diff --git a/submissionscripts/all.hits b/submissionscripts/all.hits new file mode 100644 index 0000000..f66e811 --- /dev/null +++ b/submissionscripts/all.hits @@ -0,0 +1,93 @@ +NODE_10_length_100664_cov_4.590390 +NODE_1011_length_5876_cov_3.399896 +NODE_103_length_27141_cov_4.834863 +NODE_10466_length_1265_cov_1.145870 +NODE_1084_length_5663_cov_3.230130 +NODE_11043_length_1216_cov_1.788797 +NODE_11336_length_1193_cov_1.763602 +NODE_11756_length_1163_cov_0.916023 +NODE_1191_length_5407_cov_8.549053 +NODE_12331_length_1124_cov_1.209629 +NODE_12737_length_1094_cov_2.026887 +NODE_13148_length_1072_cov_1.133333 +NODE_15132_length_972_cov_1.261538 +NODE_15181_length_969_cov_2.258907 +NODE_1527_length_4635_cov_1.427240 +NODE_15347_length_963_cov_1.683014 +NODE_1545_length_4605_cov_2.744752 +NODE_1598_length_4506_cov_5.720027 +NODE_15990_length_938_cov_1.263872 +NODE_16617_length_913_cov_1.552163 +NODE_16873_length_904_cov_1.060489 +NODE_169_length_19337_cov_6.098334 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+NODE_757_length_6935_cov_7.169066 +NODE_7608_length_1592_cov_2.047782 +NODE_7661_length_1584_cov_2.420041 +NODE_7745_length_1573_cov_2.330567 +NODE_7859_length_1558_cov_2.531097 +NODE_802_length_6659_cov_3.376607 +NODE_8049_length_1529_cov_1.796006 +NODE_84_length_30851_cov_5.003190 +NODE_8507_length_1465_cov_2.865471 +NODE_896_length_6269_cov_2.658417 +NODE_9187_length_1389_cov_4.857369 +NODE_921_length_6179_cov_4.912095 +NODE_961_length_6057_cov_2.800843 +NODE_9720_length_1333_cov_1.264511 +NODE_9822_length_1324_cov_2.765246 +NODE_9971_length_1309_cov_1.916244 diff --git a/submissionscripts/assembly.sh b/submissionscripts/assembly.sh new file mode 100644 index 0000000..504e218 --- /dev/null +++ b/submissionscripts/assembly.sh @@ -0,0 +1,17 @@ +#!/bin/bash +#SBATCH --job-name=raxml +#SBATCH -N 1 +#SBATCH -n 1 +#SBATCH -c 16 +#SBATCH --partition=amd +#SBATCH --mail-type=END +#SBATCH --mem=20G +#SBATCH --mail-user=yutian.feng@uconn.edu +#SBATCH -o racks_%j.out +#SBATCH -e racks_%j.err + + + +module load RAxML/8.2.11 +raxmlHPC ­f i ­t extein.te ­z inteinaa.align.ufboot ­m GTRCAT ­n T4 + \ No newline at end of file diff --git a/submissionscripts/autest.sh b/submissionscripts/autest.sh new file mode 100644 index 0000000..b3d19a6 --- /dev/null +++ b/submissionscripts/autest.sh @@ -0,0 +1,17 @@ +#!/bin/bash +#SBATCH --job-name=tblastn +#SBATCH -N 1 +#SBATCH -n 1 +#SBATCH -c 6 +#SBATCH --partition=amd +#SBATCH --mail-type=END +#SBATCH --mem=250G +#SBATCH --mail-user=yutian.feng@uconn.edu +#SBATCH -o tblastn_%j.out +#SBATCH -e tblastn_%j.err + + + +module load iqtree/1.5.5 +iqtree-omp -s inteinaa.align -st AA -m LG+F+I+G4 -n 0 -z exteinaa.ufb -zb 1000 -au -nt AUTO +iqtree-omp -s exteinaa.align -st AA -m LG+F+R5 -n 0 -z inteinaa.ufb -zb 1000 -au -nt AUTO \ No newline at end of file diff --git a/submissionscripts/bbcsub.bash b/submissionscripts/bbcsub.bash new file mode 100644 index 0000000..ef03739 --- /dev/null +++ b/submissionscripts/bbcsub.bash @@ -0,0 +1,16 @@ +#!/bin/bash +#$ -N ass +#$ -M yutian.feng@uconn.edu +#$ -q all.q +#$ -m ea +#$ -S /bin/bash +#$ -cwd +#$ -pe smp 16 +#$ -o ass_$JOB_ID.out +#$ -e ass_$JOB_ID.err + +cd /home/yuf17006/metagenomes +module load SPAdes/3.10.0 +spades.py --meta --only-asembler --pe<1>-1 ERR1739731_1.fastq --pe<1>-2 ERR1739731_2.fastq -o test1 + + diff --git a/submissionscripts/contigtrimmer.pl b/submissionscripts/contigtrimmer.pl new file mode 100644 index 0000000..255c7b7 --- /dev/null +++ b/submissionscripts/contigtrimmer.pl @@ -0,0 +1,69 @@ +#!/usr/bin/perl -w + +use strict; + + +my $infasta=$ARGV[0]; + +open FH1 , "$infasta" or die "$!"; + + + +my @sequence =""; +my $first = ""; +my $second =""; +my $begin=""; +my $end=""; +my $front = ""; +my $back = ""; +my $final = ""; +while(){ + chomp; + @sequence = split /\t/, $_; + $first = $sequence[6]; + $second = $sequence[7]; + if ($first > $second) { + $begin = $second; + $end = $first; + } + else{ + $begin = $first; + $end = $second; + } + my $frontflank = int($begin)-1000; + my $backflank = int($end+1000); + my $seqname = $sequence[0]; + open FH2, "$seqname".".seqfile"; + my $worthless =""; + my $cds= ""; + while(){ + chomp; + if(/^\>(.*)/){ + $worthless = $worthless . $_; + } + else{ + $cds = $cds . $_; + } + } + + my @readin = split //, $cds; + + + while ($frontflank < $backflank){ + $front = $front . $readin[$frontflank]; + $frontflank += 1; + + } + + $final = $front ; + + print ">".$sequence[0].".seqfile2\n".$final."\n"; + @sequence =""; + $front =""; + $final =""; + $back =""; + $first = ""; + $second =""; + $begin=""; + $end=""; +} diff --git a/submissionscripts/extein.pl b/submissionscripts/extein.pl new file mode 100644 index 0000000..c64c51d --- /dev/null +++ b/submissionscripts/extein.pl @@ -0,0 +1,70 @@ +#!/usr/bin/perl -w + +use strict; + + +my $infasta=$ARGV[0]; + +open FH1 , "$infasta" or die "$!"; + + + +my @sequence =""; +my $first = ""; +my $second =""; +my $begin=""; +my $end=""; +my $front = ""; +my $back = ""; +my $final = ""; +while(){ + chomp; + @sequence = split /\t/, $_; + $first = $sequence[6]; + $second = $sequence[7]; + if ($first > $second) { + $begin = $second; + $end = $first; + } + else{ + $begin = $first; + $end = $second; + } + my $seqname = $sequence[0]; + open FH2, "$seqname".".seqfile2"; + my $worthless =""; + my $cds= ""; + while(){ + chomp; + if(/^\>(.*)/){ + $worthless = $worthless . $_; + } + else{ + $cds = $cds . $_; + } + } + + my @readin = split //, $cds; + my $i =0; + + while ($i < $begin){ + $front = $front . $readin[$i]; + $i += 1; + } + + while ($end < $#readin){ + $back = $back . $readin[$end]; + $end += 1; + } + $final = $front . $back; + + print ">".$sequence[0].".ext\n".$final."\n"; + @sequence =""; + $front =""; + $final =""; + $back =""; + $first = ""; + $second =""; + $begin=""; + $end=""; +} diff --git a/submissionscripts/ictest.bash b/submissionscripts/ictest.bash new file mode 100644 index 0000000..a6b79da --- /dev/null +++ b/submissionscripts/ictest.bash @@ -0,0 +1,15 @@ +#!/bin/bash +#SBATCH --job-name=raxml +#SBATCH -N 1 +#SBATCH -n 1 +#SBATCH -c 16 +#SBATCH --partition=amd +#SBATCH --mail-type=END +#SBATCH --mem=20G +#SBATCH --mail-user=yutian.feng@uconn.edu +#SBATCH -o racks_%j.out +#SBATCH -e racks_%j.err + + +module load RAxML/8.2.11 +raxmlHPC -f i -t extein.te -z inteinaa.align.ufboot -m GTRCAT -n T4 \ No newline at end of file diff --git a/submissionscripts/iqtree.sh b/submissionscripts/iqtree.sh new file mode 100644 index 0000000..1414be1 --- /dev/null +++ b/submissionscripts/iqtree.sh @@ -0,0 +1,15 @@ +#!/bin/bash +#SBATCH --job-name=reroot +#SBATCH -N 1 +#SBATCH -n 1 +#SBATCH -c 6 +#SBATCH --partition=amd +#SBATCH --mail-type=END +#SBATCH --mem=50G +#SBATCH --mail-user=yutian.feng@uconn.edu +#SBATCH -o reroot_%j.out +#SBATCH -e reroot_%j.err + + +module load iqtree/1.5.5 +iqtree-omp -s cdsall7.align -nt AUTO -bb 1000 -st AA diff --git a/submissionscripts/kraken.sh b/submissionscripts/kraken.sh new file mode 100644 index 0000000..38d1216 --- /dev/null +++ b/submissionscripts/kraken.sh @@ -0,0 +1,16 @@ +#!/bin/bash +#SBATCH --job-name=kraken +#SBATCH -N 1 +#SBATCH -n 1 +#SBATCH -c 24 +#SBATCH --partition=himem4 +#SBATCH --mail-type=END +#SBATCH --mem=250G +#SBATCH --mail-user=yutian.feng@uconn.edu +#SBATCH -o kraken_%j.out +#SBATCH -e kraken_%j.err + + + +module load kraken/1.0 +kraken -d /isg/shared/databases/kraken/standard contigs.fasta --threads 24 diff --git a/submissionscripts/metabat.pl b/submissionscripts/metabat.pl new file mode 100644 index 0000000..8a919ac --- /dev/null +++ b/submissionscripts/metabat.pl @@ -0,0 +1,14 @@ +#!/bin/bash +#SBATCH --job-name=metabat +#SBATCH -N 1 +#SBATCH -n 1 +#SBATCH -c 24 +#SBATCH --partition=himem4 +#SBATCH --mail-type=END +#SBATCH --mem=250G +#SBATCH --mail-user=yutian.feng@uconn.edu +#SBATCH -o metabat_%j.out +#SBATCH -e metabat_%j.err + +module load metabat/2.12.1 +metabat -i contigs.fasta.gz -o binout \ No newline at end of file diff --git a/submissionscripts/metabat.sh b/submissionscripts/metabat.sh new file mode 100644 index 0000000..9aa4a7f --- /dev/null +++ b/submissionscripts/metabat.sh @@ -0,0 +1,14 @@ +#!/bin/bash +#SBATCH --job-name=metabat +#SBATCH -N 1 +#SBATCH -n 1 +#SBATCH -c 24 +#SBATCH --partition=himem4 +#SBATCH --mail-type=END +#SBATCH --mem=250G +#SBATCH --mail-user=yutian.feng@uconn.edu +#SBATCH -o metabat_%j.out +#SBATCH -e metabat_%j.err + +module load metabat/2.12.1 +metabat -i contigs.fasta.gz -o binout \ No newline at end of file diff --git a/submissionscripts/metagenomepipeline/0assembly.sh b/submissionscripts/metagenomepipeline/0assembly.sh new file mode 100644 index 0000000..063927a --- /dev/null +++ b/submissionscripts/metagenomepipeline/0assembly.sh @@ -0,0 +1,18 @@ +#!/bin/bash +#SBATCH --job-name=assing +#SBATCH -N 1 +#SBATCH -n 1 +#SBATCH -c 16 +#SBATCH --partition=himem4 +#SBATCH --mail-type=END +#SBATCH --mem=500G +#SBATCH --mail-user=yutian.feng@uconn.edu +#SBATCH -o assing_%j.out +#SBATCH -e assing_%j.err + + + +module load SPAdes/3.11.1 + +spades.py --pe1-1 /UCHC/LABS/Gogarten/metagenomes/meyghan/ERR1739732_1.trim.fq --pe1-2 /UCHC/LABS/Gogarten/metagenomes/meyghan/ERR1739732_2.trim.fq -o assembly2 +spades.py --pe1-1 /UCHC/LABS/Gogarten/metagenomes/meyghan/ERR1739731_1.trim.fq --pe1-2 /UCHC/LABS/Gogarten/metagenomes/meyghan/ERR1739731_2.trim.fq -o assembly3 \ No newline at end of file diff --git a/submissionscripts/metagenomepipeline/1trim.sh b/submissionscripts/metagenomepipeline/1trim.sh new file mode 100644 index 0000000..ca7f8b8 --- /dev/null +++ b/submissionscripts/metagenomepipeline/1trim.sh @@ -0,0 +1,16 @@ +#!/bin/bash +#SBATCH --job-name=trimm +#SBATCH -N 1 +#SBATCH -n 1 +#SBATCH -c 4 +#SBATCH --partition=amd +#SBATCH --mail-type=END +#SBATCH --mem=250G +#SBATCH --mail-user=yutian.feng@uconn.edu +#SBATCH -o trim_%j.out +#SBATCH -e trim_%j.err + + +module load sickle/1.33 +sickle se -f DL24m30.fastq -t sanger -o tDL24m30.fq +sickle se -f DL24m08.fastq -t sanger -o tDL24m08.fq diff --git a/submissionscripts/metagenomepipeline/2map.sh b/submissionscripts/metagenomepipeline/2map.sh new file mode 100644 index 0000000..e433e35 --- /dev/null +++ b/submissionscripts/metagenomepipeline/2map.sh @@ -0,0 +1,16 @@ +#!/bin/bash +#SBATCH --job-name=mapping +#SBATCH -N 1 +#SBATCH -n 1 +#SBATCH -c 10 +#SBATCH --partition=amd +#SBATCH --mail-type=END +#SBATCH --mem=30G +#SBATCH --mail-user=yutian.feng@uconn.edu +#SBATCH -o mapping_%j.out +#SBATCH -e mapping_%j.err + + +module load bowtie2/2.3.3.1 +bowtie2 -x extein30 -U /home/CAM/yfeng/metagenomes/deeplake/DL24m30.fastq -S ex30map.sam -p 10 +bowtie2 -x both30 -U /home/CAM/yfeng/metagenomes/deeplake/DL24m30.fastq -S comb30map.sam -p 10 \ No newline at end of file diff --git a/submissionscripts/metagenomepipeline/3samtobam.bash b/submissionscripts/metagenomepipeline/3samtobam.bash new file mode 100644 index 0000000..86c0190 --- /dev/null +++ b/submissionscripts/metagenomepipeline/3samtobam.bash @@ -0,0 +1,16 @@ +#!/bin/bash +#SBATCH --job-name=samsort +#SBATCH -N 1 +#SBATCH -n 1 +#SBATCH -c 1 +#SBATCH --partition=amd +#SBATCH --mail-type=END +#SBATCH --mem=20G +#SBATCH --mail-user=yutian.feng@uconn.edu +#SBATCH -o samsort_%j.out +#SBATCH -e samsort_%j.err + + +module load samtools/1.7 +samtools view -b -F 4 comb30map.sam > both30map.bam +samtools view -b -F 4 ex30map.sam > ex30map.bam \ No newline at end of file diff --git a/submissionscripts/metagenomepipeline/4samsort.bash b/submissionscripts/metagenomepipeline/4samsort.bash new file mode 100644 index 0000000..5cc7131 --- /dev/null +++ b/submissionscripts/metagenomepipeline/4samsort.bash @@ -0,0 +1,16 @@ +#!/bin/bash +#SBATCH --job-name=samsort +#SBATCH -N 1 +#SBATCH -n 1 +#SBATCH -c 4 +#SBATCH --partition=amd +#SBATCH --mail-type=END +#SBATCH --mem=250G +#SBATCH --mail-user=yutian.feng@uconn.edu +#SBATCH -o samsort_%j.out +#SBATCH -e samsort_%j.err + + +module load samtools/1.7 +samtools sort bothmap.bam -o bothsort08.bam +samtools sort exmap.bam -o exsort08.bam \ No newline at end of file diff --git a/submissionscripts/metagenomepipeline/5genomecov.bash b/submissionscripts/metagenomepipeline/5genomecov.bash new file mode 100644 index 0000000..3acf509 --- /dev/null +++ b/submissionscripts/metagenomepipeline/5genomecov.bash @@ -0,0 +1,14 @@ +#!/bin/bash +#SBATCH --job-name=samsort +#SBATCH -N 1 +#SBATCH -n 1 +#SBATCH -c 4 +#SBATCH --partition=amd +#SBATCH --mail-type=END +#SBATCH --mem=250G +#SBATCH --mail-user=yutian.feng@uconn.edu +#SBATCH -o samsort_%j.out +#SBATCH -e samsort_%j.err + +module load BEDtools/2.27.1 +bedtools genomecov -ibam workedsort.bam \ No newline at end of file diff --git a/submissionscripts/metagenomepipeline/Metagenome Pipeline.ipynb b/submissionscripts/metagenomepipeline/Metagenome Pipeline.ipynb new file mode 100644 index 0000000..b21a586 --- /dev/null +++ b/submissionscripts/metagenomepipeline/Metagenome Pipeline.ipynb @@ -0,0 +1,280 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# Metagenome Pipeline" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "This contains every line of code I use for my pipeline with explanations for some, it may be more efficient to copy and paste some of these lines into a script. This assumes you have already quality trimmed and assembled the metagenomes, and that you have 25 intein PSSMs generated from NR database (5 iterations)." + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## Searching a Metagenome with PSSM" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "This searches a metagenome with a PSSM (inteins used in this example but can be anything).\n", + "Requirements:
\n", + "assembled contigs = contigs.fasta
\n", + "intein pssms = *.pssm
\n", + "
\n", + "
\n", + "\n", + "You have 25 intein PSSMs (amino acid), that have been generated from NR database; you will now use them to search a nucleotide database (assembled metagenome) for inteins.\n", + " " + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "module load blast/2.7.1\n", + "for b in *.pssm; do tblastn -in_pssm \"$b\" -db contigs.fasta -out \"$b\".search -outfmt 6 -evalue 1e-10; done" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "PSSM searches like these will generate a ton of duplicate hits, since PSSMs have a fairly low specificty. The following will organize all your hits and get rid of duplicates.\n", + "mg_name.hits contains your final file with unique hits, sorted." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "cat *.search |cut -f 2 >all.hits\n", + "sort all.hits >sort.hits\n", + "uniq sort.hits >mg_name.hits" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "You will now use grep to get the sequences of the contigs that were identified as hits above. But first, grep only works on fasta files that are single line. You will remove \\n to get rid of linebreaks in your assembled contigs file, then use grep to get the hit sequences.\n", + "contigs.eol will be the one line multifasta.
\n", + "At the end of the next block you will have *.seqfiles* which are the sequence files of the hits from above." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "awk '!/^>/ { printf \"%s\", $0; n = \"\\n\" } \n", + "/^>/ { print n $0; n = \"\" }\n", + "END { printf \"%s\", n }\n", + "' contigs.fasta >> contigs.eol\n", + "\n", + "\n", + "for filn in `cat mg_name.hits`; do grep -A 1 $filn contigs.eol> $filn.seqfile;done" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "Your *.seqfiles* are all **possible** intein hits, but some of these are low quality, or bacteria like inteins, hedgehogs etc. You need to cull some of these hits via bitscore to make sure they can be reliably mapped later on.
\n", + "\n", + "
\n", + "You now need to blast your *.seqfiles* against a database (AA) of all recorded inteins to make sure they are the real thing.
\n", + "\n", + "Requirements:
\n", + "inteindatabase (i can email) = intein.db" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "for filn in `cat mg_name.hits`; do blastx -query $filn.seqfile -db intein.db -outfmt 6 -out $filn.blast ;done\n", + "for f in `cat all.hits`; do head -1 $f.blast >> all.tsbh; done" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "all.tsbh contains only the top hit for each seqfile. You need to sort this file by bitscore and get rid of anything under 100-150. I highly recommend excel (data-> sort -> bitscore).
\n", + "
\n", + "Now that your all.tsbh file only contains those hits with high bitscore, you can delete the seqfiles that didn't make the cut.\n", + "
\n", + "
" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "cat all.tsbh |cut -f 1 > contigs.list #contigs.list is list of contigs that made it\n", + "mkdir genes #just a directory containing the good hits\n", + "for f in `cat contigs.list`; do mv $f.seqfile genes; done" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "You now have the good contigs, but some of these contigs will be extremly large. I usually have a maximum length of 10k bp sequence. To trim large contigs, look at all.tsbh , and make a separate file with only the large contigs (longcontigs.tsbh ). I usually do this in Excel, sort by query start or stop.
Use the attached script: **contigtrimmer.pl**, which looks at the blast output of a large contig, gets about 1000 bases upstream and down stream of the intein and outputs that sequence." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "perl extein.pl longcontigs.tsbh" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## Mapping" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "You now have appropriately sized *.seqfiles* that contains inteins in them. You need to map metagenome reads back to them to determine the frequency of these \"rare\" genes.

\n", + "You need to prepare 2 sets of nucl sequences:
\n", + "1) *.seqfiles* as they are , which represents extein/intein/extein
\n", + "2) *.seqfiles* with the inteins removed, which represetns extein/extein
\n", + "
\n", + "Requirements:
\n", + "**extein.pl** which is attached
\n", + " *.seqfiles* \n", + "all.tsbh (you need to remake this file with the short contigs)
\n", + "\n", + "
\n", + "To make the second set of sequences 2):" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "perl extein.pl all.tsbh > extonly.txt\n", + "cat *.seqfile > fullseqs.txt" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "After you have both sets of sequences, you will use bowtie2 to map reads to these sequences (also called reference genomes)." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "module load bowtie2/2.3.3.1\n", + "bowtie2-build extonly.txt extonly #builds bowtie indices\n", + "bowtie2-build fullseqs.txt fullseqs\n", + "\n", + "\n", + "bowtie2 -x extonly -U reads.fastq -S exmap.sam -p 10 #maps\n", + "bowtie2 -x fullseqs -U reads.fastq -S fullmap.sam -p 10 \n", + "\n", + "samtools view -b -F 4 exmap.sam > exmap.bam #makes files much smaller, and convert to bam\n", + "samtools view -b -F 4 fullmap.sam > fullmap.bam\n", + "\n", + "samtools sort exmap.bam -o exsort.bam #sorts based on position\n", + "samtools sort fullmap.bam -o fullsort.bam\n" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "After this you can now visualize your mapped reads, using Integrated Genome Viewer (or equivalent). For this you need to create an index file for the bam files and reference genomes." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "samtools faidx name.fasta \n", + "samtools index -b name.bam" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## Extein Background\n", + "You can then identify the gene/organism the intein is inserted to with an NR blast of the extein file. " + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "blastx -query extonly.txt -db /isg/shared/databases/blast/nr -outfmt \"6 qaccver salltitles qseq\" -max_target_seqs 1 >> exteinbackground.tab" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## The end?\n", + "At this point you should have mapped reads (.bam), list of all inteins in a metagenome (all.tsbh), and their host information. I do not have a great way to parse and catalogue all of this information at the moment, but collectively you can do phylogenetic analyses, create intein distribution tables, etc from all this." + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.6.4" + } + }, + "nbformat": 4, + "nbformat_minor": 2 +} diff --git a/submissionscripts/metagenomepipeline/gilist.txt b/submissionscripts/metagenomepipeline/gilist.txt new file mode 100644 index 0000000..77f7471 --- /dev/null +++ b/submissionscripts/metagenomepipeline/gilist.txt @@ -0,0 +1,573 @@ +WP_011276942.1 +WP_011276944.1 +WP_011276956.1 +WP_011276961.1 +WP_011276972.1 +WP_011276987.1 +WP_011276988.1 +WP_011276991.1 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+NFDSEKLDLSQPHNSGNQELENHLIFWDELVNVLAKFATSKNQSLKNRTTKRNSPKNSEN +LTTTETICRKNILANMENLPSDNQNFDSEKLDLPQPHNSGNQELENHLIFWDELVNVLAK +FAASKNQSLKNRTTKRNSPKNSENLTTTETICRKNILANMENLPSDNQNFDSEKLDLPQP +HNSGNQELENHLIFWDELVNVLAKFATSKNQSLKNRTTKRNSPKNSENLTTTETICRKNI +LANMENLPSDNQNFDSEKLDLSQPHNSGTQELENHLIFWDELVNVLAKFAASKNQSLKNR +TAKGKSPKNSENLTTTETICRKNILANMENLPSDNQNFDSEKLDLSQPHNSGNQELENHL +IFWDELVNVLAKFATSKNQSLKNRTTKRNSPKNSENLTTTETICRKNILANMENLPSDNQ +NFDSEKLDLPQPHNSGNQELENHLIFWDELVNVLAKFATSKNQSLKNRTTKRNSPKNSEN +LTTTETICRKNILANMENLPSDNQNFDSEKLDLPQPHNSGNQELENHLIFWDELVNVLAK +FATSKNQSLKNRTTKRNSPKNSENLTTTETICRKNILANMENLPSDNQNFDSEKLDLPQP +HNSGNQELENHLIFWDELVNVLAKFATSKNQSLKNRTTKRNSPKNSENLTTTETICRKNI +LANMENLPSDNQNFDSEKLDLPQPHNSGNQELENHLIFWDELVNVLAKFATSKNQSLKNR +TTKRNSPKNSENLTTTETICRKNILANMENLPSDNQNFDSEKLDLSQPHNSGTQELENH +LIFWDELVNVLAKFAASKNQSLKNRTTKRNSPKNSENLTTTETICRKNILANMENLPSDN +QNFDSEKLDLPQPHNSGTQELENHLIFWDELVNVLAKFAASKNQSLKNRTTKRNSPKNSE +NLTTTETICRKNILANMENLPSDNQNFDSEKLDLPQPHNSGNQELENHLIFWDELVNVLA +KFAASKNQSLKNRTTKRNSPKNSENLTTTETICRKNILANMENLPSDNQNFDSEKLDLPQ +PHNSGNQELENHLIFWDELVNVLAKFATSKNQSLKNRTTKRNSPKNSENLTTTETICRKN +ILANMENLPSDNQNFDSEKLDLPQPHNSGNQELENHLIFWDELVNVLAKFATSKNQSLKN +RTAKGKSPKNSENLTTTETICRKNILANMENLPSDNQNFDSEKLDLPQPHNSGNQELENH +LIFWDELVNVLAKFATSKNQSLKNRTTKRNSPKNSENLTTTETICRKNILANMENLPSDN +QNFDSEKLDLPQPHNSGNQELENHLIFWDELVNVLAKFATSKNQSLKNRTTKRNSPKNSE +NLTTTETICRKNILANMENLPSDNQNFDSEKLDLPQPHNSGNQELENHLIFWDEL +VNVLAKFATSKNQSLKNRTAKGKSPKNSENLTTTETICRKNILANMENLPSDNQNFDSEK +LDLPQPHNSGNQELENHLIFWDELVNVLAKFATSKNQSLKNRTTKRNSPKNSENLTTTET +ICRKNILANMENLPSDNQNFDSEKLDLPQPHNSGNQELENHLIFWDELVNVLAKFATSKN +QSLKNRTTKRNSPKNSENLTTTETICRKNILANMENLPSDNQNFDSEKLDLPQPHNSGTQ +ELENSDIFWDKIVSIEPVGEKQVYDLTVPETHNFVANDICLHNT +>Dge_DnaB +KCVTADTLIDVPGTGERITVEAFVRRQWPVVLSVSADGRVRESRVGAWIDSGVKPV +RRVTTRTGRVVETTPHHPFLGVDGWTPLYDLKVGDRIA +VPRAVPVFGQRDVLSAERVRLLAYLLAEGGL +TQSGPRWTNADPELVQDFRACLAAEFPEVEMMADAWTGIDDRLSRRWQPGERQD + + + + + + + + + + + + +RPNPLIGWLRELGVWGQ +PTDAKRFPAVVWTFTRPS 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+AKQVKLLEILSALPEEAAGLDRDFVPGLARFIRQHSGGRWADKEWLRKHNVDRISRWQR +NGAEILGRIADPEVRAVATDLTDGRFYYATVASVADAGVQPVYSLRVDTEDHAFITNGFV +SHNT +:::::::::::::: +gyrBa.ina +:::::::::::::: +>Hwa_GyrB +GCFSGDTEIALASGDSITFESLVDAYERGETHYCYTIGDDGRIRIEEIMNPRVTQEDAAL +LAVTLDNGEVIRCTPDHEFMLRDGNYCEAQNLTDGQSLMPLYRTTTEMTETTETTETTGT +AEMVKQPFAQNNWESVSQLANRYNRRHTTTDHIVETQQIQS +QQQ + + +SQIETVQISERADVHNHTVISVESLTETADVY +DLEVPVTHNFALASGVFVHNS +>Ssp_GyrB +CFSGDTLVALTDGRSVSFEQLVEEEKQGKQNFCYTIRHDGSIGVEKIINARKTKTNAKV +IKVTLDNGESIICTPDHKFMLRDGSYKCAMDLTLDDSLMPLHRKISTTEDSGITIDGYEM +VWSPRSDSWLFTHLVADWYNRWQGIYIAEEKQHCHHKDFNKRNNNPDNLIRLSPEKHLAL +HRKHISKTLHRPDVVEKCRRIHQSPEFRRKMSARMQSPETRAILSKQAQAQWQNETYKLT +MMESWRSFYDSNEDYRQQNAEQLNRAQQEYWAQAENRTAQAERVRQHFAQNPGLRQQYSE +NAVKQWNNPELLKWRQKKTKEQWTPEFREKRREALAQTYYRKTLAALKQVEIENGYLDIS +AYDSYRISTKDKSLLRFDRFCERYFENDENLAREAVLNYNHRIVNIEAVSETIDVY +DIEVPHTHNFALASGVFVHNS +>Ter_GyrB +CFAGNQKVILADGRRLSFAEIVAEQAEGKEHFCYTINQSGNVAIERIINARITKKNASV +IKIILDNNETIICTPDHLFMLRDGSYKPAALLTGNDSLMPLSQKSSQKTENSQELDGYEM +VWSPQKESWIYTHLLPDFYNLKAGVYQSANGDSCYHVGFKKLNSTKTEGLLTEKHLEF +HKTNLE + + +LAYRCSERDEFLARDIIPNYNDHYNYRVVSIEPLEERLDVY +DIEVPNTHNFALASGVFVHNS +>MchtPCC7420_GyrB +CFDGDTRVALADGRSLSFKEIVAEQAMGKEHFCYTIRHDGKIGLERIIHPRITKANAQV +IQVTLDNGETLICTPDHPFMVRDGSYKAAALLTPEDFLMSLNAKLSERSRGQRLAEIDAA +GFNTRLSEVAFSRDVQANAVYPTVGAVGTPSLRPPHSGQDTKESSV + + + +ALLVREESPSRKDNHRVVAIERLEKRVDVY +DIEVPHTHNFALASGVFVHNS +>CraCS505_GyrB +CFVGNTLVSLTDGRNLTFTDLIAEQAAGKQNYCYTIQENGEVGIEKILHVRTTKTNAEV +VRVTLDNDQVLICTPDHLFMLRDGNYQAAGLLTPQDSLMPYY +DQSI + + + +PAVMQSAVTTYNHRVVSVESLAEKFDVY +DLEVPHTHNFALTAGVFVHNS +>RbrD9_GyrB +CFVGNTLVSLKDGRNLTFTDLIAEQAAGKENYCYTIRENGEVGIEKILHVRRTKTNAEV +VRVTLDNDQVLICTPDHLFMLRDGNYQAAGLLTPQDSLMPYY +DQSI + + + +PTVIRSAVTTYNHRVVSVESLPEKFDVY +DLEVPHTHNFALAAGVFVHNS +:::::::::::::: +gyrBb.ina +:::::::::::::: +>LspPCC8106_GyrB +GCFTGDTLVPLADGKSYPLVELASWRREFVVYSCTDTGRIVAAKASARLTRRNAPLVKVV +LDNGAEIKCTPDHQFMLRDGSYQEAKDLKNGTSLMPFYSKKDKDGYTLIQQNYSGRYQKA +HWMIARSGLLGKIPKFPGQRTVIHQKNFDPVDNRPENLEFI + +NKEIANRIYPLETCGTEVKSPIGLHNHRRKEHGYNHKVVGVIFLSEKQ +DVYCLTVPEYHNFALTDGVFVHNC +>Npu_GyrB +GCFIGDTLIPLADGKSYRIKDLMDWGTEFIVYACTPTGKIVAAQATAKLTRRNAPLVKVI +LDNGEEIICTPDHQFMLRDGTYKEAQLLQAETSLMPFYSKTDKDGYTLITQPYSSRWQKA +HWIIARSGLLGKVPRFEGQKTFIHHQNFDESDNRPENLEFMGNRDHSAYHRSLVERNQHW +HSAEFEEKRVASLAQKAKTSEGYQYYAERGTRNIFQYMEQQPEHFKNAVAGNGNRGKQYL +VEYNKTEKGRGKSQEIANRYYTCEICGVDVKTPIGLHNHRRKEHQCNHKVVAVNLLNYTE +DVYCLTVPEYHNFALKAGVFVHNC +:::::::::::::: +helicaseA.ina +:::::::::::::: +>Mja_Helicase +LCLNANTEILQESGFRKITELNKDEKVFALCGKEIKPVDGWKVHKTPQHEYNIVVKT +VNGLEITTTPNHIFLVKENGSLKEKEAKDLKVGDYVATVDRIRVKEKDIDL +SNGDLYFIGYFIGDGYTGVIEKNTLKATPDLAFNPKYPPNFDDSELHKKYFLKCRISKGV +AHYIYSKKLRKIFNKLNMLTKDNKNIDAFCNLPLDKLAYLIAGLFDSDGYIYLNRKNIE +FYSISEKLVEQLQFVLLRFGIHSSIRKKKTKTMV +SPTNGKEYKCKDIYVLTIRDFMSIKRFYENIPLRHEEKRRKLEEIIKNKE +IGQIPSEFVALRFTPIAKIWCDCGFSVDLTMFKPRTKRQRELNKKRVKLLFELLDGKKLI +TNYKEYYSKRKNPYFDFIVREKINGNNYYSLNEKGRVLMSLLNKHIKDKENL +EEMYNFLVNLEKCPICGKPIHKEMRYSWKKECYDGDIYWDRIKEIKKIKVN +DKYAYDIELPDDGSNSHYIVANGFIVHNS +>Tko_Helicase +LCMHPDTYVVTKSGAKKVSELTEGDEVLTHTGTFKKVIQPLRREHKGRLLVIKA +YGTVPVKITPEHMVWVVKQIRHKSHYSDGRQVIWWEFEGPEWMTAQELKERLESETDPKV +SYMLLQPIPEPSVDADKIPLRKEVYVVNQHGK +TDKLHPSVKRTPEYLPLNFETARLIGLWIAEGSTSKNGVIKFD +ISSNEEDLTEFITGTIRKYFPHAKIVVKDHERNR +RTVRFCNKRFAEWLRENIGHGADNKSIPPLLLLNKNREV +RLGLLRGLIEGDG +YVRRESQRRANYISYSTVSPSLAYQLQLLVASLGYTSSIHRSIR +TEGIGKTRKPIYDVKVSGKSYYSLLEELGFEVPQRGNRTYNVNRTWKNYLLLKVRSIEE +EEYEGDVYNLEVEGDESGSVGFIVHNS +>MaeoN3_Helicase +CLNANTEILQESGFKKITELNKNEKVFALCGNKIRPVDCWKVHKTPQHEYNIVVKT +ANGLKITTTPNHLFLVKKGKETCEKEAKDLKVGDYVATADKIVVEERDIDL +SYGDLYFIGYFIGDGYTGVIEKNVFRGSPDITFNPKYPPNFDDSKLHKKYFLKIKEEGNV +SHYVYSKRLREVFNELNMLTKDNKNIDVFYILPLEKLSHFIAGLFDSDGYINANRKKIG +FSSISENLIKKLQLALLRFGIHSTIRKRKGKVMKLNKTFRFCKSRRNRRFRESANLRFAS +TANPKDSLRSPTNNKEYKSRDIYELIIGDFVSVKRFYENIPLRHKEKRRKLEEIVKSKE +IAKMWCDCGFSIDLTMFKPRTKSQNELNKERVKLLFELLNGKKLV +MNYNNYYSKRKNPHFEFIIREKIGGNKKGVYYSLNDKGKILMNLLNKNIKDKENL +EEMYDFLVNLEKCPICGKPLYKEMRHSWKKEYYDGDIYWSMIKEIKKIKVN +DKYAYDIELPDDGTNDHYVVANGFIVHNS +>MvuM7_Helicase +LCLNAKTEILQENGYRKITELNKNEKIFALCGGKIKPIGRWKIHKTPQHDYNITIKT +ENGLEITTTPNHIFLVKNGKSIKEKEAKDLKIGDLVATVGKIIVDEDINT +SN +FVKFPIRRLSQFIAETFNSKGVINNSIE +IYSTSELFIKRLQVALLRFGIHSQIEIK +NSDKKDDKTYLLKISDLEGLKLFYKNFPIDLKEKEK +LF +YLIKKKINNKPYEDNL +EHIDFDNSFNNIAICWKKILEIKKVKVE +DEYVYDIELPNDGSNDHYFVANGFVVHNS +:::::::::::::: +helicase_b.ina +:::::::::::::: +>Mex_helicase +CFAAGTLIKTPKGPVPIEQIQSGDLVFNAIGIGVVEGIVCQQKQTITLELS +DGTSIVCTHDHPFFCPRGWVAAGDLEVGSGLFSHEDLRRLWSGGASLGLESGSSD +GRGAVRSSEVLLRILREEAREPDAGYCGPAEDVRNASTDRAHAEGAWWQWQADPIASDEA +ARSAGRRVADRVRDEDRREARPEPTAVLLQDRHCEPLANDRNRSGREHSSRGTGEAEGQR +QGDVPCSVR + +VVSISREERGGPEAVYNLRVSG +HPSYFAGGVLVHNC +>Ssp_DnaX +CLTGDSQVLTRNGLMSIDNPQIKGREVLSYNETLQQWEYKKVLRWLDRGEKQTLSIKT +KNSTVRCTANHLIRTEQGWTRAENITPGMKILSPASVDVDNLSQSTALTASLGGLSGAIN +YEAINTDKKNTTLSLSLKKQKPQDPFVNADVAKNLIFQHFCSAKEEKLKVSNPIGEDIP +TKKATDFGISEQKKLHQGQNRWEQKFSVLSTEPCLGMEVLTIPTHIADSPACDGPTAPSS +QNGWNIKRQDWDVCHPKYDSQPIKAMGKVPSAVKPVVPQTLLMFSAQSNLEVKENKFLRN +GSRISLKKEWLGGTWTTVPSLFPNLGVHQFSYTQRAFSRKKINLLLNGLPIEDIPPVQNP +IAEALTAKPITTQKWEQWPPASGYRTWKSIPSPQWHTNFEEVESVTKGQVEKVYDLEVED +NHNFVANGLLVHNC +>AmaxCS328_DnaX +ECLTGDALILSDRGWLRIDDPTLQECRVLSYNESTQQWEWQQVLRWLDQGVRETWKIKT +FQTEIKCTGNHLIRTDKGWIKAANITPKMKILSP + + +EIDAAVK + +TALQDVESIEKLGVNHVYDIEVEH +NHNFVANGLLVHNC +>AplC1_DnaX +ECLTGDALILSDRGWLRIDDPTLQECRVLSYNESTQQWEWQQVLRWLDQGVRETWKIKT +FQTEIKCTGNHLIRTDKGWIKAANITPKMKILSP + + +EIDAAVK + +TALQDVESIEKLGVNHVYDIEVEH +NHNFVANGLLVHNC +>Spl_DnaX +CLTGDALILSDRGWLRIDDPTLQECRVLSYNESTQQWEWQQVLRWLDQGVRETWKIKT +FQTEIKCTGNHLIRTDKGWIKAANITPKMKILSP + + +EIDAAVK + +TALQDVESIEKLGVNHVYDIEVEH +NHNFVANGLLVHNC +:::::::::::::: +hypothetical.ina +:::::::::::::: +>Mja_Hyp1 +CLTGDAKVIANGELTTIGELVERISNGKLGPTPVRGLTVLGIDEDGKLVELPVEYVYKDK +TSELVKIRTRLGRELKVTPYHPLLVNRRNGKIEWVKAEELKPGDRLAIPSFLPAMLND +NPLAEWLGYFFGNGYTDSEERVVFESKSKELRKRFMELTRKLFQDAEIKEDSGKVYVSSS +EVKRLVKSLNKDSIPEQAWKGLRSFLRAYFDCNAEIKDKIIVSTAGKEIAEQISYALAGL +GIVAEVDDKGSVIISDPENVSRFLDEIGFSVEEKKEEAKALIKKSTLNLGIYVDKE +LISYVREKLKLSFYENETMWSPEKAREIAWKLMKEIYYRLDELERFKKALSK +SVIIDWSEVEKKKEEISEKTGISVNEILEYAKGKRKPSLEEYVKIAKALGVELKETL +EAIFTFGKKYLGYVISDEIETLEEVRKEELKRLKELLNDEKLKKGVAYLIFLAQNELLWD +EIIEVEKLKGDFVIYDLHVPKYHNFIGGNLPTVLHNT +>Mja_GF6P +CVPPDTLLILENGFKRIVDIKVGDKVLTHENRFKKVEKVYKRR +YIGDIIKIKVRYFPEEIILTPEHPVYAIKTEKRCDGSHGICKFNCLTQYT +NPSCKKRYRKYKREWIIAKDLKVGDVIVYPIPN +RVRDIKYLSLDKYLSNIKREFCRSRIPEKIEVSEEFCRLVGYFLS +EGYCFRDGIGFALGENEKKIIDDIEYLMKKIFNLKPKIRDD +GRSEGIELKYYSRVLRDFFGDMFYCGDEKRAWNKALPNEFLYLPKN +KQLQIFIGWWRGDKGVTTSEILMNQLRLISLRLGFIITFSKHVPKNPKIGD +REVIKYHARWQGRVSILDEKIVDELKNEDIKLPKKDVRYGWIKGNYLYA +PIIRIGREYYDGFVYNLEVEDDSSYVTVSGTLHNC +:::::::::::::: +if2a.ina +:::::::::::::: +>Pfu_IF2 +KCLLPEEKVVLPEIGLVTLRELFELANEVVVKDEEKEVRKLGKMLTGVDERGNVKL +LNALYVWRVAHKGEMIRVKVNGWYSVTVTPEHPFLTNRGWVKAGELKEGDYI +AIPRRVYGNEDlMKFSK +IAKELGIKGDEKEFY +LAGAS +lDIPIKVLFLAPSKLVSAFLRGYFDAKGVVRENYIEVP +LFEDLPLLlLRFGIVSRIEKSTLKISGKRNLELFRKHVGFTDSEKAKA +LDELISKAKESERYPIlEELRRLGLLFGFTRNELRIEENPT +YEVlMEILERIERGSPNLAEKIAVLEGRIKEENYLRILEEEGLIENGKLTELG +KELLEVWRNREFDSKDVDYVRNIVENLVFLPVEKVERIEYEGYVYDVTTETHNFVANGI +LVHNT +>Pho_IF2 +KCLLPEERVILPDYGPITLEELFNMTKETVFKDEEKEVRKLGIRMPVAGVDGRVRL +LEGPYVWKVRYKGKMLRVKLKDWHSVAVTPEHPFLTTRGWVRADQLKPGDYV +AVPKILPGKDDKEKFLQYVHEKLKGKV +HIKLPSSDEEWETFFY +FAGTIFGRENSVNPEGLTHEVKALLELFK +VLFEYPREVLRVLFMAPVRYVANFLRGFFDINGYVNGEELRVEVRGAPHE +VLEELSLILLRLGIVSKIYPTSLAISGRRNLELFRRYIGFSEKQKAKE +LEGIIRRSENSESYPIFEELRRIRLLFGFTRAELSSTIPLYSKYESKEAPS +YEILMKILNTIEKGSKDLNKKITILEGRVRDHEYIEEFKREGLIKDGKLTELG +KELLEVWRNREFDSRDVNYLRNIIENFVFLPVEKIEEFEYDGYVYDVTTETHNFIANGI +LVHNT +>BdeJEL423_eIF5B +KCFGRDTPLLMADGTTKFVQDIKALDQLMGDDCTPRIVQERSLVHESGALYRV +VPKNANGHDAFVCNKEHILVMVNVKQPWVSQTVIDGVDQFHVSEVV +CIGNIPTVRSSGNFAS +AVEATKALPAWTLLIW +EISVLEYLAVDADLRQHFMIYKPAGG +IEYPTTTNLDIVQHFGAESVPNLEHAVMWCIGLWILLGDVDTAGNPVLILSGIDHLHP +LIKTLHSHSQKLSISFTNQLDEGVADISKPTIIALGDKFGLLFKSLGIESAEC +IPDALLRSSKLHRAALLAGLVEGSNAFSIVKDTPKHWDISCKNNMI +FENIKRLSSSLGLCVDTVTPATITQQVSVKTLQIRISGPRMHYVSELISNDSLKTTS +VVSIDSWLNVKSNACEFEIESIGCGEYFGFTVMGPNSRFLLGDFT +VTHNT +>Mja_IF2 +KCLMPHEKVLTEYGEIKIEDLFKIGKEIVEKDELKEIRKLNIKVHTLNENGEIKI +INAPYVWKLKHKGKMIKVKLKNWHSITTTPEHPFLTNNGWIKAENIKKGMYV +AIPRKIYGNEDFEKFIEFINSKILTNELIVKVNEKDLKNVEL +PSTKIYKKQKNVFRSEDIIEHNLNIEKISFSPRIHRCGKPQHYIKLPKSLNEWKAIFY +FAGVMFGDGCVDRIANNDEEVFNKLKSLNNLGIEVERIKRKSSYEIIFKNGKNALINLLK +ILFDYPSEKKSHNIKIPQILYIAPKELVAEFIKGYFDADGYVNLRQNRIEVISASKE +FIEGLSILLLRFEITSKIYEIKKSYKETKKKYYQLNIVGKRNLKNFKNIGFSIKYKEEN +LNKIIEKSRKSEKYPINKDMKRLRILFGMTRNEVNVSYYAKYENGKEIPS +YEIVKKFLNSLKPKNLDKKIKVLEGKERDVNYLKAFESDGLIENGRLTKLG +REALNIWKNHEFGKENIDYMKSLIENIAFVEVEDVEIIDYDGYVYDLTTETHNFIANGI +VVHNT +>Mka_EF2 +KCVAPETKICLADGRFVRADELFEELKERGRLVKCDESEEVYELREPVGVSSLDKDAVEI +VEGKITHVWRLKADKLVEVEVKNGRSIRTTPEHKFLVLDPSGEIVEKRADELEIGDYIV +CTQKLVHEGMSEEELKREVFRRLGRDFFVHLPEEEAESVLELAKERGIKALWETLEVDIE +ENSFYYQLRKGRIRADILVDLAEELGLDLADLYDAVEVSYRSNTKSTKPIRLPEPEDLFY +LAGLMFGDGCWNQLTNGSEAIQGEVKRIASDMGLEVRVRRYEGKTARIDFPETVPRILE +ALFDYPRRKKAHRIRVNDFLTRAPLDCIAEFIRGYFDADGTVEEGRSAVSVTSVSRE +FLEDLQLLLQKFDVASYLREGDGAYTLYVSGARSLERFPGFREPEKAEK +LKKLMEKASSSELEKVPISGEILREVRGDVPTTRMFNCYSNYEGGQVGLT +KSSLEKVISTLEAVGVEGEALERLKALA +RDDVCFLEVVRVEEVEYDGYVYDFTVEEHHNFAAEGF +VVHNT +>Pab_IF2 +KCLLPDEKVVVPSVGFVTLKELFETASKVVERDDEKEIRELDERITSVNGDGKTGL +VKASYVWKVRHKGKVIRVKLKNWHGVTVTPEHPFLTTKGWKRADQLRPGDYV +AVPRFIHGNEDEKIFLS +YVKVKKSGEEWKEYFY +LAGRKGNID +VNLLFVAPKRYVVEFLRGYFEERSEVKGESVIVEARE +LVEPLSLALLRFGIFSKIQGSKLIVTGKRNLEAFKDYIGFKDEREKA +LEEAIEKVKGSEVYPIFEEIRRLRLLFGFTREELGSYAKYENSEAPT +YEELMEILDFIERGSPSLSKKIAILEGKLKAELRVLEEEGLIKDGKLTPLG +RELLEVWRNREFDSKDVDYIRNIAETLVFIPVENVEEEEYDGYVYDLTTETHNFIANGI +LVHNT +>Tko_IF2 +KCLLPDEKVILPEHGPITLKGLFDLAKETVVADNEKEIRKLGAKLTIVGEDGRLRV +LESPYVWKVRHRGKMLRVKLKNWHSVSVTPEHPFLTTRGWVRADQLKPGDYV +AVPRVIHGNESDERFVSFVYEKLKNDELIAKLRGEVLSKISSEF +KGDRAYKVERNVFRWEDIERLNLWDEVERVAFTPRMHRSGKPLHYVKLPRSPEEWEAFFY +FAGVMFGDGSQDKIANNDVEVYEELKKLSVLGVAVKRVERTTSYEIELTNGKNALLRLLR +VLFEYPERQKAKSIRVPRILFIAPRKYVSRFLRGYFDADGHVSLKDARIEVTSASQE +FLEDLSLLLLRFGIVSKIYRSDYTTLVISGRRNLDLFRRYIGFSVKNKAEA +LEKAIKKSRRSESYPIFEELKRLRLLFGFTRTELNSNVPFYGKYESEEAPS +YETLMRILDAIEKGSINLDKKIAVLEGRIRDHNYIKAFEKDGLIKDGKLTELG +RELLEVWRNREFDSSDVDYIRNLAENLVFIPVEDIEEFEYEGYVYDVTTETHNFVANGI +LVHNT +:::::::::::::: +klbA.ina +:::::::::::::: +>Pab_KlbA +GALYYFSEIQLPNGKEFIGKLVDELFEKYHDKIGKYKDMEYVELNEEDTFEVISIGPD +LSARRHKVTHVWRRKVKDGEKLVKIRTASGKELVLTQDHPVFVLLGRDVARRDAGNVKVG +DEIAVLNTRPDFSVLSPPA + +MPELLSEPFN + + +YELSS +IGDVAWDEVVEVDEIDAKGLGVEYLYDLTVDINHNYVANGIVVSNC +>Tko_KlbA +GALYDFSVIQLSNGKFVLIGDVVEELFNKYSDRIKTYKDLEYIELDPEDQFEVVSVGPN +LKAGKHTVTAVWRRKVRNGEKLIRIRTRTGNEVILTKTHPFFVFSDGDVVRKEAEKVRPG +DRVAVMMRPPKAPQSPAVVPVEVYAGISDYYLVPNGNGMKKVPNRGVPPEDAEYLLSRNS +KPVKLVREVGTSLAYVAGVILGDGYLSSDGYNLSVTFDDPDYMNSFTSAMSEFLPESAPR +IKDNGTSTVVTYGSRIFNEMLSRIFGIPRGKKSSIWDVPDVVLTNDDLMRYFIAGLFDAD +GSVDETGPAVILTTKSESAARKIWYALQRLGIISTVSRVRNRGFKEGHIFRVIISSVEDL +KKFDALIPLSHSRKREKLKAILKEKRPYRGRYTYRVPISPEMIKPLRTRLNLTVAELSKL +ASKYAGETITESLIRHVEKGRTSEIRRSALKGIALALQRIAQDIGDEDAWVMAKRLELIA +DGDVYWDRVVEVEEVDPEEIGIEYLYDLTVDEDHNYVANGILLSNC +>Pho_KlbA +GALYDFSIIQLSNGRFVLIGDLVEELFKKYSDKIERYKDLEYIELNDEDRFEVVSVGPD +LKANKHIVSRVWRRRVREGEKLIRIKTRTGNEVILTRSHPLFAFSNGDVVRKEAGNLKVG +DRVAVMMNPPKPPQTKAVVDLSIYAKISDYYLVPNGKGMIKVPNKGLPPEKAQYLVSVNS +HPVKLVREVDEKLSYLAGVILGDGYISSNGYYISATFDDEDYMEAFVSVISDFIPNYIPN +VKENGKYMVVTVGSKIFAEMLSRIFGIPKGRKLEWDVPDIVLSNDDLMRYFIAGLFDAD +GYVDENSIILVTKSENVARKIWYALQRLGIISTVSRVKNKGFKEGEIFRVIISGVDDL +AKFARSIPLHHSRKRAKLMEVLKTKKTHRGRRAYRVPISAEMIAPLRQMLGLTVSELSKL +ASHYAGEKVSESLIRHVEKGRVKEIRRSTLRGIALALQQVAKDVGDEEAWVKARRLQLIA +EGDVYWDEVVSVEEVDPKELGIEYVYDLTVEDDHNYVANGILVSNC +>Mja_Klba +GALAYDEPIYLSDGNIINIGEFVDKFFKKYKNSIKKEDNGFGWIDIGNENIYIKSFNKLS +LIIEDKRILRVWRKKYSGKLIKITTKNRREITLTHDHPVYISKTGEVLEINAEMVKVG +DYIYIP + + + + +K +NNTINLDEVIKVETVDYNGHIYDLTVEDNHTYIAGKNEGFAVSNC +>Pfu_KlbA +GALYDFSVIQLSNGRFVLIGDLVEELFKKYAEKIKTYKDLEYIELNEEDRFEVVSVSPD +lKANKHVVSRVWRRKVREGEKLIRIKTRTGNEIILTRNHPLFAFSNGDVVRKEAEKLKVG +DRVAVMMRPPSPPQTKAVVDPAIYVKISDYYLVPNGKGMIKVPNDGIPPEKAQYLLSVNS +YPVKLVREVDEKLSYLAGVILGDGYISSNGYYISATFDDEAYMDAFVSVVSDFIPNYVPS +IRKNGDYTIVTVGSKIFAEMLSRIFGIPRGRKSMWDIPDVVLSNDDLMRYFIAGLFDAD +GYVDENGPSIVLVTKSETVARKIWYVLQRlGIISTVSRVKSRGFKEGELFRVIISGVEDL +AKFAKFIPLRHSRKRAKLMEILRTKKPYRGRRTYRVPISSDMIAPLRQMLGLTVAELSKL +ASYYAGEKVSESLIRHIEKGRVKEIRRSTLKGIALALQQIAKDVGNEEAWVRAKRLQlIA +EGDVYWDEVVSVEEVDPKELGIEYVYDLTVEDDHNYVANGILVSNC +:::::::::::::: +lhr.ina +:::::::::::::: +>Pho_LHR +VCVSGDSKVLTEKGPVEIRHLNSGMIVGINGFKSRFVKFQELHQVKYQEYGVKIRTQLG +FEVKCTREHRFLTIDKNGELRWVEAWRLKEGDYVGIIRKLPSPNSKVLILDFLPESTYLW +LNKEFLKKLKVSIKEKFGSIKNYAKERGFNSSYLVKQLNGLSPFRWGRLRVILNDVSIEI +SRDDIERITSRRGKYSLPPELTPGIARLLGFWMASGSLNRNTLIFYSQDKKILERYEDL +CKREFRVKGRIKAQDKGTYILEIPSSLLSFVFKNLARPKLEVPPIIYILPEKHK +EEFLAGYFDGNGFIKIENGRIHSLGFFAFNRKFAEGIRDILLQLGILSSINEQ +TFEVSIIEGEKFLKIVNSWRSNYYKEWEDVIPNLE +KRLKEIEEKLGYPGTYNRREIRRSELKAIIKLYEKVARERGLNDVL +KELSYLKELSEGDIFFDRITSIEPVYLDVAYGIINSETGNYVVNGFVSKNS +>MspFS40622_LHR +VCVSPDTKILTNNGLIEIKDLKSNNKILGIDNFKGKFTEFDKPHIRDYNNDGFLIKTNLG +FEIKCTKEHRFLTIANGELKWVESRTLKVGDYIAVLRKYPNDGEKINILDLLPDNAYVG +LKKSTLEKIRMKIKEKYGTSKNFSKIIGMEKSHFNAKLRGESPFKLKVLREIEKILSIKI +ESEDIEIIRTNKKKYPMEIKTFTPFLARLLGFWMADGSWTSGCLRLFSSDLQLLKEYEKR +IIEELNMKPHYRRANKSTYCLEISSSVLETMFKNLVGNKKRKSKNGMFPEILYKLPLEHK +KAFLSGYFDGDGFLEIKKDNKLYSIGFSTFNKRFAEGIRDLLLYFGIMSSVRKQEINYEN +ELNGRIIKKRGVSYTVSILGGEYLEKAINILDIWRTKDRELIKKAFSAGYCNIDIIPNIG +KKLREIREKLRISTYKLQKEKFYNPQRVEVGERQISRRNLIKLMNKYLDYAKKTNNKEVI +EEIESLLRLAEGDIFFDRIKEIKSIKLKKVYGIINSKTGNYIVNNFISKNS +>Tko_LHR +VCVSGDSKILTGKGPVEIGRLNSNMIAGIWRFQTELVRFEEPHRVEYRREGVKIRTRLG +FEIKATKEHKFLTVDENGELRWVEAWKLKEGNWVGVVRRLPSPNVKVSILDLLPPNAYLK +LKGEFLRELKLSIQAKFGSIRTYAKKKRWSESYLVKQLNGVYPFRWERLSAVLKDLDLRM +TENDVERITSDKGKYSLPIEFTPSMARLLGFWMADGSWKGGTLTLFSSDRKMLEKYKEL +CKEEFGVVGRIRMLNESTYSLEISFNLLPAIFKNLTGNTERKSKLGTFPSIIYSLPEEHK +REFLAGYFDGDGFLEVKGGRVYSAGFSTFNKRFAEGIRDILLQLGIVSSIRAREYDEVQ +KFKGRVIPKKGASYTVSVLGGEYLKRFFDAVRPWRSDYEGWEGMYNEGYSNSDVVPNLG +KRLRSIRERLGISAYRMSKMGFYNPVRVELGEREISRRNLRLLVEFYERVAKEKRVEDVL +EELSYLRELAEGDVFFDRITSVEPAYIDVAYGIINSETENYIVEGFISKNS +>TonNA1_LHR +VCVPGHSKIFTAEGTRRIDRLGEKTAIVGVEETRSRFVGFDGTHKIEYNTKGVKIRTRLG +FEVEATLGHKFLTVKDGRLTWVEAGELKPGDYVGVLRRLPSPEKEVPIFEVLPGSAYLH +LRAEFLRELKRNIQAKFGSIKAFAKRWNMGESHLSKQLRGEYPFSWERLKLILSEVDMTI +EEDDVERITSDKNSYKLSKKFTPGMARLLGFWLADGSWKGGTVTLFSGDLEMLKRYAEL +AKQEFGIDGHIRRQNESTYALELSFNVLLHLFSGLVGKNKKSKFGVFPEILYRLPMKHK +IQFLSGYFDGDGYLEVKGGRIYSAGFVTFNPEFAEGIRNLLLQLGIVSSLRSQDYDEEQ +FFRGRTVPKKGTSYTVAVLGGDYLRTFGELIEPWRPNLRKIKGLSTGYSNRDVIPNLG +KKLREIRETLGISSYRLQKMGIYNPMKVELGTREISRRNLVRLLDFYEMVAKEREMSDVL +AEIQRLKELAEGDVFFDRIESIEPVFIKEAYGILNSETGNYVVNGFVSKNS +>TspAM4_LHR +VCVPGHSKIITSRGIRRIDGLSVDEEIVGVKESRSRFVEFGGTHRIEYNSTGVKLKTRLG 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+IILDRFDVARTYNEEKKLKDYFRWKDYYEKTGNGYKRVAKELGIKESTLRWWTQGAKPKS +LKMAEELEKLGLLPLKNEDERLEEIAKVMGILFSDGNIDKNLNTLSFVSSEREAIEKFVR +ILGNLFGEFEYEIKENREAMGESILFRTWDRRVIRFFVALGAPVGNKTMVKLELPWWIKL +KPSLFLAFIDGLYSGDGSVPRFAHYRDGIKFNGTLEIAQLTDELEKKLPFFEEIAWHLGL +FGIEAKVRVDKADGKYKVRLIFSQSIDNVLNFLEFIQISLSPSKRERFLGEVEKYINAVP +DSSLAEKLKEFKERFERIKKEERRNFIESSEEVEVTYNVTTETGNLLANGLFVKNS +>TspAM4_Lon +QCFSGNESVVIRENGKIKAVKLKNFVENALKNPSGEGTDGDVRVVYHDFRNENVEVLTRE +GFTKLLYANKRVGKQRLRRIVNLEKDYWLALTPDHRVYTPSGLKEVGELTERDELISVPV +VVLDEFGIAGTYGEEDKLRDYFRWMEHRERTGHGYKRASKELGIKASTLRWWEKGAKPKS +LKMAEKLKGLDLLPLRSDDERLEKVALLVGALFSDGNIDRNLNTLSFISSEKEAVERFVD +TLRELFGEFDYEIKENREAKGRSVLFRTWDRRVIRFFVALGAPVGNKTRVRLELPWWVKL +KPSLFLAFFDGFYSGDGSVPRFARYKEGIKFNGTLEVAQLAEELEDKLPFFEELAWHLGL +FGIDAKVRVDEARGKHKVRLILSQSIDNVLTFLELVPISLSPAKREKFIAEVEKYLNEAG +DSRHADRLDELRKWFERVKKSEKRTFVETWEEVEVTYNLTTERGNLVANGLFVKNS +:::::::::::::: +mupF.ina +:::::::::::::: +>AgPS1249_MupF +NCFPGQSELKGLPRPEKLYRRWYSGKLTELVTDNGTVLLATPNHPILTSNGIKSIDSVNV 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+:::::::::::::: +>Mja_PEP +TCIEGDAKILTDRGFLKMKEVYKLVKNGEKLKVLGLNAETLKTEWKEIIDAQKREARRYE +IGVYRKNKNTKDTIKITPDHKFPVFVNGELSKVQLCDIIDNNLSVLSIDYIPMIEEKYES +LAEVMYLGGAVLSDGHIVRRNGKPIRVRFTQKDTEEKKDFIEKVKGDVKLIGGNFIEISN +RNNVIEYQTSRKIPSEILGFIEVNINTIPLYATKDEIADLIAGFVDG +DGCLSGKRRVEIYQNSSHIKKIEGLIVGLYRLGIIPRLRYKRSSTATIYFNNNLETILQR +TRRIKLDKLKEFKKPVEDKKLIDISQILPELKEFDYKGYLYKTYKEKLFIGINKLEEYL +SKIDKDGIERIKQKIKLLKESDIYSIRIKKVGEDYGEVYNITVKAENEFNHNYVVWTKH +YTPIVVFNC +>Cwa_PEP +TCFDGKTKILTNQGFMTLRQVYEQGYEGLSTLSLNTKTHKIEWKPILDTMKRQSEMID +ISVSQTGRITDNTLRLTPDHKMVNLRGGKYTKTEIQDLLKQQEMLTVAQTIPSLGNNKHQ +EADLAYFLGGIITDGSIYTSSTRGEVQFIQKDVPEKQAFISKMNDLANSLYGKSFTAHI +KPVSSSYIRGQKVTGQATAYRLHSKAIAYDVKERENNITQLLLENEAELSYHFLGGVIDG +DGCYHKNRLHIYISEENLLQAVIIACLKMNTVPQVTKNRNIYHLQIVEKLEVILRY +TQRVKGEVTPRTIQTRFFATRQLFENQETGQIKLRQDNNCLISDKQL +REMGEFEELIDGDTRMQRVIQVGEKSDGDVYNITVAEHHNYVVFTAK +YTPVVVCNC +>MeinME_PEP +TCIEGDAKILTDRGFITMREAYELVKNGEKIRVLGLNAKTLRTEWKEIIDAQKREAKRFE 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+ADEVLLKYEREDNQIPTGFGMDDWLELVGWFVTAGRFAHEAKRIVLRR +QDEEGRSAIRSLLERMELPYDADGTRVTVSNRVLYDWFVKNCGDGATET +RLPEWVFELDAAHLRTLLETLVDGDGSRTDSGLGEFWTQSDRLKDDVVRLAVRCGEKP +TVSENQDGTWYVSVGTRGSMKKSNATVEDHDGDVHCITAEDNHVVLAGRNGHL +QWVGQS +>Tfu_Pol1 +RCHPADTKVIVKGKGVVNISEVREGDYVLGID +GWQKVQRVWEYDYEGELVNINGLKCTPNHKLPVVRRTERQTAI +RDSLAKSFLTKKVKGKLITTPLFEKIGKIEREDVPEEEILKGELAGIILAEGTLLR +KDVEYFDSSRGKKRVSHQYRVEITVGAQEEDFQRRIVYIFERLFGVTPSVYRKKN +TNAITFKVAKKEVYLRVREIMDGIENLHAPSVLRGFFEGDGSVNKVRKTV +VVNQGTNNEWKIEVVSKLLNKLGIPHRRYTYDYTEREK +TMTTHILEIAGRDGLILFQTIVGFISTEKNMALEEAIRNRE +VNRLENNAFYTLADFTAKTEYYKGKVYDLTLEGTPYYFANGIL +THNS +>Tag_Pol1_(TspTY_Pol1) +RCHPADTKVIVKGKGIVNISDVKEGDYILGID +GWQRVKKVWKYHYEGKLININGLKCTPNHKVPVVTENDRQTRI +RDSLAKSFLSGKVKGKIITTKLFEKIAEFEKNKPSEEEILKGELSGIILAEGTLLR +KDIEYFDSSRGKKRISHQYRVEITIGENEKELLERILYIFDKLFGIRPSVKKKGD +TNALKITTAKKAVYLQIEELLKNIESLYAPAVLRGFFERDATVNKIRSTI +VVTQGTNNKWKIDIVAKLLDSLGIPYSRYEYKYIENGK +ELTKHILEITGRDGLILFQTLVGFISSEKNEALEKAIEVRE 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+KVRGDELKPGDLVVVPGRLKLPESKQVLNLVELLLKLPEEETSNIVMMIPVKGRKN +FFKGMLKTLYWIFGEGERPRTAGRYLKHLERLGYVKLKRRGCEVLDWESLKRY +RKLYETLIKNLKYNGNSRAYMVEFNSLRDVVSLMPIEELKEWIIGEPRGPKIGTFIDVDD +SFAKLLGYYISSGDVEKDRVKFHSKDQNVLEDIAKLAE +KLFGKVRRGRGYIEVSGKISHAIFRVL +AEGKRIPEFIFTSPMDIKVAFLKGLNGNAEELTFSTKSELLVNQL +ILLLNSIGVSDIKIEHEKGVYRVYINKKESS +NGDIVLDSVESIEVEKYEGYVYDLSVEDNE +NFLVGFGLLYAHNS +>MespFS406_PolB3 +NSILPNQWMPIVEDNDIKFVKIDNYINQLMDRNKYKIKFDGNSEILEVDNL +KAFSFNRQSKKCEIKRVKALIRHKYSGKAYKIKLRSGREIEVTMGHSLFKYENGKIV +EVKGEDVKVDDLIVVPKSIVAIEEDITINIPKVLAKLDDDSLILEIPKEKRN +EIKKKISTIKDKSL +RKFYELILKHSKYTKNGNYIIKLSKVKDIIDYIPDKEFINFKIGTRGGKRINAIIKLDE +DVAKFLGYYVSEGYARCSKNQKNGYSYEIYIANHDKDILKDMERVTT +KIFDKCKVCKDRVRVMSKIAYLFVNYVVPCGI +KAENKQIPEIIFKAKKSIKLAFLEGYFIGDGDIHPSKRLRLSTKSEKLAYQL +MFLLNSLGISAVKIGFDSGVYRVYINEDLPFITTNRKRNKYYSNVIPKEILEYIFNKKF +QNNMSIDKFKEFIKDKDINGFEWLLNGDITFDRVKEIEEFDYNGYVYDLSVEDNE +NFLINNIYAHNS +>Hma_PolB +NCFTPDTDVLTPEGVQNIRDLDIGD +EVYSLDPETEEMEVKPVVETQSYPDYRGDLVDIETSKMDFRVTPNHRMLVRKNETNGIT +EDGYSFVEAGDLDDATNYELPHDWDGPDGDPLDTVDLTEYVDDYE +VWVRPSVHGHTFAAEIGHYPDTVLKNDIGEEGYVFGPKEFEAN +REYIESVAERTYIHAESGRKWIPRTFDGD +DFLELLAWYITEGNVYTSETKQFGEKTRGASTTVKIAQQAIADGGESDHAAIGDLLD +RLGFDYYVDDRSYQFTSALLGDLLCNICGE +DSFEKRIPEFVFDLSHRQKRRFLDTLIAGDGDRQKNSWRYTTSSDQLRDDV +LRLCAHLGLTANYNRDSGSWRIYVTEDNKN +TLRMHRSGSRSTADDGVYCVTVADNH +TLMAGRNGKFQFVGQS +>TspGE8_Pol1 +NSILPDEWLPLLVNGRLKLVRIGDFVDNTMKKGQPLENDGTEVLEVSGI +EAISFNRKTKIAEIKPVKALIRHRYRGKVYDIKLSSGRNIKVTEGHSLFAFRDGELV +EVTGGEIKPGDFIAVPRRVNLPERHERINLIEILLGLPPEETSDIVLTIPVKGRKN +FFKGMLRTLRWIFEEEQRPRTARRYLEHLQKLGYVKLMKRAYEIVNKEALRNY +RKLYEVLAERVKYNGNKREYLVHFNDLRNEIKFMPDEELEEWKVGTLNGFRMEPFIEVGE +DFAKLLGYYVSEGYARKQRNQKNGWSYSVKIYNNDQRVLDDMEKLAS +KFFGRVRRGKNYVEISRKMAYVLFESLCGT +LAENKRVPEVIFTSPESVRWAFFEGYFIGDGDLHPSKRVRLSTKSEELVNGL +VVLLNSLGISAIKIRFDSGVYRVLVNEELPFLGNRKRKNAYYSHVIPKEILEETFGKQF +QKNMSPAKLNEKVEKGELDAGKARRIAWLLEGDIVLDRVEKVTVEDYEGYVYDLSVEENE +NFLAGFGMLYAHNS +>Hwa_PolB2 +NCFTPDTNVLTPNGVRNIRDLTVGD +SVYSLNPETMQMEIKPVTQTHEYPDYQGDLIDIQTNEIDFRVTPNHRMLVEATGTDTTS +TNDYDFIEAGNLDISSRYELPHGWSVDHTDSLGAYIDLITLLREQSD +TYNVLSDGGMTTAATADINHNNVTRRVDS +D +TFVSLIGWYVATGRVSRTQNGSDRVYLQLSQTNTKARTQLTMLLD +ELGVDWQADNEKIHFVSHVWTELFDTTCGR +TEKNKHIPELIFDASASQKRAFFDAIINGSGVKNDDSYQYHTSSEDLRDDI +LRLCVHIGIVARYDYINDESWRIECTETANP +DFTLTHSGRQSTAEDGVYCVTVADNQ +TLLAGRNGTFQWTGNS +>MvuM7_Pol2 +NSILPDEYLTVIEDDGVKIVKIGEYINRLMEKYPNKIKLSEVLEVKNL +KTFSFNKLTKKCEIKKVKGLIRHKYEGKAYKIKLRSGRTIRVTEGHSLFKYENGEIV +EVKGNEIKINDLIVVPRKIAHINKKIVINIPKRLVDADEEDIKNLVITKHKDKI +HFIKLKKTLEDIERNKFNVIFDDCILYLKKLGLIDYNIIKAINKVEIKILDKKKFKIY +KKYIDTIIEHGNFARGRSNIQYLKIKDLINDIPDEEFEDCEIGALCGKINALLKLDE +NLAKFLGYFVTRGGLNKYKAKEGTTHEVAIFKSLPDYQKEIVKIFK +KTFGAGCISKDKVIMDNKIVYLILKYIFKCG +NKNKKHIPEEIFLADEKVIKSFLDGFLKAKKNSHKGTTTFMAKDEDYLNQL +MILFNLVGIPTRFTPVKNKGYKLTLNPNYKLIN +DLMLDEVKEIEEFNYNGYVYDLSVEDNE +NFLVNNIYAHNS +>MespFS406_PolB2 +NSILPDEYLTVIEEDGVKIIKIGDYIDDLMRKHKDKIKYDGLSEILEVDNL +KTYSFNRKTKKCSINRVKALIRHPYSGKAYKIKLRSGRTIKVTEDHSLFKFEKGRPV +CVRGDEIQPGDLIVVPRKLKFVNKKDVIINIPKRLVDADEEELKDLTITKHKDKE +FLVRLRKTLEDIKNNKLKIIFDDCISYLENLGLIDYSIIKKINKIDIKILDEEKFDAY +KKYIDTFVEYGTFRKDRCNIQYIRIKDYIPNIPDKEFEDCEIGAYSGKINALLKLDE +KLAKFLGYFVTRGRLKKLKIKGETVYEISVYKSLPEYQKEIAEVFK +EAFGAGSIAKDKVTMDNKIIYLVLKYIFKCG +NRDKKHIPEEIFLANENIIKSFLEGFLKAKKNSHKGTTTFMAKDEKYLHQL +ILLFSLVGIPTRFTPVKNKGYKLTLNPNYTIVE +DLMLDEVKEVEAFDYTGYVYDLSVEKYE +NFLINNIYAHNS +>Tko_PolII +NSILPEEWLPVLEEGEVHFVRIGELIDRMMEENAGKVKREGETEVLEVSGL +EVPSFNRRTNKAELKRVKALIRHDYSGKVYTIRLKSGRRIKITSGHSLFSVRNGELV +EVTGDELKPGDLVAVPRRLELPERNHVLNLVELLLGTPEEETLDIVMTIPVKGKKN +FFKGMLRTLRWIFGEEKRPRTARRYLRHLEDLGYVRLKKIGYEVLDWDSLKNY +RRLYEALVENVRYNGNKREYLVEFNSIRDAVGIMPLKELKEWKIGTLNGFRMRKLIEVDE +SLAKLLGYYVSEGYARKQRNPKNGWSYSVKLYNEDPEVLDDMERLAS +RFFGKVRRGRNYVEIPKKIGYLLFENMCGV +LAENKRIPEFVFTSPKGVRLAFLEGYSSAMATSTEQETQALNEKRALANQL +VLLLNSVGVSAVKLGHDSGVYRVYINEELPFVKLDKKKNAYYSHVIPKEVLSEVFGKVF +QKNVSPQTFRKMVEDGRLDPEKAQRLSWLIEGDVVLDRVESVDVEDYDGYVYDLSVEDNE +NFLVGFGLVYAHNS +>NmaATCC43099_PolB2 +NCFTPDTEVLTPDGVRDITDLEVGD +EVYSLDPETEALEVKPVVETHAYPEYDGDLVDIETNKIDFRVTPNHRMLVRKNETNGIT +EDEYSFIEAGDLDRATNYELPHDWDGPDGNELDTVDLTELIDGEYE +VWVRPSVHGHTFTTELGWKPRRVPKADVGKTGYVFTAEEFEAH +REYIEEVCETSFIHRDSGRKWIPRTYDGD +KFLDLLAWFVTEGNVYTSEDKQFGENFRGSATTVKLAQDKLPIADGGLGHHATIGELLD +EMGFDYYVDDRSYTVTSKLLGNFLTSCCGD +GSFEKRIPELVFECSHRQKRRFLEVLIDGDGDRQTNSWRYTTSSNRLRDDV +LRLCAHLGLTANYSRDSGTWRIYVTEGSKN +TLRMHRSSTQSTADNGVYCVTVEDNH +TLLAGRNGKFQFVGQS +>MfeAG86_Pol1 +NSILPDEYLVVIEDDKVKVTKIGEYVDNLIEKNKEKVKYEKKSEILEVDNL +KTYAFSKIDKKCRIRKVKALIRHPYSGKAYKIKLRSGRSIKVTKGHGLFKYENGKIV +AVKGDEIKIKDLIVVPRKIPYINKEVIINIPKGLIDADEEEINDLTITKHKDKE +FLVKLKKTIEDIEKNKLNVVFEDCLKYLEDLGLIRYEGIKRINKLEIDIPNKRKLSIY +KKYIETILDYGTFRKGKCNIQYIKVKEYIPDIPDKEFEDCEIGAYSGKIKALLRLNE +NLAKFLGYFVARGRLKEIKLKGETVYEACVYKSLPEYQEEIAEVFK +KAFGAGAIARDKVTLDKKIVYLVLKYIFKCG +YKGRKHIPEQLFLANEEVIKSFLDGFLKAKKNSHKGTSTFMAKDEEYLNQL +MLLFNLVGIPTRFTPVKNKGYKLTLNPNYELVK +DLMLDEVKEIEEFDYNGYVYDLSVEEDE +NFLVNNIYAHNS +>Tzi_Pol +NSILPDEWIPLLINGRLKLVRIGDFVDSAMKELKPMKRDETEVLEVSGI +GAISFNRKTKRSETMPVRALLRHRYSGKVYGIKLSSGRKIKVTAGHSLFTFRDGELV +EIKGEEIKPGDFIAVPGRINLPERQERINLVEVLLGLPEEETADIVLTIPVKGRRN +FFKGMLRTLRWIFGEEKRPGTARRYLEHLQTLGYVRLGKIGYEIVNEEALRDY +RGLYETLTGKVKYNGNKREYLVHFNDLRDIIRLMPEKELKEWKVGTLNGFRMETSIEVKE +DFAKLLSYYVSEGYAGKQRSQKNGWNYSVKLYNNDQNVLDDMETLAS +KFFGKVRRGKNYVEIPRKMAYVLFESLCGT +LAENKRVPEIIFTSPESVRWAFLEGCFIGDGDLHPGKGVRLSTKSEELVNGL +VILLNSLGVSALRIWLDSGVYRVLVNEELPFLDKGKKKTPYVTSKEIPEEAFGKRF +QRNISLEKLREKVEKGEPDAEKVKRVVWLLEGDIVLDRVEEVAVDDYEGYVYDLSVEENE +NFLAGFGMLYAHNS +>S42459__Tli_Pol1 +NSILPNEWLPIIENGEIKFVKIGEFINSYMEKQKENVKTVENTEVLEVNNL +FAFSFNKKIKESEVKKVKALIRHKYKGKAYEIQLSSGRKINITAGHSLFTVRNGEIK +EVSGDGIKEGDLIVAPKKIKLNEKGVSINIPELISDLSEEETADIVMTISAKGRKN +FFKGMLRTLRWMFGEENRRIRTFNRYLFHLEKLGLIKLLPRGYEVTDWERLKKY +KQLYEKLAGSVKYNGNKREYLVMFNEIKDFISYFPQKELEEWKIGTLNGFRTNCILKVDE +DFGKLLGYYVSEGYAGAQKNKTGGISYSVKLYNEDPNVLESMKNVAE +KFFGKVRVDRNCVSISKKMAYLVMKCLCGA +LAENKRIPSVILTSPEPVRWSFLEAYFTGDGDIHPSKRFRLSTKSELLANQL +VFLLNSLGISSVKIGFDSGVYRVYINEDLQFPQTSREKNTYYSNLIPKEILRDVFGKEF +QKNMTFKKFKELVDSGKLNREKAKLLEFFINGDIVLDRVKSVKEKDYEGYVYDLSVEDNE +NFLVGFGLLYAHNS +>Thy_Pol1 +NSLLPEEWIPLVENGKVRLHRIGEFVDKLMETDSELVKRNGDTEVLEVRGI +RALSFDRKSKKARVMPVKAVIRHRYSGDVYEIVLGSGRRITVTEGHSLFAYGDGELR +EVTGGEIKAGDLLAVPRRVNLPEKKERLNLVELLRRLPEEETGDIILTIPVKGRKN +FFKGMLRTLRWISGEEKRPRTARRYLEHLEGLGYVRLKKIGYEVTDREGLERY +RKLYERLVEAVRYNGNKREYLVEFNAVRDVIALMPEEELRDWLVGTRNGFRMRPFVEIEE +DFAKLLGYYVSEGNARKWRNQKNGWSYTVKLYNENQRVLDDMESLAE +RFFGRVKRGKNYIEIPRKMAYIIFENLCGT +LAENKRVPEAIFTSPESVRWAFIEGYFIGDGDVHPSKRVRLSTKSELLVNGL +VLLLNSLGVSAIKIRHDSGVYRVYVNEELPFTDYRKKKNAYYSHVIPKEILEETFGKVF +QRSVSYEKFRELVKSEKLDGEKAKRIEWLLNGDVVLDKVLEVKKRPYEGYVYDLSVEEDE +NFLAGFGLLYAHNS +>PspGBD_Pol +NSILPEEWVPLIKNGKVKIFRIGDFVDGLMKANQGKVKKTGDTEVLEVAGI +HAFSFDRKSKKARVMAVKAVIRHRYSGNVYRIVLNSGRKITITEGHSLFVYRNGDLV +EATGEDVKIGDLLAVPRSVNLPEKRERLNIVELLLNLSPEETEDIILTIPVKGRKN +FFKGMLRTLRWIFGEEKRVRTASRYLRHLENLGYIRLRKIGYDIIDKEGLEKY +RTLYEKLVDVVRYNGNKREYLVEFNAVRDVISLMPEEELKEWRIGTRNGFRMGTFVDIDE +DFAKLLGYYVSEGSARKWKNQTGGWSYTVRLYNENDEVLDDMEHLAK +KFFGKVKRGKNYVEIPKKMAYIIFESLCGT +LAENKRVPEVIFTSSKGVRWAFLEGYFIGDGDVHPSKRVRLSTKSELLVNGL +VLLLNSLGVSAIKLGYDSGVYRVYVNEELKFTEYRKKKNVYHSHIVPKDILKETFGKVF +QKNISYKKFRELVENGKLDREKAKRIEWLLNGDIVLDRVVEIKREYYDGYVYDLSVDEDE +NFLAGFGFLYAHNS +>TonNA1_Pol +NSILPDEWVPLLIDGRLKLTRIGDFVDNAMDEGNPLKSNETEVLEVLGI +NAISFNRKTKISEVRPVRALIRHRYRGKVYSIKLSSGRKIKVTEGHSLFTVKNGELV +EVTGGKVKPGDFIAVPRRINLPERHERINLADVLLNLPEEETADVVLTIPTKGRKN +FFRGMLRTLRWIFEGEKRPRTARRYLEHLQKLGYVRLKKIGYEVLDEKALRKY +RALYEVLAEKVRYNGNKREYLVAFNDLRDKIEFMPEEELREWKIGTLNGFRMEPFIEVNE +DLAKLLGYYVSEGYAGKQRNQKNGWSYSVKLYNNDQKVLDDMERLAS +KFFGKVRRGKNYVEMPKKMAYVLFKSLCGT +LAENKRVPEVIFTSPENVRWAFLEGYFIGDGDLHPSKRVRLSTKSETLVNGL +IILLNSLGISAVKIRFESGVYRVLVNEELSFLGNSKKKNAYYSHVIPKEILEDVFEKRF +QKNVSPKKLREKIKRGELNQEKAKRISWLLEGDIVLDRVEEVEVEDYNGYVYDLSVEENE +NFLAGFGMIYAHNS +>P77933___Tko_Pol2_(Psp_KOD_Pol2) +SVTGDRPVVVRDPGGTVRILPIEDLFARGTTESEVLIAADGDVVASATPGKTRRALDGW +DALSVNEDGEAEWQPIAQAIRHNTDKPVVNLQHKFGESTTTRDHSYVVPGEDGLT +TVSPDDVAEPYRVSGVPDVEPVEQVDVYEVLRGYEREYEDGRSVGSDNSITKRKQ +IHADDEYVWFGHEHHRDVDSTVKVKRFVD +IDSEDGAA +LIRLLGAYVPEGSASTGETATSKFGASLAESDREWLAQLQRDYS +RLFENTTAGIITSDRRAERTVEYQTDTGGASVTYNDETLKLQMMNELAAVFFREFAGQ +TSRGKRIPSFVFHLPEEKQDLFLTLLVEGDGSREFPRYTEAYAQRNFDFETTSRELAAGL +SMLLTQRGQKHSLKYRDSKDSYTIRTCSTYREGR +DPVLTEADHDGYVYDLSVEENE +NFVDGVGGIVLHNT +>Tma_Pol +NSLLPEEWIPVVENGKVKLVRIGEFVDGLMKDEKGRAKRDGNTEVLEVSGI +RAVSFDRKTKKARLMPVKAVIRHRYSGDVYKITLSSGRKITVTKGHSLFAYRNGELV +EVPGEEIKAGDLLAVPRRVHLPERYERLDLVELLLKLPEEETEDIILTIPAKGRKN +FFKGMLRTLRWIFGEEKRPRTARRYLRHLEGLGYVKLRKIGYEIIDREGLKRY +RKLYERLAEVVRYNGNKREYLIEFNAVRDVISLMPEEELNEWQVGTRNGFRIKPLIEVDE +DFAKLLGYYVSEGYAGKQRNQKNGWSYTVKLYNEDERVLDDMENLAR +EFFGKARRGRNYVEIPRKMAYIIFESLCGT +LAENKRVPEVIFTSPEDVRWAFLEGYFIGDGDVHPSKRVRLSTKSELLANGL +VLLLNSLGVSAVKLGHDSGVYRVYVNEELPFTGYKKKKNAYYSHVIPKEVLEETFGKVF +QRNMSYEKFQELVESEKLEGEKAKRIEWLISGDIILDKVVEVKKMNYEGYVYDLSVEEDE +NFLAGFGFLYAHNS +>Tthi_Pol +NSLLPEEWVPVIVGDEVKPVRIGEFVDALMKTDSELVRRDGDTEVLEVKEI +RALSFNRKSKKARTMPVKAVIRHRYAGDVYEIVLSSGRRIRVTTGHSLFAYRNGELV +EITGGEVKPGDLLAVPKRVSLPERKERLDIVELLLKLPESETEDIVMTIPVKGRKN +FFSGMLRTLRWIFGEEKRLRTARRYLEHLERLGYVKLRKIGYEVIDGGGLESY +RKLYEKLAQTVRYNGNRREYLVDFNAIRDVIPLMPVEELKEWLIGTRNGFRMRPFIDVNE +DFAKLLGYYVSEGNARKWKNHTGGWSYSVKLYNEDESVLDDMERLAS +KFFGRTRRGKNYVEIPRKMAYIIFEGLCGV +LAENKRVPEVVFTSPENVRWAFLGGYFIGDGDVHPGKRVRLSTKSELLVNGL +VLLLNSLGISAIKIRHDSGVHRVYVNEELPFTEYRKKKNVYYSHVIPKEVLEETFRKVF +QKNMSREKFRELVESGKLDEERAKRIEWLLDGDIALDKVVEVKREHYDGYVYDLSVEEDE +NFLAGFGLLYAHNS +>TspOGLP20_Pol +NSLLPEEWVPVIVGDEVKPVRIGEFVDALMKTDSELVRRDGDTEVLEVKEI +RALSFNRKSKKARTMPVKAVIRHRYAGDVYEIVLSSGRRIRVTTGHSLFAYRNGELV +EITGGEVKPGDLLAVPKRVSLPERKERLDIVELLLKLPESETEDIVMTIPVKGRKN +FFSGMLRTLRWIFGEEKRLRTARRYLEHLERLGYVKLRKIGYEVIDGGGLESY +RKLYEKLAQTVRYNGNRREYLVDFNAIRDVIPLMPVEELKEWLIGTRNGFRMRPFIDVNE +DFAKLLGYYVSEGNARKWKNHTGGWSYSVKLYNEDESVLDDMERLAS +KFFGRTRRGKNYVEIPRKMAYIIFEGLCGV +LAENKRVPEVVFTSPENVRWAFLGGYFIGDGDVHPGKRVRLSTKSELLVNGL +VLLLNSLGISAIKIRHDSGVHRVYVNEELPFTEYRKKKNVYYSHVIPKEVLEETFRKVF +QKNMSREKFRELVESGKLDEERAKRIEWLLDGDIALDKVVEVKREHYDGYVYDLSVEEDE +NFLAGFGLLYAHNS +>HmuDSM12286_PolB +NCFTPDTEVVTPEGVRDITDLEVGD +EVYSLDPETMRMEVKPVVETHDYPDYRGDLVDIETSKIDFRVTPNHRMLVRKNETNGIT +EDEYGFVEAGELDRATNYELPHDWDGPDGERLNEVDLVDILEGAFE +VWCDNDDHGHTLAAEVGYRPDKMQKQGEDGTGYVFDAESFREH +RAYIDESCSGFYVHSERGRKWIPRFYDGD +DFLELLAWYITEGSIYTSADKQFGEHFRGSSTTVNIAQDAVPDGGSGDDHTRIGSLLD +GMGFDAYVDEKGYQFTSKLLGDLFERLCGS +DSFEKRIPEFVFETSQAQKRTFLDTLIAGDGDWQTNSWRYSTASERLRDDV +LRLCAHLGLTASYNEDSGTYRIYVTEDSKN +TLRMHRSGGESTAENGVHCVTVEDNH +TLLAGRNGKFQFVGQS +>Nph_PolB2 +NCFTPDTEVLTPDGVRNIRALDIGD +EVYSLDPETMEMEVKPVVDTHAYPDYRGELVDIQTGEIDFRVTPNHRMLVRKNGTNGIT +DDEYRFVEAGALDLATTYELPHDWAGPDGEDVTQIDLTELIDEEYE +VWVRPEVHGRTFTAELGWKPRRVPKADIDTVGYVFTADEFKQH +REYIESVCEQSYIRRESGLKWIPRVYDGD +DFLELLAWYVTEGNAHTSERKEFDGQRHGSSTVQIAQEPVVADGGDTHATIGTLLD +RMGFDYDNDNGSYQVTSKLLGDLFCTLGGG +GSEDKRIPQLVFEASRRQKERFMQTLISGDGDRQPNSWQYNTASERLRDDV +LRLCAHLGVPASYSEESGVYRIYVTEDGTN +TLRMDRSAERTTADDGVYCVTVEDNH +TLLAGRAGKFQFVGQS +>Tag_Pol2_(TspTY_Pol2) +NSILPNEWLPIIENGEVKFVKIGEFIDRYMEEQKDKVRTVDNTEVLEVDNI +FAFSLNKESKKSEIKKVKALIRHKYKGEAYEVELNSGRKIHITRGHSLFTIRNGKIK +EIWGEEVKVGDLIIVPKKVKLNEKEAVINIPELISKLPDEDTADVVMTTPVKGRKN +FFKGMLRTLKWIFGEESKRIRTFNRYLFHLEELGFVKLLPRGYEVTDWEGLKRY +RQLYEKLVKNLRYNGNKREYLVRFNDIKDSVSCFPRKELEEWKIGTXKGFRXKCILKVDE +DFGKFLGYYVSEGYAGAQKNKTGGMSYSVKLYNENPNVLKDMKNIAE +KFFGKVRVGKNCVDIPKKMAYLLAKSLCGV +TAENKRIPSIIFDSSEPVRWAFLRAYFVGDGDIHPSKRLRLSTKSELLANQL +VFLLNSLGVSSIKIGFDSGVYRVYINEDLPFLQTSRQKNTYYPNLIPKEVLEEIFGRKF +QKNITFEKFKELADSGKLDKRKVKLLDFLLNGDIVLDRVKNVEKREYEGYVYDLSVEDNE +NFLVGFGLLYAHNS +>TspGT_Pol1 +NSLLPEEWIPLVENGKVRLHRIGEFVDKLMETDSELVKRNGDTEVLEVRGI +RALSFDRKSKKARVMPVKAVIRHRYSGDVYEIVLGSGRRITVTEGHSLFAYGDGELR +EVTGGEIKAGDLLAVPRRVNLPEKKERLNLVELLRRLPEEETGDIILTIPVKGRKN +FFKGMLRTLRWISGEEKRPRTARRYLEHLEGLGYVRLKKIGYEVTDREGLERY +RKLYERLVEAVRYNGNKREYLVEFNAVRDVIALMPEEELRDWLVGTRNGFRMRPFVEIEE +DFAKLLGYYVSEGNARKWRNQKNGWSYTVKLYNENQRVLDDMESLAE +RFFGRVKRGKNYIEIPRKMAYIIFENLCGT +LAENKRVPEAIFTSPESVRWAFIEGYFIGDGDVHPSKRVRLSTKSELLVNGL +VLLLNSLGVSAIKIRHDSGVYRVYVNEELPFTDYRKKKNAYYSHVIPKEILEETFGKVF +QRNVSYEKFRELVKSEKLDGEKAKRIEWLLNGDVVLDKVLEVKKRPYEGYVYDLSVEEDE +NFLAGFGLLYAHNS +>Mja_pol2 +NSILPDEYLTIIEEDGIKVVKIGEYIDDLMRKHKDKIKFSGISEILETKNL +KTFSFDKITKKCEIKKVKALIRHPYFGKAYKIKLRSGRTIKVTRGHSLFKYENGKIV +EVKGDDVRFGDLIVVPKKLTCVDKEVVINIPKRLINADEEEIKDLVITKHKDKA +FFVKLKKTLEDIENNKLKVIFDDCILYLKELGLIDYNIIKKINKVDIKILDEEKFKAY +KKYFDTVIEHGNFKKGRCNIQYIKIKDYIANIPDKEFEDCEIGAYSGKINALLKLDE +KLAKFLGFFVTRGRLKKQKLKGETVYEISVYKSLPEYQKEIAETFK +EVFGAGSMVKDKVTMDNKIVYLVLKYIFKCG +DKDKKHIPEELFLASESVIKSFLDGFLKAKKNSHKGTSTFMAKDEKYLNQL +MILFNLVGIPTRFTPVKNKGYKLTLNPKYGTVK +DLMLDEVKEIEAFEYSGYVYDLSVEDNE +NFLVNNIYAHNS +>Sru_PolBc_ +NCFDPETEVVTVDGIRHVEEIEVGD +RVYSLNPDTGAVEIKPVTATQSQHYAGPMVEIKNQHTDFLVTPNHRFLTQRFTSGEYT +DLEWETAGDMLGDRIRRRLPSLRSLPATQERPGPISLSAVCDRLAI +EHKTGPRGIKELRRQARWQPEEY +ELTDW +LRILGWFATEGTLYKSKARQYENGNVRGVSYQTTLCQKNDIGRSEIATLLN +RTGITYSSDQNDHSFCSKVLYEILEAECGS +DSFSKHLPPWIFQLGPKDLKIVFDTLMQGDSAANGDRFTTSSNQLAEDF +IRLAMHIGRRAFHMPNDGSHRIQVNT +VRGQRPTIKPKHRQQVDYDGMIHCLTVADNH +TVLAGRNRKFNWTGQS +:::::::::::::: +polBc.ina +:::::::::::::: +>Hwa_PolB3 +DSVTGDRPVVVRDPSDYIQIVPIKLLFEQATAPEQNMRLTADGAPSVNSELPKERR +HLDQWEALSLSDTGETEWQPINQIIRHQTDKEILTLQHEYGESTTTRDHSYITADD +GEYVETSPENVDEPLPIPNIASVKTIETIDIYQTLTTDTQAQIGNDTEPDKWLPSADC +IHANDEYVWIGTTDKQQDRDDSTPAIPRYIDLTSDTGHALIRFLAVYLSDWSKSTITTTE +RGQCLHITGPQESALKTCAADADQLFTHITPSIAVDAESNTNT +VDSGFRCHIPTTLATTLISAFAGHPAHTKQIPSIVYHLPAAEQSLFIRHLIQAESTPE +SDGVSGRPQKSDKPILLENEFITTNRELAAGVSMLLTQCGQSYTISKQDTKGAYTIHINN +SSSSGCTPTLTETTH +SGYVYDLSVATNQNFVDGLGGLVLHNT +>MvuM7_Pol3 +DSVVKDAKVIIKEDGKIKEIKIEDLFKKVDYTIGDKEYC +ILNNVETLTIEDTKLVWRKVPYIMRHRTNKKIYRVKVKDRYVDITEDHSII +GVKNNKLVELKPTEIKDDETKLIILNKDL + + + + +KSYNFASVEEINCIKY +SDYVYDIEVENTHRFFANGILVHNT +>Thy_Pol2 +DSVTGETEIIIKRNGKVEFVAIEELFQRVDYRIGEKEYC +VLEGVEALTLDNRGRLVWKSVPYVMRHRTNKRIYRVWFTNSWYLDVTEDHSLI +GYMNTSKVKPGKPLKERLVEVKPGELGESVKSLITPNRAIAHGIR +VNPIAVKLWELIGLLVGDGNWGGQS +NWAKYNVGLSLGLDKEEIEEKILKPLKNTGIISNYYDK +SKKGDVSILSKWLARFMVRYFKDESGSKRIPEFMFNLPREYIEAFLRGLFSA +DGTVSLRKGVPEVRLTSVNPELSSSVRKLLWLVGVSNSMFVETNPNRYLGKESG +THSVHVRIKDKHRFAERIGFLLDRKATKLSENLGGHTSKKRAYKYDFDLVYPKKVEEIAY +DGYVYDIEVEGTHRFFANGILVHNT +>Tfu_Pol2 +DSVTGDTEVTIRRNGRIEFVPIEKLFERVDHRVGEKEYC +VLGGVEALTLDNRGRLVWKKVPYVMRHKTDKRIYRVWFTNSWYLDVTEDHSLI +GYLNTSKVKPGKPLKERLVEVKPEELGGKVKSLITPNRPIARTIK +ANPIAVKLWELIGLLVGDGNWGGQS +NWAKYYVGLSCGLDKAEIERKVLNPLREASVISNYYDK +SKKGDVSILSKWLAGFMVKYFKDENGNKAIPSFMFNLPREYIEAFLRGLFSA +DGTVSLRRGIPEIRLTSVNRELSDAVRKLLWLVGVSNSLFTETKPNRYLEKESG +THSIHVRIKNKHRFADRIGFLIDRKSTKLSENLGGHTNKKRAYKYDFDLVYPRKIEEITY +DGYVYDIEVEGTHRFFANGILVHNT +>TsiMM739_Pol2 +DSVTSDTEIIVKRNGRVEFVPIEKLFERVDYRLGEKEYC +ILESVEALTLDNRGRLVWKKVPYVMRHKAKKKVYRIWITNSWYIDVTEDHSLI +VAEDGLKEAKPIEIEGKSLIATKDDLS + +GV +EYIK + +PRTLEEIPY +DGYVYDIEVEETHRFFANGILVHNT +>Tag_Pol3_(TspTY_Pol3) +DSVTGDTEIIVKRNGRIEFVPIEKLFERVDYRIGEKEYC +ILEDVEALTLDNRGKLIWKKVPYVMRHRAKKKVYRIWITNSWYIDVTEDHSLI +VAEDGLKEARPMEIEGKSLIATKDDLS + +GV +EYIK + +PHAIEEISY +NGYVYDIEVEGTHRFFANGILVHNT +>TspGE8_Pol2 +DSVAGNTEVIIRRNGKVEFVPIEKLFQRVDYRIGEKEYC +ALEGVEALTLDNRGRLVWRKVPYIMRHKTNKKIYRVWFTNSWYLDVTEDHSLI +GYLNTSKVKSEKPLKERLVEVKPRELGEKVKSLITLNRAIARSIK +ANPIAVRLWELIGLLVGDGNWGGHS +KWAKYYVGLSCGLDKAEIEEKVLRPLKEAGIISNYYGK +SKKGDVSILSKWLAGFMVKYFKDENGNKRIPSFMFNLPREYIEAFLRGLFSA +DGTVSLRRGIPEIRLTSVNRELSNEVRKLLWLVGVSNSMFTETTPNKYLGNESG +TRSIHVRIKNKHRFAKRIGFLLDRKATKLSDNLREHTNKKMAYRYDFDLVYPKKIEEINY +DRYVYDIEVEGTHRFFANGILVHNT +>Neq_Poln_Nterminal___) +DSIMDTEIEVIENGIKKKEKLSDLFNKYYAGFQIGEKHYA +FPPDLYVYDGERWVKVYSIIKHETETDLYEINGITLSANHLVL +SKGNWVKAKEYENKNN + + + + + + +>S42459__Tli_Pol2 +DSVSGESEIIIRQNGKIRFVKIKDLFSKVDYSIGEKEYC +ILEGVEALTLDDDGKLVWKPVPYVMRHRANKRMFRIWLTNSWYIDVTEDHSLI +GYLNTSKTKTAKKIGERLKEVKPFELGKAVKSLICPNAPLKDENTK +TSEIAVKFWELVGLIVGDGNWGGDS +RWAEYYLGLSTGKDAEEIKQKLLEPLKTYGVISNYYPK +NEKGDFNILAKSLVKFMKRHFKDEKGRRKIPEFMYELPVTYIEAFLRGLFSA +DGTVTIRKGVPEIRLTNIDADFLREVRKLLWIVGISNSIFAETTPNRYNGVSTG +TYSKHLRIKNKWRFAERIGFLIERKQKRLLEHLKSARVKRNTIDFGFDLVHVKKVEEIPY +EGYVYDIEVEETHRFFANNILVHNT +>MfeAG86_Pol2c +DSVTENTEIIVKINGEIKFMKIKDLFKKVDYAVGEKEYC +LLDDVYALTLNDDGKLIWKKVPYVMRHRANKDIYRVWITNTWYVDVTEDHSLI +GYLNTTKKRNAKKIGDRFIEIKPNNLGKDVKSLITINNSLVDDKP +VNNISIRFWELVGLLIGDGSWGGKT +NSAKYYLRLSAGLDKDEIIKKVLEPLKEIGVISNYYLE +NEKGDIRILSKKLVRFMNKFKDENNKKIIPKFMFKLSKRKIEAFLRGLFSA +DGTVIVRRGNAEIRFTNTNENIIENVRKLLYLVGISNSVFKENNPNKYKGKVSK +TFSYHINIKNKIRFAERVGFILDRKNERLINLNNKWKSTIRNYDFDIARVKKIEKIDY +NGYVYDIEVEDTHRFFANGILVHNT +>Neq_Polc_Cterminal + + + + + + + +MRYLGK +KRVILYDLSTESGKFYVNGLVLHNT +>CroV_Polc +DSVIGDTPLLLKNKFTNEILINKIKDLSSNWSNYHNGKESC +EIDTYQTWTETGWTDIKRVIRHKLESNKKLLKIQTHNGEVIVTDEHSLLNKN +GKTINAKNVKVGDNILHSFPSYINNIDNTNSINYHNKFYNKKM +CNELAYILGCFMKYGLCDSSK +KCFTINNKDINLIESLKKMCENIFDEFKWKISSSSHLSDNI +YKLVPFQNEIKLIDFIKYFTNKMYNNGEKKVPQCILNSSKEYIKIFLIGLYP +EYKLENNQQFIYTCKNNEFSLGIYYLIKKLGYHVKLNSNDSSDSSDSIYTF +EISHKLENNNNVITKITEWEH +KETYVYDLTTENHHFHAGVGSIIVHNT +>APMV_Polc +DSVTGDTPIITRHQNGDINITTIEELGSKWKPYEIFKAHEKNSNRKFKQQSQ +YPTDSEVWTAKGWAKIKRVIRHKTVKKIYRVLTHTGCIDVTEDHSLL +DPNQNIIKPINCQIGTELLHGFPESNNVYDN +ISEQEAYVWGFFMGDGSCGSYQ +TKNGIKYSWALNNQDLDVLNKCKKYLEETENIQFKILDTMK +SSSVYKLVPIRKIKYMVNKYRKIFYDNKKYKLVPKEILNSTKDIKNSFLEGYYAA +DGSRKETENMGCRRCDIKGKISAQCLFYLLKSLGYNVSINIRSDKNQIYRLTFS +NKKQRKNPIAIKKIQLMNETSNDH +DGDYVYDLETESGSFHAGVGEMIVKNT +>HaV01_Polc +DSVTKETPLMLRTMETCGNHKHEVISIENVFTDNMRSIDMYSIIGEKEHV +MLSRNEEIWTGENWSRIIRVIRHKTQKKIYGVLTENGYVEVTEDHSLI +SSDYELLKPKNCIVKETQLLQSFPDIVENST +IENNMIDIP +K +GQPCRLTVFGQVSAMIIYTYLKRKNYSITLNVCNVNSNKFYISFMERPRFKN +TKKNIIKKIFF +IRNTDN +EEYVYDVETEDGIFHAGIGEIIVKNT +>Tpe_Pol +SVTGDSEVIIRRNGRIEFIPIEKLFERVDYTVGEKEYH +VLSSNVEALTLDDNGKLTWRKVPYVMRHKTEKKIYRVWLTNSWYLDVTEDHSLI +GYLNTSRVRAGKPLKDRLCEVKPLELGKSVKSLITPRAPLSRGIK +PNEIALKFWELVGLLVGDGNWGGTS +NWAKYYVGLACGEDKEEIAEKVLDPLKRAGVISNYYDK +SKKGDVSILSKGLAKLMVRYFKDEDGNKKIPEFMFNLPKEYLEAFLRGLFSA +DGTVSVKRGVPEVRLTTISDRLASDVRKLLWLVGISNSIFREQNPNRYNGKSSG +TYSKHVRIKDKLQFAQRIRFIINRKQEKLIKNLKESQYKRTTFKYEFDITPVKKVEEVTY +NGYVYDIEVEGTHRFFANGILVHN +>TspGT_Pol2 +DSVTGETEIIIKRNGKVEFVAIEELFQRVDYRIGEKEYC +VLEGVEALTLDNRGRLVWKSVPYVMRHRTNKRIYRVWFTNSWYLDVTEDHSLI +GYMNTSKVKPGKPLKERLVEVKPGELGESVKSLITPNRAIAHGIR +VNPIAVKLWELIGLLVGDGNWGGQS +NWAKYYVGLSLGLDKEEIEEKILKPLKNTGIISNYYDR +SKKGDVSILSKWLARFMVRYFKDESGSKRIPEFMFNLPREYIEAFLRGLFSA +DGTVSLRKGVPEVRLTSVNPELSSSVRKLLWLVGVSNSMFVETNPNRYLGKESG +THSVHVRIKDKHRFAERIGFLLDRKATKLSENLGGHTSKKRAYKYDFDLVYPKKVEEIAY +DGYVYDIEVEGTHRFFANGILVHNT +>Hvo_PolB +DSVTGDRPVVVRDPGGTVRILPIEDLFARGTTESEVLIAADGDVVASATPGKTRR +ALDGWDALSVNEDGEAEWQPIAQAIRHNTDKPVVNLQHKFGESTTTRDHSYVVPGE +DGLTTVSPDDVAEPYRVSGVPDVEPVEQVDVYEVLRGYEREYEDGRSVGSDNSITKRKQ +IHADDEYVWFGHEHHRDVDSTVKVKRFVDIDSEDGAALIRLLGAYVPEGSASTGETATSK +FGASLAESDREWLAQLQRDYSRLFENTTAGIITSDRRAERTVEYQTDTGGASVTY +NDETLKLQMMNELAAVFFREFAGQTSRGKRIPSFVFHLPEEKQDLFLTLLVEG +DGSREFPRYTEAYAQRNFDFETTSRELAAGLSMLLTQRGQKHSLKYRDSKDSYTIRTCS +TYREGRDPVLTEADH +DGYVYDLSVEENENFVDGVGGIVLHNT +:::::::::::::: +polBd.ina +:::::::::::::: +>Hwa_polB1 +CLPSDARIQMADGTETEIHAVEIGDNVIGTTDQRSVTATVTNKWKSEREIYEFSLADGT +SLRSSGDHRIMISDSNTVDWKSGSDIEQGEYVLKPRQLPVDDPTIPIINNLLSSESANII +DTLEVDALDSTGRSMNIHSSNPRESIAHTATLSMADGGD +QKQRNETTNNTLDLNRTVTKQDLYAIGRVLHNRITPRQDGITPVSQATLIDNSVLSSP +SPANTQHQSDSILTEVISSLRGLVSPGAHAIDFSAIYEMPKSHIAQFLAGTLDGS +ETGETTSSNLTVTTESASIARWYAQLYRRLGIYAQYQADAVHIANNACDLQRLSDAILPR +LRCSDTIDYVKTQIDTVCDSSLKHSRASSTGLSGDEANIRQFSDDGPQNKSYAAQPDSSD +YDDDWNAYVFVEIEAITLNGTETTYDIETTTHNFVADDCLVHNC +>NmaATCC43099_PolB1 +NCLPADSDVLMADGTEKEIQEIEIGDSVVGSDSQQTSVAEVTNKWESEKEIREFSLADGT +SLRSSADHRIMVGGDDAVDWKEGSEIESGDYVLKPRRLSVEETATPTLSDLIPIENQRYA +DKQSVSEFKTDLPYGAVSELADQFDVTTGTLHHPHTSVWTPKRCRDAASQYDVPVPDGG +VEYRGTGVALERKITPEELYYAGLILTDGSMSTDDGVRFYNTREELHRQFPGENHL +EPDGKGCYKQNVLDYATMYAFHGLGIPFGNKNDGPVDLSTIYEMPSEYIGRFLAGAIDGD +GNIAQSGITVAAENRSIGTWYVKLFKRLGIYAQQRENVVRIPDAKRDIDRLKDCVLPY +MSHSEKKDALTEFEGGKSGQTENIPYALFEADVGSDAKRIGNDKHRRGINLKRHET +HSEEWEEYVFVEVTDVSVTGTETTYDIETTTHNFIAEGCLVHNC +:::::::::::::: +pol_c.ina +:::::::::::::: +>CroV_Pol +CLHPETDVITFSGTVIKAKDLRPGMQLMGLDSTPRRVLDIGRGREMMYEIV +PIKGEPWKCNETHVLSLIYNEHGSIQKTKSNTYFVKFHEYTSDGRGV +FKYPTVKTLKEAQDIVARLNPNHIVDIPLNEYLNLPKHVKNSLKLFR +SGPITFPNKPEPKFHPYILGAWLGDGKSSTAEITIDVKEKPLLNH +VSNLLRPLGMIASKRTGASSLKRTDHYRIQYPDNNSRKGKSNPFMDALKSYDLISN +KHIPDDIKCGSLNVRLQILAGLLDTDGYLGGNCFEITQKNKRLSEDIAFVARSLG +YAAYLKMVKKSCTYKGEKKCGTYYKVSISGEGLEKIPTILERKCAKPRQQVKDARR +TGFTVRKLSVGDYVGPVLDKDHRYLLGDFTVTHNT +>HaV01_Pol +CLAKGTRLLRYDGSEIEVQDVKEGDLLLGPDGGPRRVFNIVNGEDRLYRIK +IDRGIEDLVVTPNHILVLHREKKAKNNED +DELPEVPAAERYDTVEMTAAEFAALSTEERSLYRAFR + +CPGFELSEKAVPANHS +FTIKDIRL + +ELETTEWAGFRVDKDQLYLRHDYLVLHNS +>APMV_Pol +CFAKGTNVLMADGSIECIENIEVGNKVMGKDGRPREVIKLPRGRETMYSVVQKSQHRAHK +SDSSREVPELLKFTCNATHELVVRTPRSVRRLSRTIKGVEYFEVITFEMGQKKAPDGRIV +ELVKEVSKSYPVSEGPERANELVESYRKASNKAYFEWTIEARDLSLLGSHVRKATYQTYA +PILYENDHFFDYMQKSKFHLTIEGPKVLAYLLGLWIGDGLSDRATFSVDSRDTSLMER +VTEYAEKLNLCAEYKDRKEPQVAKTVNLYSKVVRGNGVRNNLNTENPLWDAIIGLGFLKD +GVKNIPSFLSTDNIGTRETFLAGLIDSDGYVTDEHGIKATIKTIHTSVRDGLVSLARSLG +LVASVNAEPAKVDMNGTKHKISYAIYMSGGDVLLNVLSKCAGSKKFRPAPVATFVRECQG +FYFELQELKENDYYGITLSDDSDHQFLLANQVVVHNC +:::::::::::::: +pol_IIa.ina +:::::::::::::: +>Hwa_PolII1 +NCFHPETKIWFRDTDNEWHHETIQTFVEDRLDDPEIDAVGTLVQEVDDNTDREISVPS +IDDNGNERLQSVTAVSKHRAPNHLVQIETISGREITITPDHEMHIFEQGNLVSKQAS +KITSGEYAVIPKRLQTISPSSHTPQHDLLREFLTRDELTADRLIIHTSDPVRLCNRVFPE +EVTSCKDAVEIMQNTACHLDKNKETLIGWLGEGRIPVALLRGFVETDEALLMSIPDDVQI +GLRGEKVRIDRHIGFTEELTSLLGYYAAAGIVHTQTNPISYESAQQEQSRITFYNIDTQT +QTDLLNALNSVFEIEPIQYNLDGEILGVPGELIRRVFDTVFDVGTQPSHKRIPQALFDAS +ESHITSYLRCFFSTHDSLTTDTRDISATTVSREFKEDIIAALRRLGITAEVTTQQSRSVP +EVLPDWYAIDDITHHDADNSLNLTRSYVISIASSDAVTLQRDRQAQEQIKYDAQGLIANN +NAIHQSRQVTDGGRKDYITEPITDIEYVDADIDYTYCLTVSETHSLIVNDLSQKQC +>Memar_PolII +NCFAGDTEITVSDGRRWMSLPIRQFVTENFDISKPGLDHVGTFYSDPRQPFYVRS +IDSQGKTSLKRVTSVSVHRAPAHLVRFATRRGRVLTVTPDH + +AMLVWDTDY + +LRKI +KALEVAVGDRVPVE + +EGGLVVADEVVSRETVQALDDRVYCLTVAENHTLVANGIFCGQC +>Maeo_PolII +NCFPPNTTILVNINGEVKRITIEELYNLYDNEYYKNMAYIKKDIKNNNNIKVYS +FDTLNKKMVLTDIEEVLKIQSPNHLVNIGLDTGRSFETTPDHPVMVYDEKEDKFIKKNAM +DVEENDLMLIPKLDFEEDEEQEQDNIEHIDLLAELSKEEYKNMWELLRIRGISD +WIKNNIQKHCLKEKNENGKENLIKNIAKYIKQDTIPLNLLLKILKNAELNITDVPKDAFI +AVRRDKVNIRRIIKIEPLLKIIGYYLAEGYMRKTSSVYQINFSNYDEEV +IKDIKNSLNEAFGDGFGIYEKDGKITVGSRIIYLLFTEILKTGINAHNKRVPSFIFKLP +KEKVKLMLSAYFTGDGSAVKTRPIVVIYSANKKLLEDIDTLMISKFGLYGNWGAD +KNANGRKGNVVMKYHEKRETEIPKSTVYRIDYNGIQAMKYFENIGFTSSKKQNIYELHTH +KNFKAKKGLKEYGYIVKVRNKSIIKAEDEFVYSLNAKKYHNVVINSNIQMHNC +>Pho_PolII +NCFPGDTRILVQINGTPQRVTLKELYELFDEEHYESMVYVRKKPKVDIKVYS +FNPEEGKVVLTDIEEVIKAPATDHLIRFELELGSSFETTVDHPVLVYENGKFVEKRAF +EVREGN +IIIIIDEST + +LEPL + + +KVAVKKIEFIEPPEDFVFSLNAKKYHTVIINENIVTHQC +>Tko_PolIIa +NCFPGDTRILVQINGLPQRITLRELYDLFEDERYENMAYVRKKPKADVKVYS +FDPESGKVVLTDIEDVIKAPSTDHLIRFELELGRSFETTVDHPVLVYENGKFVEKRAF +EVREGDRILVPNLKLPEKNIDYLDLLKEFSREEFAHLHDRIMVRGIAE +WLRSVEADVKEDYLRRDSIPLSVLLRVLTEKEISIEEVPSCWL +GFKRDKVRIKRFVPLKPLLRVVGYYLAEGYARESKSVYQLSFSMAEKEV +REDLKRALREAFGDGFGIYERGGKVTVGSRILYLLFTEVLKAGKNAYSKRVPSLVFTLP +REAVAEMLKAYFEGDGSALKSVPRVVAYSVNKALLEDIETLLLAKFGIRGYYTFD +NNANRGNARGRLYHVERGTEAPVSKVYALNIAGEHYHRFFNSIGFVSERKNSIYELHAE +KSPAQDRYSSQNGWLVKVRRIEYITPKDDFVFSLNAKKYHNVIINESIVTHQC +>Mhu_PolII +NCFHGDTLIEIYADGILEEIPIRRFVLEHLDLSQAGVDALGTFYADPVRPAHVRS +VDTGGIPHLRKITSVSVHKAPANLIQFSTSRGKNLLVTPDH + +AMLVWDVSY + +LRKI +RALEVKIGDAVPVW + +ESGVVISDRIVSIDYVPCEDERVYCLTVDRDHNVVGNGIFTGQC +>Pab_PolII +NCFPGDTRILVQIDGVPQKITLRELYELFEDERYENMVYVRKKPKREIKVYS +IDLETGKVVLTDIEDVIKAPATDHLIRFELEDGRSFETTVDHPVLVYENGRFIEKRAF +EVKEGDKVLVS +ELELVEQSS + + +SSQDNPKNENLGSP + +EHDQLLEIKNIKYVRANDDFVFSLNAKKYHNVIINENIVTHQC +>Tba_PolII +NCFPGDTRILVQLNGMPQRITLRELYELFEEESYENMAYVRKKPKVDIKVYS +FDEESGKVVLTDIEDVIKLPSTDHLIRFELELGRSFETTVDHPVLVYENGRFIKKRAF +EVKEGDLILVPKIEFPEEDIDSIDLLEEFSKDEFKELRERIMVRGIAE +WLMKIGAEVNPDYIRRNSIPLAVLLEVLKEKGLSIKDVPDCYI +GFKPDHVKIRRFVPIGPLLRLIGYYLAEGYARESDSVYQISFSNGDEEV +REDIKRALRKAFGDGFGIYERGEKITVGSRVIYLLFTRVLKIGKGAKDKRVPAFVFKLP +KEKVRHLLQAYFEGDGTAIKSRPMIVVYSVNKPLLEDIDTLMIAKFNLYASWGVD +KNANSRPGNIVQRYHEHRGRRVPVSTVYRLDYYGIQAKRFFEEIDFISERKNSVVNAWTN +HKFQPYRRANEMGILVRVRRVEYVKPPEEWVYSLSVAKYHTVIVSDNITTSNC +>HspNRC1_PolII +NCFHPETNVWFRDESGEWHHDPIETLVEARLDPDTADEDDFGALVQALDGDVFVPS +VTEDGEETLQRVEAVSKHPAPDHLLAVETKRGRELTVTPDH + +SMRRWTGDG + +IERV +DARELTAGDALPAP +TQVPGDGETATSELRSESL +DGTHPQRRFGDGGSVRTDEVVSVEPVRSSVDHTYSLTVAETNTLVANGLFTGQC +>Cmeboo_PolII +NCFYGETKIEIFDGRSWATFPIRKFVMENFDVSRPGLDRLGTYYSDPVRPYYTRT +VDTNGGMHLRRITSVSIHRSPASMIRFVTARNRELTVTPDH + +AMVVWDTGY + +LRKI +KALEIKAGDAVPIL + +EGGVVIADRIVTAETVASLEDRVYCLTVAEDHTLVANGVFTGQC +>Hma_PolII +NCFHPDTRLWYEDENDDWEYGTIEELVESRLDDPQEDDFGTLVQELDGDLTVSS +LGENGPCRQPVDAVSKHPAPDHLVEVAVGDRTLRVTPDH + +TMLRAGPDG + +IEEV +PASDLAAGDDLPAY +DGGETTTM +TARGEASTAATDGAAPTDTVEAVEYVESDVDHVYCLTVADTHRVAVEGTYVGQC +:::::::::::::: +primase.ina +:::::::::::::: +>ShPSfv2a2457Tn_Primase +KACPLNEPILLADGTWTTHGNVKIGDQVASVDGNPSTVTGIFPQGVRDVYRVTFEDGRYV +DCAGDHLWEVTSRGFTKGEKRRVIDTFGLKRLSETKRHKNGVRIPEITGDFGDHSEPLAW +VIGSLLGDGSLSNGSVKFSNVEPYMIERMKAELPDYNFSGDGKDWLISTARGQVNPLMET +LRGYGLMGCTAKNKFIPRVFFSANKSTRIGMLCGLLETDGYVEKDGTLVFSSASEELRNE +VVN +KNWPPS +>ShPSfv2a301_Primase +KACPLNEPILLADGTWTTHGNVKIGDQVASVDGNPSTVTGIFPQGVRDVYRVTFEDGRYV +DCAGDHLWEVTSRGFTKGEKRRVIDTFGLKRLSETKRHKNGVRIPEITGDFGDHSEPLAW +VIGSLLGDGSLSNGSVKFSNVEPYMIERMKAELPDYNFSGDGKDWLISTARGQVNPLMET +LRGYGLMGCTAKNKFIPRVFFSANKSTRIGMLCGLLETDGYVEKDGTLVFSSASEELRNE +VVN +KNWPPS +>EPMin27_Primase +KACPLNEPILLADGTWTTHGDVKIGDQVASVDGNPSTVTGIFPQGVRDVYRVTFEDGRYV +DCAGDHLWEVTSRGFTKGEKRRVIDTFELKRLSETKRHKNGVRIPEITGDFGDHSEPLAW +VIGSLLGDGSLSNGSVKFSNVEPYMIERMKAELPDYNFSGDGKDWLISTARGQANPLMET 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+DDNHEKTTNHNIHEENVREFLVNHAAELDMYLAWQGLIDYATVANPAPMMVRLPPTNP +DTIEHRPVVCQARQSIRKLRLAAKNIAQPEVVLSTSPRPESQMQPKRELPSNTETALRSE +AEASSISAILDSKAGHSSLDTGDPNSDVVPESIPNDVADFGLDGVPELTSSGFSELTSDS +ELMRLIEQVERSSQGSTEEPSQASVVEQEADLNLLETDSEDEEA +DSADDDEFGDPEASEFRPEPESQLSQSHFSNRRRNHRLRTGRRVYGDLNGEEEGILLDQI +VEQSEGSRVNSLLRALDALGIIAQKGTGPETNRKHIPSIYMKNS +RSVRLAVLAGLIDSDGWYVYPENVLGFAQSERWHSKLFWDVVALARSLGLSVLTKRRMMW +NPARTERYPQLFAQISGNVAEVPCLIARKKGVERLIPQTHSFMIKDISLEPEATEWAGFR +VDKDQLYLRHDYLVLHNS +>AcaG186AR_PRP8 +ACLAKGTQLLRYDGTKVGVENVREGDLLLGPDGEPRRAFNIVSGRDRL +YRISIDADKEDLVVTPNHILVLHHEKEN + + + +QKRQSELSASATERYD +TVEMTAADFAALDPEERRWYRLFRSPGFEFGQQNVPIDPYFVGFWLC +DGIRASTTIYTSPEEATREFIINHAAELDLQLAS +KEYMQHSVRRVARQTILEQRLAVQCTAPQETDRTLLSHILQKA +AKSGLASSTRTMSTSRNRQPLSETSAATSMNILPGFASNSTSVVSPGIHSHEILS +LRSSCSQLVQITEKSGLREECMINPPSSREDLGLDLFDTHIEAD +EIQGLDENLTGQKHRLRTGCRAYGDLTVHEEGQILDNI +ISRPVGTPDIGTLLRALEELGLPTNRAEGHGVENKRIPFMYMKSS +RSIRLALLAGLIDSDGWYCQPQNTFCFGESERISPTLFWDIVTLARSLGLSVSTEQHTMR +SPACTAYKPRFVAQISGNVAEVTCLLARKGGVKSPVSQAHSFTIKGIHLESEMTEWAGFR +VDKDQLYLRHDFLVLHNS +>NglFRR1833_PRP8 +ACLAKGTRLLRYDGSEIEVQDVKEGDLLLGPDGGPRRAFNIVNGEDRL +YRIKIDEGIEDLVVTPNHILVLHREKKA + + + +GNNEDDGLPEVSAAERYD +TVEMTAAEFAALSTEERSRYRAFRCPGFELSEKAVPAN + + + + + + + +HSFTIQDIRLELESTEWAGFR +VDKDQLYLRHDYLVLHNS +>NglFR2163_PRP8 +ACLAKGTRLLRYDGSEVEVQDVKEGDLLLGPDGGPRRAFNIVSGEDRL +YRIKIDGSVEDLVVTPNHILVLHRESAA + + + +ESYD +TVEMTAAEFAALSTEERGRYRAFRSPSFELSEKAVRVN + + + + + + + +HRFMIKDIRLELETTEWAGFR +VDKDQLYLRHDYLVLHNS +>Eni_PRP8 +ACLANGTQLLRYDGTKVNVEDVKEGDLLLGPKEDLVVTANHILVLGPRRAFNVVSGKDRL +YRIKIDGDKEDLVVTANHILVLHRAKAM + + +NTSV +CFDRSKEQQGGAGEQLDISEVSAAERYD +TVEMTAAEFAALHPQERSWYRAIRCPGFELPEQDVPVNPYFLGLWLG +DESRNQSAIYSNHEEALREFLVSHAAELDMHLVYHGQSAYSTVCNKDRPTNKRIGPAN +QTQTVRPTIRQTRRTIRQQRLAAEHAAAEYTTQRETASLTPLLESPTS +DKHGLLSSVETPGRLSDSVTTELPMSRSASAMRSIRTASGLSEFNDVTNVSASMPDIQNS +GIKNQGRIAKVTRQQDSKGEVDFRQQYSQAIKDDLELLETDIED +DVASSDEIEDVCVVGSENELIGSEKQDQSGRRRQIHRLRTGHRGYGDLSDDEQEQLLDSV +VERYAGDSRLNTLQQELSKMGILNPETGPINDKKRIPQVFMQNS +RSVRLSVLAGLLDSDGWYIYPENMFGFAQSELCHKELFWDVVTLARSLGFGVWTKKRMMP +DPTGKRMSPMLVAQISGDLAEIPCVLARKKAMPRLIPQSHSFAIKDISLESEATEWAGFR +VDKDQLYLRHDYVVLHNS +>BfuB05_PRP8 +ACLAWDTKLLRYDGTDVVVQDVKEGDLLLGPDGGPRRAFNIVSGKDRL +YRIKVGSRKEDLVVTGNHILVLHREKGHGNVYDGPSVGGNRQRFVDQLGDLPVPSSN +PADATRPNNLTKVRPDFLAALKSAIAWALNAERGKKGADTIRNTLNGTTGITSRQESYIV +NIPVGKGTRAEYATFAWGNPDRTVKGHAKHPPEFFPTKEDAFSASVAKSRQIHDKGDVT +LATLRRRFLDKSSDGKGGELRIDTGLPNMFLLWNANGANLKIRVYCSRNYTKYGRSYTFP +SLPDINLSEAGSDDSDDNEETENEDDETEDEDDEREETLTLQNFQSTASRDVSSAERYD +TVLMTATQFAALDENERSKYRLFRSPGFELPEQDVPVNPYFLGLWLG +DGSRSSTTIFSNHEQEVREFLISHAAELDLHLVWHGNLSYATVGRTRIANRPLPKAN +IDVVDRPSRRFSRQTIKKQREAAELPSRPAPAVANL +KHGLNSSVPNSPQRRLRQRIDDVDVQNLVDGMDNLTSSPIPSSPPVIPAESIPTEALPQ +LRSDRSIMDMAGPSVVPEEPVDVNNLPEDEEDEFDMDLIETMSD +DEDDVTEYQVENDEGSNVGAGDSNLSDDSVSQRRIHRLQSGRRAYGDLQPEEQDQLLSQI +IDTVDSPVGSSFDPSTDKKHIPSIYMKNT +REVRLAVLAGLIDSDGWYVYPENMLGFAQSEIWHKTLFWDVVALARSLGLSVWTTRRMMW +VPSHSRKTPMLVAQMFGNVKEVPCLLLRKKGSERYIPQMHSFMIKDITLESEATNWAGFR +VDKDQLYLRHDYLVLHNS +>Ure1704_PRP8 +ACLAKGTRLLRYDRTEINVEDGQEGDQLLGPDGHPRRAFNIVSGQDRL +YRIKIGEGVEDLVVTPNHILVFHREKRA + + + +ENMPSGQQAGVTEERPPEASEAARYD +TVEMTAAEFAACDPKERVLYKVFKSPAFTMPEKSESVN + + + + + + + +AEAHSFVVNDISLESEETEWAGFR +VDQDQLYLRHDYLVLHNS +>AcaH143_PRP8 +ACLAKGTQLLRYDGTKVGVENVREGDLLLGPDGEPRRAFNIVSGRDRL +YRISIDADKEDLVVTPNHILVLHHEKEN + + + +QKRQSELSASATERYD +TVEMTAADFAALDPEERRWYRLFRSPGFELGQQNVPIDPYFVGFWLC +DGIRSSTTIYTSPEEATREFIINHAAELDLQLAS +KEYMQHPVRRVTRQTILEQRLAVQCTAPQETDGILLSHILQKA +AKSGLASSTRTMSTSRNRQPLSETSAATSMNILPEFASNSTSVVSPGIHSHEILS +LRSSCSQLVQIAEKSGLREECMVNPPSSREDLGLDLFDTHIEAD +EIQGLDENLTGQKHRLRTGCRAYGDLTVHEEEQILDNI +ISRPVGTPDIGSLLRALEEALDQS +RLALLAGLIDSDVWYCQPQNTFCFGESERISPTLFWDIVTLARSLGLSVSTEQHTMR +SPACTACKPRFVAQISGNVAEVTGLLARKRGVKSPVSQAHSFTIKGVHLESEMTEWAGFR +VDKDQLYLRHDFLVLHNS +>AcaNAm1_PRP8 +ACLAKGTQLLRYDGTKVRVEDVREGNLLLGPDGEPRRAFNIVSGRDRL +YRISIDADKEDLVVTPNHILVLHLEKEN + + + +QKRQSELPASAAERYD +TVEMTAADFAALDPEERRWYRLFRSPGFELGQQNVPIDPYFLGFWLC +DGIRASTTIYTSPEEAAREFIINHAAELDLQLAS +KEYMQHPVRRVARQTILEQRLAVQCTAPQETDGTLLSHILLKA +AKSGLAPSTRTMSTSRNRQPLSETSAATSMNILPGFASNSTSVVSPGIHSHEILS +LRSSCSQLVQIAEKSGLREECMINPPSSREDLRLDLFDTHIEAD +EIHGLDENLTGQKHRLRTGCRAYGDLTVHEEEQILDNI +ISRPVGTPDI +ALLAGLIDSDGWYCQPQNTFCFGESERISPTLFWDIVTLARSLGLSVSTEQHTMR +SPACTACKPRFVAQISGNVAEVTCLLARKKGVKSPVSQAHSFTIKGIHLESEMTEWAGFR +VDKDQLYLRHDFLVLHNS +>Nau_PRP8 +ACLAKGTRLLRYDGSEIEVQDVKEGDLLLGPDGGPRRAFNIVSGEDRL +YRVKIDGSVEDLVVTPNHILVFHREQKA + + + +RDKEDDQLPESYD +TVEMTAAEFAALSAEDRSRYRAFRSPSFDLSEKAVPTN + + + + + + + +HRFAIKDIRLELETTEWAGFR +VDKDQLYLRHDYLVLHNS +>Pex_PRP8 +ACLAKGTRLLRYDGTEINVEDVREGDQLLGPDGEPRRAFNIVNGIDRL +YRIKIAGEKEDLVVTPNHILVLYREEEA + + + +SDGPKNAERQ +TVEITAAEFAALSTEERGLHSAFTSSRVEKDVENSA + + + + + + + +PQMHSFKIEHINLEYEETEWAGFR +VDKDQLYLRHDYLVLHNS +>PbrPb18_PRP8 +ACLAKGTLLLRYDGTKVEVENVREGDLLLGPDGGPRRAFNIVGGRDRL +YRIKMEGGKEDLVVTPNHILVLHREKRD + + +GVDKVYAR +PFALPLLQEDATDDGEDLSEISAIEHFD +TMEITAADFASLDPNERKLYRLFTSPGYELNGRPVPIDPYFLGLWLG +DRSRTKSSIYTNHEEEIREFIADHAAELDLQLVSYVSNRPSLAAM +KNGNQLPLRHQARQTIRKQRIAAKSITQPGGARSSSYPA +TNGGLSSNTVTSLHSRERHPLSESSAAATMNLLPRSTSVSTSVAAQPKSSMSTFITDA +ILPSESSNISVISDSGIEISKSSKMLSEEEADLDLFDIDSEDE +EIEDLDEKKNVSNVDEFPKRRRIHYLRTGCRTYGELCPGEEDQILEDI +VGRPDGTTSVESLLLALEALGLHTCGTNDSGSDKKRIPSVYMKNS +RAVRLALLAGLIDSGGWYVDSENTFGFSQTEDSNSTLIWDVVTLARSLGFSVSTKRRMTH +KPTRTQHKAQEFAQISGNVAEIPSLLARERGVERPISQAHSFKIKDIQLETEATEWAGFR +VDQDQLYLRHDFLVLHNS +>CneJEC21_PRP8 +ACLQNGTRLLRADGSEVLVEDVQEGDQLLGPDGTSRTASKIVRGEERL +YRIKTHEGLEDLVCTHNHILSMYKERSG + + + +SERAHSPSADLSLTDSHE +RVDVTVDDFVRLPQQEQQKYQLFRSTASVRHERPSTSK + + + + + + + +LDTTLLRINSIELEDEPTKWSGFV +VDKDSLYLRHDYLVLHNS +>EniFCSGA4_PRP8 +ACLANGTQLLRYDGTKVNVEDVKEGDLLLGPDGGPRRAFNVVSGKDRL +YRIKIDGDKEDLVVTANHILVLHRAKAM + + +NTSV +CFDRSKEQQGGAGEQLDISEVSAAERYD +TVEMTAAEFAALHPQERSWYRAIRCPGFELPEQDVPVNPYFLGLWLG +DESRNQSAIYSNHEEALREFLVSHAAELDMHLVYHGQSAYSTVCNKDRPTNKRIGPAN +QTQTVRPTIRQTRRTIRQQRLAAEHAAAEYTTQRETASLTPLLESPTS +DKHGLLSSVETPGRLSDSVTTELPMSRSASAMRSIRTASGLSEFNDVTNVSASMPDIQNS +GIKNQGRIAKVTRQQDSKGEVDFRQQYSQAIKDDLELLETDIED +DVASSDEIEDVCVVGSENELIGSEKQDQSGRRRQIHRLRTGHRGYGDLSDDEQEQLLDSV +VERYAGDSRLNTLQQELSKMGILNPETGPINDKKRIPQVFMQNS +RSVRLSVLAGLLDSDGWYIYPENMFGFAQSELCHKELFWDVVTLARSLGFGVWTKKRMMP +DPTGKRMSPMLVAQISGDLAEIPCVLARKKAMPRLIPQSHSFAIKDISLESEATEWAGFR +VDKDQLYLRHDYVVLHNS +>Abr_PRP8 +ACLAKGTRLLRYDGTEIEVQDVKEGDLLLGPDGGPRRAFNIVNGEDRL +YRIKIDEGIEDLVVTPNHILVLHREKKA + + + +RNNEDEASAAERYD +TVEMTAAEFAALSTEERSQYRAFRCPGFESPEKAVPEN + + + + + + + +HSFMIQDIRLELETTEWAGFR +VDKDQLYLRHDYLVLHNS +>AfuAf293_PRP8 +ACLAKGTRLLRYDGSEIEVQDVKEGDLLLGPDGGPRRAFNIVNGKDRL +YRIKIGGSKEDLVVTPNHILVLHREKRARNVYTGPSVQGHIQRSENGHGNLPMLSSS +PAAAHHPNNLVKNRGDFWSALKSAIAWVLHAERSSTGANMVRNVLNGTVGLTAHKESYTV +TNPQQKGVYYTYVWGNPQRTSIKGHRDHPPVFLPTKEDAFSAAIAKSRELYSQSEVT +LATLRQRFLAKSADGKGGEILVDANLPNIFLLWDKNRSNLKFRVLCSRNFKTYGRVYTFE +SMPSTNAEEPGYGDDDELPQVSAEERYD +TVEMTAAEFASLSTEERSRYRVFRCPGFELPEQPVPVNPYFLGLWLG +DDNHEKTTNHNIHEENVREFLVNHAAELDMYLAWQGLIDYATVANPAPMMVRLPPTNP +DTIEHRPVVCQARQSIRKLRLAAKNIAQPEVVLSTSPRPESQMQPKRELPSNTETALRSE +AEASSISAILDSKAGHSSLDTGDPNSDVVPESIPNDVADFGLDGVPELTSSGFSELTSDS +ELMRLIEQVERSSQGSTEEPSQASVVEQEADLNLLETDSEDEEA +DSADDDEFGDPEASEFRPEPESQLSQSHFSNRRRNHRLRTGRRVYGDLNGEEEGILLDQI +VEQSEGSRVNSLLRALDALGIIAQKGTGPETNRKHIPSIYMKNS +RSVRLAVLAGLIDSDGWYVYPENVLGFAQSERWHSKLFWDVVALARSLGLSVLTKRRMMW +NPARTERYPQLFAQISGNVAEVPCLIARKKGVERLIPQTHSFMIKDISLEPEATEWAGFR +VDKDQLYLRHDYLVLHNS +>Bci_PRP8 +ACLAWDTKLLRYDGTDVVVQDVKEGDLLLGPDGGPRRAFNIVSGKDRL +YRIKVGSRKEDLVVTGNHILVLHREKGHGNVYDGPSVGGNRQRFVDQLGDLPVPSSN +PADATRPNNLTKVRPDFLAALKSAIAWALNAERGKKGADTIRNTLNGTTGITSRQESYIV +NIPVGKGTRAEYATFAWGNPDRTVKGHAKHPPEFFPTKEDAFSASVAKSRQIHDKGDVT +LATLRRRFLDKSSDGKGGELRIDTGLPNMFLLWNANGANLKIRVYCSRNYTKYGRSYTFP +SLPDINLSEAGSDDSDDNEETENEDDETEDEDDEREETLTLQNFQSTASRDVSSAERYD +TVLMTATQFAALDENERSKYRLFRSPGFELPEQDVPVNPYFLGLWLG +DGSRSSTTIFSNHEQEVREFLISHAAELDLHLVWHGNLSYATVGRTRIANRPLPKAN +IDVVDRPSRRFSRQTIKKQREAAELPSRPAPAVANL +KHGLNSSVPNSPQRRLRQRIDDVDVQNLVDGMDNLTSSPIPSSPPVIPAESIPTEALPQ +LRSDRSIMDMAGPSVVPEEPVDVNNLPEDEEDEFDMDLIETMSD +DEDDVTEYQVENDEGSNVGAGDSNLSDDSVSQRRIHRLQSGRRAYGDLQPEEQDQLLSQI +IDTVDSPVGSSFDPSVSHNTGVNTLLRALQHLGVSSNTTGSETDKKHIPSIYMKNT +REVRLAVLAGLIDSDGWYVYPENMLGFAQSEIWHKTLFWDVVALARSLGLSVWTTRRMMW +VPSHSRKTPMLVAQMFGNVKEVPCLLLRKKGSERYIPQMHSFMIKDITLESEATNWAGFR +VDKDQLYLRHDYLVLHNS +>BdeJEL423_PRP82 +ACFAGHTSLLLADGTTKHASDITTNDQLMGDDGKPRLIREVVNGISPM +YHITPKDGDELVVTGNHILCLVATSRA + + +CLSWSDASSTFSVFWFDGVYQTK +QFKVTTSTCAGDFASATAACDAAYQFYSS +LRACSFIPIKDYRIEITVREYLALPFAEQKVWHLHRTILDCPSSPVTVDPYFVGLWLG +EYVQNRVALQTFYPLETHIIDLIARESVALDTNLGVS +LPAP +LAINTNAVEEVFIMNTHFNQVDDSYSVDVISLQNTALT +DADYLPCLQTEMEAD +SFMSSSDKTVCVDEMIFRI +LNHKTNTTSICCHLATQLILLGVAPAFNCIKDIKSFIPRIPSAYKFNS +IDVRMRLLAGYASCFVFENKPSAVSFTDLHDTDLAPLFGDLETVSRGCGLNLS +DLSLCAESFARQLYKNCSTFTAISRNAGSLATPIVSVKYNCAPQPYYGFK +VDGNQRFLGSDFMVLHNS +>AdeSLH14081_PRP8 +ACLAKGTQLLRYDGTKVGVESVREGDLLLGPDGGPRRAFNIVSGRDRL +YRIKIDAEKEDLVVTPNHILVLHREKKD + + + +QNGQGGGASVSVAEHYD +TVEMTASDFAALDPEEMHLYRLFRSPGFELAEQSVPIDPYYLALWLC +DGVRPSTTIYTSPEEEAREFLINHAAELDLHHVSHALPSYTTCLSGLPS +KGETQRPIPREARQTIFKQRLAAVQAEAADSHHHHIFQTP +AKHGLASGTKTSSSRHSRHPLSESSAMTSMNLLS +LRSPGLDLAQVVDKGGLRKETMINQASSGEEPEVDLFDTERIED +ETQGLTERVPGHKHRLRTGFRAYGDLAPHEEEQILGNI +LTRPTSSTSVGSLLRAFEELGLVARGTAGHAVEKKHIPSVYMNNS +RSIRLALLAGLIDGDGWYCQHENTFGFSESERIAPSLFWDIVVLARSLGLSVSTDQPKMH +NPAGAECKSHLSARISGNVAEVPSLLARKRGVKRIISQDHSFAIKGIHLERDMTEWAGFR +VDKDQLYLRHDFLVLHNS +>CneA_Prp8 +ACLQNGTRLLRADGSEVLVEDVQEGDQLLGPDGTSRTASKIVRGEERL +YRIKTHEGLEDLVCTHNHILSMYKERFG + + + +REGAHSPSAGTSLTESHE +RVDVTVDDFVRLPQQEQQKYKLFRSTDFVRREQPSASK + + + + + + + +LATLLHINSIELEEEPTKWSGFV +VDKDSLYLRYDYLVLHNS +>CneAD_prp8 +ACLQNGTRLLRADGSEVLVEDVQEGDQLLGPDGTSRTASKIVRGEERL +YRIKTHEGLEDLVCTHNHILSMYKERSG + + + +SERAHSPSADLSLTDSHE +RVDVTVDDFVRLPQQEQQKYQLFRSTASVRHERPSTSK + + + + + + + +LDTTLLRINSIELEDEPTKWSGFV +VDKDSLYLRHDYLVLHNS +:::::::::::::: +radA.ina +:::::::::::::: +>Tfus_RecA1 +KCLTADTYVWTDRGLETVAEVFGRAGLPLSSTSRVTDVRDRDIRVVNEKG +ELEQVAALTHNGRQPVVRITVASGRQVTVTRNHPLRVMNDDGFIVWREAGQLREGDVL +VSAAFGAVQAASGGGLSEDEAVLLGYLTAAGSLDPAGHVCFTTTDIETGAEFAALAEWLL +DTTVTAVPGDGQVAYVLSDPAARHTLAERYGVDYAAAARIPQCVRTAGDKMQRAFLAALY +TAAGWTDTSAAVGLRTASAPLAREVQYLLYGLGIPADLDRSHGNGQHPWAVTISPAAAPR +FHTEVGFRTAQQSPQTGLHEPTPQVEAI +PNLTGLIHALRDSIGDRAESTDDPFPAASGGAYDRDQVRRVIDWAKRRT +DEAPATANAILGYLTQLTDARYTYEPITAVEDAGQQPTFDLMV +PRTHSFLANGILSHNT +>Pho_RadA +KCFARDTEVYYENDTVPHMESIEEMYSKYASMNGELPFDNGYAVPLDNVFVYTLDIASG +EIKKTRASYIYREKVEKLIEIKLSSGYSLKVTPSHPVLLFRDGLQWVPAAEVKPGDVV +VGVRE +EVLRRRIISKGE + + + +LEFHEVSSVRIIDYNNWVYDLVI +PETHNFIAPNGLVLHNT +>Tko_RadA +KCFAKDTKVYYENDTLVHFESIEDMYHKYASLGREVPFDNGYAVPLETVSVYTFDPKTG +EVKRTKASYIYREKVEKLAEIRLSNGYLLRITLLHPVLVFRNGLQWVPAGMIKPGDLI +VGIRSVPANAATIEESEAYFLGLFVAEGTSNPLSITTGSEELKDFIVSFIEDHD +GYTPTVEVRRGLYRILFRKKTAEWLGELATSNASTKVVPERVLNAGESAIAAFLAGYL +DGDGYLTESIVELVTKSRELADGLVFLLKRLGITPRISQKTIEGSVYYRIYITGEDRKT +FEKVLEKSRIKPGEMNEGGVGRYPPALGKFLGKLYSEFRLPKRDNETAYHILTRSRNVWF +TEKTLSRIEEYFREALEKLSEARKALEMGDKPELPFPWTAITKYGFTDRQVANYRTRGL +PKRPELKEKVVSALLKEIERLEGVAKLALETIELARRLEFHEVSSVEVVDYNDWVYDLVI +PETHNFIAPNGLVLHNT +:::::::::::::: +recAa.ina +:::::::::::::: +>MtuCanetti_RecA +KCLAEGTRIFDPVTGTTHRIEDVVDGRKPIHVVAAAKDGTLHARPVVSWFDQGTQDVIGL +RIAGGAIVWATPDHKVLTEYGWRAAGELRKGDRVAQPRRFDGFGDSAPIPADHARLLGYL +IGDGRDGWVGGKTPINFINVQRALIDDVTRIAATLGCAAHPQGRISLAIAHRPGERNGVL +DLCRRAGVHGKLAWEKTIPNWFFEPDIAADIVGNLLFGLFESDGWVSREQTGALRVGYTT +TSEQLAHQIHWLLLRFGVGSTVRDYDPTQKRPSIVNGRRIQSKRQVFEVRISGMDNVTAF +AESVPMWGPRGAALIQAIPEATQGRRRGSQATYLAAEMTDAVLNYLDERGVTAQEAAAMI +GVASGDPRGGMKQVLGASRLRRDRVQALADALDDKFLHDMLAEELRYSVIREVLPTRRAR +TFDLEVEELHTLVAEGVVVHNC +>MtuSo93_RecA +KCLAEGTRIFDPVTGTTHRIEDVVDGRKPIHVVAAAKDGTLHARPVVSWFDQGTQDVIGL +RIAGGAIVWATPDHKVLTEYGWRAAGELRKGDRVAQPRRFDGFGDSAPIPADHARLLGYL +IGDGRDGWVGGKTPINFINVQRALIDDVTRIAATLGCAAHPQGRISLAIAHRPGERNGVL +DLCRRAGVHGKLAWEKTIPNWFFEPDIAADIVGNLLFGLFESDGWVSREQTGALRVGYTT +TSEQLAHQIHWLLLRFGVGSTVRDYDPTQKRPSIVNGRRIQSKRQVFEVRISGMDNVTAF +AESVPMWGPRGAALIQAIPEATQGRRRGSQATYLAAEMTDAVLNYLDERGVTAQEAAAMI +GVASGDPRGGMKQVLGASRLRRDRVQALADALDDKFLHDMLAEELRYSVIREVLPTRRAR +TFDLEVEELHTLVAEGVVVHNC +>MtuT92_RecA +QVPRRGHSDLRSGHRYTHRIEDVVDGRKPIHVVAAAKDGTLHARPVVSWFDQGTRDVIGL +RIAGGAIVWATPDHKVLTEYGWRAAGELRKGDRVAQPRRFDGFGDSAPIPADHARLLGYL +IGDGRDGWVGGKTPINFINVQRALIDDVTRIAATLGCAAHPQGRISLAIAHRPGERNGVA +DLCQQAGIYGKLAWEKTIPNWFFEPDIAADIVGNLLFGLFESDGWVSREQTGALRVGYTT +TSEQLAHQIHWLLLRFGVGSTVRDYDPTQKRPSIVNGRRIQSKRQVFEVRISGMDNVTAF +AESVPMWGPRGAALIQAIPEATQGRRRGSQATYLAAEMTDAVLNYLDERGVTAQEAAAMI +GVASGDPRGGMKQVLGASRLRRDRVQALADALDDKFLHDMLAEELRYSVIREVLPTRRAR +TFDLEVEELHTLVAEGVVVHNC +>MtuT17_RecAc + +ELRKGDRVAQPRRFDGFGDSAPIPADHARLLGYL +IGDGRDGWVGGKTPINFINVQRALIDDVTRIAATLGCAAHPQGRISLAIAHRPGERNGVA +DLCQQAGIYGKLAWEKTIPNWFFEPDIAADIVGNLLFGLFESDGWVSREQTGALRVGYTT +TSEQLAHQIHWLLLRFGVGSTVRDYDPTQKRPSIVNGRRIQSKRQVFEVRISGMDNVTAF +AESVPMWGPRGAALIQAIPEATQGRRRGSQATYLAAEMTDAVLNYLDERGVTAQEAAAMI +GVASGDPRGGMKQVLGASRLRRDRVQALADALDDKFLHDMLAEELRYSVIREVLPTRRAR +TFDLEVEELHTLVAEGVVVHNC +>MtuT85_RecA +KCLAEGTRIFDPVTGTTHRIEDVVDGRKPIHVVAAAKDGTLHARPVVSWFDQGTRDVIGL +RIAGGAIVWATPDHKVLTEYGWRAAGELRKGDRVAQPRRFDGFGDSAPIPADHARLLGYL +IGDGRDGWVGGKTPINFINVQRALIDDVTRIAATLGCAAHPQGRISLAIAHRPGERNGVA +DLCQQAGIYGKLAWEKTIPNWFFEPDIAADIVGNLLFGLFESDGWVSREQTGALRVGYTT +TSEQLAHQIHWLLLRFGVGSTVRDYDPTQKRPSIVNGRRIQSKRQVFEVRISGMDNVTAF +AESVPMWGPRGAALIQAIPEATQGRRRGSQATYLAAEMTDAVLNYLDERGVTAQEAAAMI +GVASGDPRGGMKQVLGASRLRRDRVQALADALDDKFLHDMLAEELRYSVIREVLPTRRAR +TFDLEVEELHTLVAEGVVVHNC +>MtuT46_RecA +KCLAEGTRIFDPVTGTTHRIEDVVDGRKPIHVVAAAKDGTLHARPVVSWFDQGTRDVIGL +RIAGGAIVWATPDHKVLTEYGWRAAGELRKGDRVAQPRRFDGFGDSAPIPADHARLLGYL +IGDGRDGWVGGKTPINFINVQRALIDDVTRIAATLGCAAHPQGRISLAIAHRPGERNGVA +DLCQQAGIYGKLAWEKTIPNWFFEPDIAADIVGNLLFGLFESDGWVSREQTGALRVGYTT +TSEQLAHQIHWLLLRFGVGSTVRDYDPTQKRPSIVNGRRIQSKRQVFEVRISGMDNVTAF +AESVPIWGPRGAALIQAIPEATQGRRRGSQATYLAAEMTDAVLNYLDERGVTAQEAAAMI +GVASGDPRGGMKQVLGASRLRRDRVQALADALDDKFLHDMLAEELRYSVIREVLPTRRAR +TFDLEVEELHTLVAEGVVVHNC +>MtuH37Rv_RecA +KCLAEGTRIFDPVTGTTHRIEDVVDGRKPIHVVAAAKDGTLHARPVVSWFDQGTRDVIGL +RIAGGAIVWATPDHKVLTEYGWRAAGELRKGDRVAQPRRFDGFGDSAPIPADHARLLGYL +IGDGRDGWVGGKTPINFINVQRALIDDVTRIAATLGCAAHPQGRISLAIAHRPGERNGVA +DLCQQAGIYGKLAWEKTIPNWFFEPDIAADIVGNLLFGLFESDGWVSREQTGALRVGYTT +TSEQLAHQIHWLLLRFGVGSTVRDYDPTQKRPSIVNGRRIQSKRQVFEVRISGMDNVTAF +AESVPMWGPRGAALIQAIPEATQGRRRGSQATYLAAEMTDAVLNYLDERGVTAQEAAAMI +GVASGDPRGGMKQVLGASRLRRDRVQALADALDDKFLHDMLAEELRYSVIREVLPTRRAR +TFDLEVEELHTLVAEGVVVHNC +>MtuEAS054_RecA +KCLAEGTRIFDPVTGTTHRIEDVVDGRKPIHVVAAAKDGTLHARPVVSWFDQGTRDVIGL +RIAGGAIVWATPDHKVLTEYGWRAAGELRKGDRVAQPRRFDGFGDSAPIPADHARLLGYL +IGDGRDGWVGGKTPINFINVQRALIDDVTRIAATLGCAAHPQGRISLAIAHRPGERNGVA +DLCQQAGIYGKLAWEKTIPNWFFEPDIAADIVGNLLFGLFESDGWVSREQTGALRVGYTT +TSEQLAHQIHWLLLRFGVGSTVRDYDPTQKRPSIVNGRRIQSKRQVFEVRISGMDNVTAF +AESVPMWGPRGAALIQAIPEATQGRRRGSQATYLAAEMTDAVLNYLDERGVTAQEAAAMI +GVASGDPRGGMKQVLGASRLRRDRVQALADALDDKFLHDMLAEELRYSVIREVLPTRRAR +TFDLEVEELHTLVAEGVVVHNC +>Mbo_RecA +KCLAEGTRIFDPVTGTTHRIEDVVDGRKPIHVVAAAKDGTLHARPVVSWFDQGTRDVIGL +RIAGGAIVWATPDHKVLTEYGWRAAGELRKGDRVAQPRRFDGFGDSAPIPADHARLLGYL +IGDGRDGWVGGKTPINFINVQRALIDDVTRIAATLGCAAHPQGRISLAIAHRPGERNGVA +DLCQQAGIYGKLAWEKTIPNWFFEPDIAADIVGNLLFGLFESDGWVSREQTGALRVGYTT +TSEQLAHQIHWLLLRFGVGSTVRDYDPTQKRPSIVNGRRIQSKRQVFEVRISGMDNVTAF +AESVPMWGPRGAALIQAIPEATQGRRRGSQATYLAAEMTDAVLNYLDERGVTAQEAAAMI +GVASGDPRGGMKQVLGASRLRRDRVQALADALDDKFLHDMLAEELRYSVIREVLPTRRAR +TFDLEVEELHTLVAEGVVVHNC +>MtuR604_RecAn +KCLAEGTRIFDPVTGTTHRIEDVVDGRKPIHVVAAAKDGTLHARPVVSWFDQGTRDVIGL +RIAGGAIVWATPDHKVLTEYGWRAAGELRKGDRVAQPRRFDGFGDSAPIPADHARLLGYL +IGDGRDGWVGGKTPINFINVQRALIDDVTRIAATLGCAAHPQGRISLAIAHRPGERNGVA +DLCQQAGIYGKLAWEKTIPNWFFEPDIAADIVGNLLFGLFESDGWVSREQTGALRVGYTT +TSEQLAHQIHWLLLRFGVGSTVRDYDPTQKRPSIVNGRRIQSKRQVFEVRISGMDNVTAF +AESVPMWGPRGAALIQAIPEATQGRRRGSQATYLAAEMTDAVLNYLDERGVTAQEAAAM +RIPT + +>MtuCPHL_RecA +KCLAEGTRIFDPVTGTTHRIEDVVDGRKPIHVVAAAKDGTLHARPVVSWFDQGTRDVIGL +RIAGGAIVWATPDHKVLTEYGWRAAGELRKGDRVAQPRRFDGFGYSAPIPADHARLLGYL +IGDGRDGWVGGKTPINFINVQRALIDDVTRIAATLGCAAHPQGRISLAIAHRPGERNGVA +DLCQQAGIYGKLAWEKTIPNWFFEPDIAADIVGNLLFGLFESDGWVSREQTGALRVGYTT +TSEQLAHQIHWLLLRFGVGSTVRDYDPTQKRPSIVNGRRIQSKRQVFEVRISGMDNVTAF +AESVPMWGPRGAALIQAIPEATQGRRRGSQATYLAAEMTDAVLNYLDERGVTAQEAAAMI +GVASGDPRGGMKQVLGASRLRRDRVQALADALDDKFLHDMLAEELRYSVIREVLPTRRAR +TFDLEVEELHTLVAEGVVVHNC +>MtuC_RecA +KCLAEGTRIFDPVTGTTHRIEDVVDGRKPIHVVAAAKDGTLHARPVVSWFDQGTRDVIGL +RIAGGAIVWATPDHKVLTEYGWRAAGELRKGDRVAQPRRFDGFGDSAPIPADHARLLCYL +IGDGRDGWVGGKTPINFINVQRALIDDVTRIAATLGCAAHPQGRISLAIAHRPGERNGVA +DLCQQAGIYGKLAWEKTIPNWFFEPDIAADIVGNLLFGLFESDGWVSREQTGALRVGYTT +TSEQLAHQIHWLLLRFGVGSTVRDYDPTQKRPSIVNGRRIQSKRQVFEVRISGMDNVTAF +AESVPMWGPRGAALIQAIPEATQGRRRGSQATYLAAEMTDAVLNYLDERGVTAQEAAAMI +GVASGDPRGGMKQVLGASRLRRDRVQALADALDDKFLHDMLAEELRYSVIREVLPTRRAR +TFDLEVEELHTLVAEGVVVHNC +>MtuK85_RecA +KCLAEGTRIFDPVTGTTHRIEDVVDGRKPIHVVAAAKDGTLHARPVVSWFDQGTRDVIGL +RIAGGAIVWATPDHKVLTEYGWRAAGELRKGDRVAQPRRFDGFGDSAPIPADHARLLGYL +IGDGRDGWVGGKTPINFINVQRALIDDVTRIAATLGCAAHPQGRISLAIAHRPGERNGVA +DLCQQAGIYGKLAWEKTIPNWFFEPDIAADIVGNLLFGLFESDGWVSREQTGALRVGYTT +TSEQLAHQIHWLLLRFGVGSTVRDYDPTQKRPSIVNGRRIQSKRQVFEVRISGMDNVTAF +AESVPMWGPRGAALIPAIPEATQGRRRGSQATYLAAEMTDAVLNYLDERGVTAQEAAAMI +GVASGDPRGGMKQVLGASRLRRDRVQALADALDDKFLHDMLAEELRYSVIREVLPTRRAR +TFDLEVEELHTLVAEGVVVHNC +>MtuT17_RecAn +KCLAEGTRIFDPVTGTTHRIEDVVDGRKPIHVVAAAKDGTLHARPVVSWFDQGTR + + + + + + + +:::::::::::::: +recAb.ina +:::::::::::::: +>Tfus_RecA2 +GCMHYDTLVTLADGTQEKIGTIVDRKLDVEVLSYDPETDRIVPRRVVNWFDNGAADHFLQ +FTVGRSGKPGGAQFTATPNHLIRTPGGWREAGELIAGDRVLVHEPHYLNEQQRQVVY +GSLMGRGTLVPDRHGGPGVHFCMAHTAEQAAYLDWKVSLLGNIAHSRTAEASATVGVE +FTPMPELSELHRVVDFGDGHTHLTWEFLKQLTPLALAVWYLDAGTLTIPQSGTDD +DARVQIDVETLSPGSRQRLVEYLRDTHELDAAVVQQGADARSLLEFTPAATVRFLELVA +PYVPESMSSMLLAQFRGRCSVTPEYSDPVQRLVAAPVLDIQVKPGSTRKFDIEVEGNH +NYFVDGVMVHNS +>Mga_RecA +GCGSWYTNVTLADGSTEKLGKIVNQKMDVEVLSYDFESGQIVPRRVTNWFNNGKAEEFLH +FKVDRAGSGTGRGHASLAMTRNHLIRTPVGWREAEDINVGDRVMLAQPRLLSDQQWEIVL +GSLMGDGCLSPPVRQDSESARLRIGHGAQQSAYFDWKVSLLANIPHSRTVNGKGAAFVD +FSPLAELHELRSAVYLGDGKKFLSEEYLKGLTPLSLAIWYMDDGSFSLRSKGLQQRTQG +GSGRIEICVEAMSEGSQVRLRDYLHDTHGLDVRLRKAGAAAKAVLVFSTAATAKFQQLVA +PYMAPCMAYKLLPRFHGRSMVTPQFVEPIMELMPARVTEIESKTDYPIMSRFDIEVEGSH +NYFADGVMVHNS +>TcuDSM43183_RecA +GCMSYGTRVTLADGTQEKIGKIVDQKMDVEVLSYDPQLDKIVPKRVVNWFDNGNAERFLQ +FTVAKSGGNGRAQFAATENHLVRTPGGYREAGELIAGDRVMVMETHRLSDQQWQVVL +GSVMGDGSLSPNRRGRTGVRFRMGHGAGQAAYLDWKVSLLGNIPCTRSVNAKGAVFAD +FTPLPELDELRRVVYFGDGKKHLTWDYLKALTPLALAIWYMDDGHLAVPSKELQDRTAG +GSGRVEICVEAFSPGSRERLVEYLRDTHGLDVRLIERGARKAGVLQFTTAASAKFQELIA +PYVHESMDYKLLPRLRGRCTVEPQFVDPEPRLVPAQILDVRVKPKTRSMRRFDIEVEGAH +NYFVDGVMVHNS +>Mfa_RecA +GCFSYGTRVQLADGSTEKIGKIVNQKMDVEVMSYDPVTDQIVPRKVVNWFNNGPAEQFLQ +FTVEKSGGNGRSQFAATPNHLIRTPAGWTEAGDLIAGDRVLAAERHLLSDQQFQVIL +GSLMGGGNLSPNLHDRNGVRFRMGHGARQADYLEWKTALLGNIGHSVRENDQGARFVD +FTPLPELGELRRAVYLGDGKKFLSEDYLKALTPLALAVWYMDDGSFTVRSKGVQQRTQG +GSGRIEICVEAMAEGTRERLRDYLRDTHGLDVRLRSAGSGKSMLTFSTEATAKFQELVA +PHMAPSMEHKLLPRFRGLGTVEPRFVEPAQRLVPARVLDVQVKPRTRSMNRFDIEVEGNH +NYFVDGVMVHNS +>Mthe_RecA +GCFDYSTRAQLADGTTEKIGKIVDNKMDVEVLSYDPDTDRIVPRKVVNWFNNGPAEQLLQ +FTVEKSGGNGRARFAATPNHLIRTPGGWTEAGDLIAGDRVLAAEPHRLSDQQFQIVL +GSLMGDGTLSPDPRGRNGVRFRMGHGADRVDYLEWKTALLGNIKHSTGENAEGARFVD +FTPLPELAELRRAVYLGDDGRKFISEEYLKALTPLALAIWYMDDGSLTVRSEGLQQGTAG +GSGRIEICVEAMTEGSRIRLRDHLRDTHGLDVRLRQAGAGGKAVLVFSTAATAEFQELVA +PYMAPSMEYKLLPRFRGQSRVVPQFVEPTQRLVPARILDVHVEPHTRSMNRYDIEVEGNH +NYFVDGVMVHNS +>MleTN_RecA +GCMNYSTRVTLADGSTEKIGKIVNNKMDVRVLSYDPVTDRIVPRKVVNWFNNGPAEQFLQ +FTVEKSGSNGKSQFAATPNHLIRTPGGWTEAGNLIAGDRVLAVEPHMLSDQQFQVVL +GSLMGDGNLSPNLCDRNGVRFRLLGYGCKQVEYLQWKKALMGNIRHTVRENSMGASFID +FTPLPELVELQRAVYLGDGKKFLSEEYLKALTPLVLAIWYMDDGSFTVGSKRVQERTAG +GSGRIEICVDAMTEGTRVRLRDYLCDTHGLDVRLREVGSAGKAVLVFSTAATAKFQSLIA +PYVAPSMEYKLLPQFRGRGSVTPQFVEPTQQLVPARVLDVHVKLSTRSMNRFDIEVEGNH +NYFVDGVMVHNS +>Msh_RecA +GCMNYSTRVTLADGSTEKIGKIVNNKMDVKVLSYDPDSDRIVPRKIVNWFNNGPAEQFLQ +FTVEKSGGNGKSQFAATPNHLIRTPAGWTEAGDLNTGDRVLAAEPHLLSDQQFQVVL +GSLMGDGNLSPNRRDRNGVRFRLGHGAKQAEYLQWKTALMGNIGHTVRENAKGASFVD +FTPLPELAELQRAVYMGDGKKFFSEEYLKALTPLALAIWYMDDGSFTLRSRGLQERTAG +GSGRIAICVEAMTEGTRVRLRDYLRDTHGLDVRLRSAGSAGKTVLVFSMAATAKFQELVA +PYMAPSMEYKLLPRFRGRSTVRPQFVEPTQRLVPARILDVHVKPHTRSMNRFDIEVEGNH +NYFVDGVMVHNS +>Mch_RecA +GCFNYSTRVQLADGTTEKIGKIVNNKMDVEVLSYDPVADQVVPRKVVNWFNNGPAEQFLQ +FTVEKSGGNGRSQFAATPNHLIRTPAGWSEAGDLIAGDRVMASEPHRLSDQQFQVVL +GSLMGDGNLSPNRRDRNGVRFRMGHGAKQGDYLQWKTDLLANIAHSAHENAKGARFVD +FTPLPELAELQRAVYLGDGKKFLSEEYLKALTPLALAIWYMDDGGFTVRSKGLQQRTEG +GSGRIEICVEAMSVGSRDRLRDYLRDTHGLDVRLRHAGAAGKAMLVFTTAASAKFQEIVA +PYMAPSMEYKLLPRFRGQGTVAPQFVEPTERLVPARILDIHVKPHTRSMNRFDIEVEGNH +NYFVDGVMVHNS +>MflATCC14474_RecA +GCFNYSTRVQLADRTTEKIGKIVTQKMDVEVLSYDPDTDRVVPRKVVNWFNNGPAEQFLQ +FTVEKSGGNGKSQFAATPNHLIRTPGGWTEAGDLIAGDRVMATEPHRLSDQQFQVVL +GSLMGDGNLSPNRRDRNGVRFRMGHGAKQVDYLRWKTELLGNIKHSTRVNDKGATFVD +FTPLPELAELQRAVYLGDGKKFLSEEYLKALTPLALAIWYMDDGAFTVRSKGLQERTAG +GSGRIEICVEAMSEGTRVRLRDYLHDTHGLEVRLRQSGKAGKAVLVFSTASSAKFQELVA +PYMAPSMEYKLLPRFRGQSTVSPQFVESTQRLVPARILDVHVKPHTRSMNRFDIEVEGNH +NYFVDGVMVHNS +>Mfl_RecA +GCFAYGTRGALADGTTEKIGKIVNQKMDVEVMSYDPDTDQVVPRKVVNWFNNGPAEQFLQ +FTVEKSGGNGKSQFAATPNHLIRTPAGWTEAGDLVAGDRVMAAEPHRLSDQQFQVVL +GSLMGDGNLSPNRRDRNGVRFRMGHGAKQVDYLQWKTALLGNIKHSTHVNDKGATFVD +FTPLPELAELQRAVYLGDGKKFLSEENFKALTPLALVFWYMDDGPFTVRSKGLQERTAG +GSGRIEICVEAMSEGNRIRLRDYLRDTHGLDVRLRLSGAAGKSVLVFSTASSAKFQELVA +PYITPSMEYKLLPRFRGQGAVTPQFVEPTQRLVPARVLDVHVKPHTRSMNRFDIEVEGNH +NYFVDGVMVHNS +:::::::::::::: +rfc_a.ina +:::::::::::::: +>Mja_RFC1 +KCLTGDTKVIVNGEIREIGEVIEEISNGKFGVTLTNNLKVLGIDEDGKIREFDVQYVYKD +KTNTLIKIKTKMGRELKVTTYHPLLINHKNGEIKWEKAENLKVGDKLATPRYILFNESD +YNEELAEWLGYFIGDGHADKESNKITFTNGDEKLRKRFAELTEKLFKDAKIKERIHKDRT +PDIYVNSKEAVEFIDKLGLRGKKADKVRIPKEIMRSDALRAFLRAYFDCDGGIEKHSI +VLSTASKEMAEDLVYALLRFGIIAKLREKVNKNNNKVYYHIVISNSSNLRTFLDNIGFSQ +ERKLKKLLEIIKDENPNLDVITIDKEKIRYIRDRLKVKLTRDIEKDNWSYNKCRKITQEL +LKEIYYRLEELKEIEKALEENILIDWDEVAERRKEIAEKTGIRSDRILEYIRGKRKPSL +KNYIKIANTLGKNIEKIIDAMRIFAKKYSSYAEIGKMLNMWNSSIKIYLESNTQEIEKL +EEIRKTELKLVKEILNDEKLIDSIGYVLFLASNEIYWDEIVEIEQLNGEFTIYDLHVPRY +HNFIGGNLPTILHNT +>Pho_RFC +KCLTGDTKVIANGQLFELRELVEKISGGKFGPTPVKGLKVIGIDEDGKLREFEVQYVYKD +KTERLIRIRTRLGRELKVTPYHPLLVNRRNGEIKWVKAEELKPGDKLAVPRFLPIVTGE +DPLAEWLGYFLGGGYADSKENLIMFTNEDPLLRQRFMELTEKLFSDARIREITHENGT +SKVYVNSKKALKLVNSLGNAHIPKECWRGIRSFLRAYFDCNGGVKGNAI +VLATASKEMSQEIAYALAGFGIISRIQEYRVIISGSDNVKKFLNEIGFIN +RNKLEKALKLVKKDDPGHDGLEINYELISYVKDRLRLSFFNDKRSWSYREAKEISWEL +MKEIYYRLDELEKLKESLSRGILIDWNEVAKRIEEVAEETGIRADELLEYIEGKRKLSF +KDYIKIAKVLGIDVEHTIEAMRVFARKYSSYAEIGRRLGTWNSSVKTILESNAVNVEIL +ERIRKIELELIEEILSDEKLKEGIAYLIFLSQNELYWDEITKVEELRGEFIIYDLHVPGY +HNFIAGNMPTVVHNT +>Pfu_RFC +KCLTGDTKVIANGQLFELGELVEKLSGGRFGPTPVKGLKVLGIDEDGKLREFEVQYVYKD +RTDRlIKIKTQLGRELKVTPYHPLLVNRENGEIKWIKAEELKPGDKLAIPSFLPLITGE +NPLAEWLGYFMGSGYAYPSNSVITFTNEDPLIRQRFMELTEKLFPDAKIRERIHADGT +PEVYVVSRKAWSLVNSISLTLIPREGWKGIRSFLRAYSDCNGRIESDAI +VLSTDNNDMAQQIAYALASFGIIAKMDGEDVIISGSDNIERFLNEIGFST +QSKLKEAQKLIRKTNVRSDGLKINYELISYVKDRLRLNVNDKRNlSYRNAKELSWEL +MKEIYYRLEELERLKKVLSEPILIDWNEVAKKSDEVIEKAKIRAEKLLEYIKGERKPSF +KEYIEIAKVLGINVERTIEAMKIFAKRYSSYAEIGRKLGTWNFNVKTILESDTVDNVEIL +EKIRKIELELIEEILSDGKLKEGIAYLIFLFQNELYWDEITEVKELRGDFIIYDLHVPGY +HNFIAGNMPTVVHNT +>Pab_RFC1 +KCLTGDAKVIANGELTTIGELVERISNGKLGPTPVRGLTVLGIDEDGKLVELPVEYVYKD +KTSELVKIRTRLGRELKVTPYHPLLVNRRNGKIEWVKAEELKPGDRLAIPSFLPAMLND +NPLAEWLGYFFGNGYTDSEERVVFESKSKELRKRFMELTRKLFQDAEIKEDS +GKVYVSSSEVKRLVKSLNKDSIPEQAWKGLRSFLRAYFDCNAEIKDKI +IVSTAGKEIAEQISYALAGLGIVAEVDDKGSVIISDPENVSRFLDEIGFSV +EEKKEEAKALIKKSTLNLGIYVDKELISYVREKLKLSFYENETMWSPEKAREIAWKL +MKEIYYRLDELERFKKALSKSVIIDWSEVEKKKEEISEKTGISVNEILEYAKGKRKPSL +EEYVKIAKALGVELKETLEAIFTFGKKYLGYVISDEIETL +EEVRKEELKRLKELLNDEKLKKGVAYLIFLAQNELLWDEIIEVEKLKGDFVIYDLHVPKY +HNFIGGNLPTVLHNT +>Hwa_RCF +KCVTGSTPILTNKGIRQIGEIVGDVDGFAPAPQNLKVCSLTADGSFQYRHPSHVFGK +RASGLQRIKTNDGATLTVTPEHKLLIRTGENTNPTWVPAADITAGMHVLRAKNLPIPAET +TGSCAASKNASEVSHIGDEYRYHDSLMADVNTRIA +TLERLIEDYAESRSDGSLKF +TLIGAHTPTVSTVSYLLATVGIASRHTSTLIDSE +KRVHAIIIDASDTV +RLEEMIETDWDTVMADQTTTVTSSSTASTTKTT +QSYLSSGETQTCGWIPYADGGVTHPSTQ +HSPLHADVVTVSESLDAEKRVYDLTVPGV +RNYVGGCIPTVMHNT +>Tko_RFC +KCLTGDAKVIANGRLFELGELVEKVSKGRFGPTPVEGLKVLGIDEDGKLREFEVQYVYKD +RAERLIKVRTRLGRELKVTPYHPLLVNRKNGEIMWVKAEELRPGDRLAVPRFLPAIAEE +DPLAEWLGYFIGDGHADSKNKVITFTNTDPSLRQRFMELTERLFPDAKIRERIHKNRA +PDVYVNSRRAWELVSSLGLAGRKADKVYIPEKGWEGIRSFLRAYFDCDCGVDKNAV +VLATASREMAEQVTYALAGFGITSKIREKKVRGKTYYHVTISGSENLERFLSEIGFSH +REKLERTLKLVKKPNPNLDSLNVNYELISYVRDRLKLNFSDDKRSWSHRKARKISWEL +MKEIYYRLDELERLKESLSRSILIDWNEMAERRKEIAEKTGIRADRLLEYIKGKRKPSL +RNYIKIAKALGIDLEPTINAMRVFARKYSSYAEIGRKLGTWNSSVRIILESNTEKIKEL +EEIRKIELELIGEILSDEKLKEGVAYLIFLSQNELYWDEITEVKELKGDFVIYDLHVPGY +HNFIAGNMPTVVHNT +:::::::::::::: +rfc_b.ina +:::::::::::::: +>TsiMM739_RFC 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+NKLPIDPYLFGYWIGNGNAVKPEITVMRDDVDEVIKNIPYKLHNRYKQEG +NSDILVYKELKSILVKNFREKRIPIEYLRASAQQRKRLLQGLIDSDGCVSTAKSQ +AIYVTILFELAKDVQDLLWSLGIKNTLKTAPSARYGIETGEICYLIKFTAFNDLEVSG +LDRKLKRGRERNIKTRSHFHYIKSIEKTGKTKMRCIQVDSPSRLYLAGKSMIPTHNS +:::::::::::::: +thrRS.ina +:::::::::::::: +>Cpa_ThrRS +NCLSEDMRIQTDKGFLFLNEIESNWKDVNFATYDPESKQIQYSKASNFIVKDSANHKMVE +FANYDIASSGDKSGVSLLVTEDHDMYVQQNAESREAPFKKVPARELLQ +KDSKYGFLV +AAEESASSAHAFVN +TTLNTTE +IRAVGDYQGRVWCVTVPTGLIVAHRVHRDTSGNVVCASKPVVIGNC +>Ctr_ThrRS +NCLSEDMRVQTNKGFLGLDEVKDQWRDLKFANYNPETKQIQYLPASNFILKDAANHKMVE +FSDYDINSDAHGSFSLFVTDNHDMYVQTGRVDKEAGDINRIVYEENLEFSKVEASQLVG +SGKGIRFTTTAPNGIDIASVASYKQVVSENQQQTFLELYGYWVGNADKVGETGVTFTAAN +EANSAWLSKAISELEGKVDGTTITDSKLSALFNGSEQSFAEWVWDLAKDELRSVVHGFAR +ASGDENKKIYTSSVILRDELVRVLLHAGYTSRFELNATKGWEITYVEDVAQCVNPVLYSD +KNVKVVDDYFGRVWCVTVPTGLIIVQRVVKNAEDVVVKASRPTIVGNC +:::::::::::::: +topA.ina +:::::::::::::: +>Tko_TopA +YCLHPDSLIPTPQGVKRIKELPEKGEVFALDFDLKLSRARYRLLERDADEPMYKV +TLSDRTELYLTADHPVLVYRDDQLIFVPAEELRENDQVVLFINRSEYSPRTESPTLLGFL +LENATSMKDYILYDPEFGGVLRNRIKDAGLKTEILWRFRIREPTYYKYLRGKMPVPIVRF +LLEEGVVSIEELREVFRGFSYSTSLTPISFEFSEEFWYLFGLVAGDGHLAKKGAITIP +AKDRTEDTVKAVKEIANSLQVPFAFDEKYKMIILRSKSLTRLFELLGCPYGNKTEIFRI +PGEIMAKPEWMAAFLAGYYDADGHIGTKPTGGKKSHSPQIVLTSKNRMAIYTVKQMWQLL +GVGTYLWEKKDRNGNFMAYELKVYSRDAWRFYEVMKNHLRIKRKDLEHVKEVAIRKRKA +YSHHYSVLNVKSWEGKIKSSNVLWKKFDMSNQTAHGRGISLDKLQRIVDY +LTDTDLRRIAMGDVYVLGIRSIEKFHYRGKVYDLVVDQYHNFIANGVVVHNC +>Pfu_TopA +FCLHPDTLILTSQGVRKIKELSREGEVFALDFNLKLSKAKYRLLERDADEQMYKV +TLLDGTELYLTADHPVLVYREGNLAFVPADKLRETDHVVLVLNKSARDNYGFLDLL +LEITDSQEDYAILENGETLSLHSLKM +LVERGEIKDIAVVGFSHNNFGKVMLRDELWYLIGYLAGKGGEIKGNGVVISS +RTKEIVGLTKSLNIDLIETEEGIVLSNKSFVRLLHLIHYTPRVPEVY +GIINNTEWLKAFLAGYYDATLLEGLTLEALYKIKVYLQLL +GIRAKIEDNKLKVHLEDLQRFRELLGKFSR +RKLYVETSQVPVFTDFDERSYDFPR +ILGGDIYIIGIKSIEKFHYKGKVYDLVVENYHNFIANGIAVHNC +>Mja_rGyr +LCLTPDTYVVLGDGRIETIEDIVNAKERNVLSLDLDNLSIKIDTAIKFWKLRYNGNLSKI +TLSNNYELKATPDHCLLVLRDNQLKWIPAKDIKENDYIAMPFNYKVERKPISLLNLL +KYLDITDVLIEFDENSTIFEKIAEYIRNNIKTSTKYKYLRNRRVPLKY +LIEWNFDLDEIEKEAKYIYKSVAGTKKIPLFKLDERFWYFAGLVLGDGSIQDSKIRIAQ +TPLKDVKSILDETFPFLHNWISGNQVIISNPIIAEILEKLGMRNGKLNGIIF +SLPESYINALIAGYFDTDGCFSLLYDKKAKKHNLRMVLTSKRRDVLEKIGIYLNSI +GILNTLHKSREVYSLIISNKSLETFKEKIAKYLKIRKEAFINGYKTYKKEHEER +FECDLLPVKEVFKKLTFEKGRKEILKDSKIHIENWYKEKTNNIPREKLKTVLRY +ANNSEHKEFLEKIVNGDISFVRVKKVENIPYDGYVYDLSIKHNQNFISNG +>Tko_rGyr +LCVTPDTLVSLADGRIMEIKDAVEKSEGNLLSVNGLKPKEAKALKFWEIDWNGPLKVI +KLKNGHEIKATPDHGLLVMREGKLGWVSAKNVREGDYVAFAYNTGHRGRDEYTLLKLM +IKLGITDVMVELDEEYFNEKVAPIVRERISTSTKYKYLRRRVLPLYL +LQEWGLDDYEAHVKSLYRQRAGSKPIPNFKLDGRFWYVFGLVLGDGTLRDSKVLISQ +TPLKDVKSVLEDVFPFLRVFETTNQVGFSNSIIAEVFRRLGARKGKLHPLVF +GLREEYINAMIAGYFDTDGTFSILNDRKGPNFRGILTSKRGDVLRMLSVYLYQI +GIMNYLRRDERTGVWDLIISNRSLEKFREKIYPYLRIRRAQFDEAYSVYRASRRA +FEGDLLPVAPVFGKLKFKNGTKNRILKETGIDVWNWLKRPEGEIPRDKLSKVLEY +AEESPEKEFLKSLVEAGVTWVKVKGVEEELYTGKLYDFTTTTENFLSNGAVSHNC +>Pho_rGyr +LCVTPDTLVSLSDGRIIEIREAVENSEESLLGINGLKPKEAKALKFWEIDWDGPIKVI +KLKNGHEIKATPDHGLLVMRDGKIGWVSAKNIREGDYVAFIYNLGHRGGKKYTLPQLL +KELGISEYENSSSQE +LNNREQEMDSKQISIELDERFWYIFGVILGKGTLKGDKVVIFQ +KDVKPVIEEALPFVRIFESADHIGFSHLILAEVFRRLGVGEGKLHSLVF +GLREEYINAMIAGYFDASGTFLRRAVLTSKRGDILRMLSVYLYQI +GIVNNLRRDEHAGVWELIISDLEKFREKIYPYLRIKKSQFDKVYSISKN +EGDFLPVASIFRKLKFRDGFKNRILDEEIPRDEVAKVLEY +AEDSPEKEFLNSLVEARVTWVRVEKIEERHYTGKLYDFTTTTENFISNGIVSHNC +:::::::::::::: +udp.ina +:::::::::::::: +>MaeoN3_UDP_GD +SCFHPDEILFVDFGDGLECMAFKELFDELSRDNNRSVKILSINKNLKLDLANLKLITKRD +YSDDLIVLKTTMGREIKITKDHPVVVLNGDKLHVKLAENIKEGDEIALPKGEFNSNSNIN +NIITIDILEEIKNTPLIEKTYLNNKNMVLNEFENIRAHLSNKYIHDIKKNGTVRAKDMLP +IRSILNKYNYNSNRLFTVRSKSTTIPSVIKIDGDFARLIGYYLAEGWISEDGKKNGAIRK +RISFSFGAHEEEYINDVKNILNKLDINYIEKIRNGSHSIIISSKLLAYIFEEALKCGNNC +YNKQIPPQIFNSPSDIKWEFLKGILRGDGGIVKLNNNKNLNIEYGTVSKKLANSLMILLQ +SLGIITSLKRCYNNKSTTLTYIIRINGLNQVKKIGELFGDKWNNYKEIADNYERNIKPIG +YKKFDNYASLKVKSVEREYYGGEVYSVETDNNLLISSYGLLIHNC +>Mja_UDP_GD +SCFHPDEVLFIDRGRGLECITFKELFELEDKDNVKILSFDGEKLSLKKLKLASKRY +YNDDLITLRFNLGREIKITKDHPVVILEDGELKIKLTSDVKEGDKVILPYGNFGEEREIE +IDILEELSKTDLIEKVWIHNKDLATNEFNIIKPYLSNKYPHDVKRNGTIRAKDILP +IKEILDKYGSKNRLFTAKSKSTTIPYKIKIDKDFARLIGYYLSEGWISKDYGRNGVVRK +RIGLCFGIHEEEYINDVKNILNKLGIKYIEKIKDGSHSILISSKILAYVFENILNCGINC +YNKNIPPQMFNAKEEIKWEFLKGLFRGDGGIVRLNNNKNLNIEFATVSKKMAHSLLILLQ +LLGIVASVKKCYNNKSTTMAYIIRINGLEQVKKIGELFGKKWENYKDIAESYKRNIEPLG +YKKSDNFAILEVKEIIKEHYSGYVYSVETENSLLITSYGILIHNC +>MvuM7_UDP_GD +SCFHPDEVLFIDRGRGLECITFKELFELEDKDDIKVLSFDGEKLSLKKLKLASKRY +YNDDLITLRFNLGREIKITKDHPVVILEDRNLKVKLAEDVKEGDKVILPYGNFGEEQEIE +IDILEELSKTDLIEKVWIHNKDLVINEFNIIKLYLSNKYPHDVKRNGTIRSKDILL +IKEILDKYGSKNRLFTARSKSTTIPYKIKIDKDFARLMGYYLSEGWISKDYGRNGVVRK +RIGLCFGIHEEEYINDVKNILNKLGIKYIEKIKDGSHSIIISSKILAYVFENILNCGINC +YNKNIPPQIFNSKEEIKWEFLKGLFRGDGGIVRLNNDKNLNIEFATVSKKMAHSLLILLQ +SLGIVASVKKCYNNKSTTMAYIIRINGLEQVKKIGELFGRKWENYKDIVENYKRNIKPLG +YSKSDNFAILEVKEIIKEHYSGYVYSVETENSLLITSYGILIHNC +:::::::::::::: +vma_b.ina +:::::::::::::: +>TacDSM1728_VMA +KCVSGDTPVLLDAGERRIGDLFMEAIQDQKNAVEIGQNEEIVRLHDPLRIYSMVGSEIV +ESVSHAIYHGKSNAIVTVRTENGREVRVTPVHKLFVKIGNSVIERPASEVNEGDEI +ACASVSENGDS + +QTVTTTLVLTF + +DRVVSKEMHSGVFDVYDLMVPD +YGYNFIGGNGLIVLHNT +>TacATCC25905_VMA +KCVSGDTPVLLDAGERRIGDLFMEAIRPKERGEIGQNEEIVRLHDSWRIYSMVGSEIV +ETVSHAIYHGKSNAIVNVRTENGREVRVTPVHKLFVKIGNSVIERPASEVNEGDEI +AWPSVSENGDS + +QTVTTTLVLTF + +DRVVSKEMHSGVFDVYDLMVPD +YGYNFIGGNGLIVLHNT +>Pho_VMA +KCVDGDTLVLTKEFGLIKIKELYEKLDGKGRKIVEGNEEWTELEKPITVYGYKDGKIV +EIKATHVYKGVSSGMVEIRTRTGRKIKVTPIHRLFTGRVTKDGLILKEVMAMHVKPGDRI +AVVKKIDGGEYIKLDSSNVGEIKVPEILNEELAEFLGYLMANGTLKSGIIEIYCDD +ESLLERVNSLSLKLFGVGGRIVQKVDGKALVIQSKPLVDVLRRLGVPEDKKVENWKVP +RELLLSPSNVVRAFVNAYIKGKEEVEITLASEEGAYELSYLFAKLGIYVTISK +SGEYYKVRVSRRGNLDTI +PVEVNGMPKVLPYEDFRKFAKSIGLEEVAENHLQHIIFDEVIDVRYIPEPQEVYDVTTET +HNFVGGNMPTLLHNT +>Pto_VMA +KCVTGDTPVLLADGTVMSIEDIYNKSSGTVEYKNENETLIRLDEPLRLYSFYNGHVN +ESTSNYIYKGKSDSIIKIRTASGREVKVTPVHKLFRFVDDKIIETEARYLNTGDFI +ASIKRFNNKDENYLSGDESELLGLYASYGSIEDGILID +ASIKDRFINLAMNIFKLKTIKIEYRNDRVLIKNDGLKDFIARMISSGIPSE +VMRSRACAASFINGYLYGKLYHDDVIKLHDNEQNILKISYMLTGLGIIHSIRN +NLIEIKAENMKILNSMENELI +DNNETLLISNNANDDFDLYPDEIESIEILPGPFDVYDVTTPD +FGSNFVGGYGAILLHNT +>Tvo_VMA +KCVSGETPVYLADGKTIKIKDLYSSERKKEDNIVEAGSGEEIIHLKDPIQIYSYVDGTIV +RSRSRLLYKGKSSYLVRIETIGGRSVSVTPVHKLFVLTEKGIEEVMASNLKVGDMI +AAVAESESEAR +DCGMSEE +CVMEAEVYTSLEATF + +DRVKSIAYEKGDFDVYDLSVPE +YGRNFIGGEGLLVLHNT +>Pab_VMA +KCVDGDTLVLTKEFGLIKIKDLYKILDGKGKKTVNGNEEWTELERPITLYGYKDGKIV +EIKATHVYKGFSAGMIEIRTRTGRKIKVTPIHKLFTGRVTKNGLEIREVMAKDLKKGDRI +IVAKKIDGGERVKLNIRVEQKRGKKIRIPDVLDEKLAEFLGYLIADGTLKPRTVAIYNND +ESLLRRANELANELFNIEGKIVKGRTVKALLIHSKALVEFFSKLGVPRNKKARTWKVP +KELLISEPEVVKAFIKAYIMCDGYYDENKGEIEIVTASEEAAYGFSYLLAKLGIYAIIRE +KIIGDKVYYRVVISGESNLEKLGIERVGRGYTSYDIVPVEVEELYNALGRPYAELKRAGI +EIHNYLSGENMSYEMFRKFAKFVGMEEIAENHLTHVLFDEIVEIRYISEGQEVYDVTTET +HNFIGGNMPTLLHNT +>Pfu_VMA +KCVDGDTLILTKEFGLIKIKDLYEKLDGKGRKTVEGNEEWTELEEPITVYGYKNGKIV +EIKATHVYKGASSGMIEIKTRTGRKIKVTPIHKLFTGRVTKDGLVLEEVMAMHIKPGDRI +AVVKKIDGGEYVKLDTSSVTKIKVPEVLNEELAEFLGYVIGDGTLKPRTVAIYNND +ESLLKRANFlAMKLFGVSGKIVQERTVKALLIHSKYLVDFLKKLGIPGNKKARTWKVP +KElLLSPPSVVKAFINAYIACDGYYNKEKGEIEIVTASEEGAYGLTYLLAKLGIYATIRR +KTINGREYYRVVISGKANLEKLGVKREARGYTSIDVVPVDVESIYEALGRPYSELKKEGI +EIHNYLSGENMSYETFRKFAKVVGLEEIAENHLQHILFDEVVEVNYISEPQEVYDITTET +HNFVGGNMPTLLHNT +:::::::::::::: +vma_bplus.ina +:::::::::::::: +>fer2_ATPase_with_Intein +MKDKGTIYSISGPVVIATDLDGKMFDVVRVGNMGLVGEVIKIVGNKFTIQVYED +TSGLKPGEPVRSTGKPLSVELGPGLLKSIYDGIQRPLDIIQSETGDFIVRGATAPSLDEE +KEWNFTPILKDGDEVEQGYILGTVQETDIIVHKIMVPYGVNGIIKNIKSGKFRVSDTV +CTIDSGNVKHEIKLKQIWPVRQARKVFLKFAPEIPLITGQRVIDSLFPVAKGGTVAVPG +PFGSGKCVAGDTPLLLADSSIKTIEEVYKEAESEGEIEYHDENETLIKLKSPLKIYSFY +DGKVSESKSDYIYKGKSDSLLKIKTRTGKQVKVTPIHKLFRLDAEGNIVETEAEYLK +AGDYIVSIRKFEAEEEYKHIDAYSLFGDARATSNEIKNKLKEVTKENRKLLKNII +NERILDQITRNEYNPAPKLNWIKTIYDELNLQRPEIKCLRGDRNGNIVTVPDYVSEDLSE +LLGFYVAEGYIRGKSTFVITDSDEKIIGRVKYLLKKVFNLNGKIEIQKNKTNNLIVNSI +ILSEFIRKLIPGKLASHKDIPQIIMKSKDKVIWAFLKGYYLGDGSYYNGNIELSTA +SKKLSISLSYLLTRLGILHTIKNDKSLNKNYRYRTFIRGLNELKKFYLNIAPGNENFQKI +DNIKKYTDSKNSTYTAIDLVPLGAQKIDDLYRTHPSYNKLKSNEVEITNYTGQNEIMSV +SSFNKFARTILLNNKEEEDNQDINTLSHLSEYLDFIYFDRIDSIEYMPGPFDVYDVTTPD +FGSNFVGGEGAILLHNTVIQHQLSKWSDADITVYVGCGERGNEMTEILSTFPELQDPKSG +KPLMEKTILIANTSNMPVAAREASIYTGVTIAEYYRDMGYDVALMADSTSRWAEALREIS +GRLEEMPGEEGYPAYLGRRISEFYERSGNAQIIPQDERTGSITLIGAVSPPGGDLSDPVV +QNTLRVTRVFWALDASLASRRHFPSINWLNSYSLYLDSLSGWFKSNVNTEWLQAHSLIMG +ILQKEAELQEIVQLVGYDSLPEKQKNILDIAKIIREDFLQQNAFDDTDTYCSIKKQYEML +MIIKTLNEMQEKAIDAGLKVIQTATLPVRMKISRMKEITENDFERFYNEVIKEINNEYDN +IMEGVENV +>gi|48477562|ref|YP_023268.1| Vtype ATP synthase subunit A [Picrophilus torridus DSM 9790] +MSGSIYSVSGPVVIAQDIENAKMFDVVRVGELGLIGEIIRISGNKATIQVYED +TSGLRPGEKVYSTGKPLSVELGPGLLSSIYDGIQRPLDVIRAKTGDFIAKGVNIPPLNEE +KLWDFKPLVNEGQQVKSNFIIGEVDETEIIKNKIMVPYGVEGTVKSIKSGKFKVSDTV +AIIETKNGDYEIKLKQIWPVREARRVFHKFPPEIPLITGQRVIDAFFPVAKGGTVAVPG +PFGSGKCVTGDTPVLLADGTVMSIEDIYNKSSGTVEYKNENETLIRLDEPLRLYSFY +NGHVNESTSNYIYKGKSDSIIKIRTASGREVKVTPVHKLFRFVDDKIIETEARYLN +TGDFIASIKRFNNKDE +NYLSGDESE +LLGLYASYGSIEDGILIDASIKDRFINLAMNIFKLKTIKIEYRNDRVLIKND +GLKDFIARMISSGIPSEVMRSRACAASFINGYLYGKLYHDDVIKLHD +NEQNILKISYMLTGLGIIHSIRNNLIEIKAENMKILNSMENELIDNNETLLISNNANDDF +D +LYPDEIESIEILPGPFDVYDVTTPD +FGSNFVGGYGAILLHNTVIQHQLSKWSDSDIVVYVGCGERGNEMTEILSTFPELMDPKTG +KPIMQRTVLIANTSNMPVAAREASIYTGVTIAEYYRDMGYNVALMADSTSRWAEALREIS +GRLEEMPGEEGYPAYLGRRISEFYERSGNAQIIAEDQRTGSVTLIGAVSPPGGDLSDPVV +QNTLRVTRVFWALDASLASRRHFPSINWLTSYSLYTNNLSKWYTENVGPDWPEIYKTMMD +LLEKESELQEIVQLVGYDALPEKEKNVLDIAKMIREDFLQQNAFDDIDTYCSIKKQYMML +KIIKTVYEMQMNALNHGMKISQITSIPARSKISRMKEVSEQDFPAFYKNIIKEINDEYNS +MIEVGGVNA +>gi|332698892|gb|AEE95833.1| H+transporting twosector ATPase alpha/beta subunit central region [Mahella australiensis 501 BON] +MSQGSIVKVSGPLVVAQGMGDANMYDVVRVSGMGLIGEIVEIHGDMAYIQVYEE +TSGLGPGEPVESTGQPLSVELGPGLIEAIYDGIQRPLNAIREQAGDRIARGVRAPSLDRD +KKWHFTPVIEKGAHVTAGDIIGVVQETPIVEHRIMVPYGIEGTVEEIYEGDFTVEDTV +ARVAVKGGIKEITMMQHWPVRRGRPYKRKLPPDRPLITGQRVIDTLFPVAKGGTACIPG +PFGSGKCVSGDTPIVLADGTLTTMDELFENALCRGKVQMQGCETLVELDQPLSVLTMD +NGVGIEAQAPIVYKGKSDTLLCVRTHSGRSVKVTPVHKLFRIDDSGHIIETQAGDLK +PGEFIAAPRRLKADAGDAAFELEISPNVRVMDDDVRRNISVILRNMRANGTLDSVV +GLSRASAESIIYGKLTASVETVGNIYAAAELELPRFNNLRGARAGHIVRLPQKVTSELAE +LAGLFIAEGHIRDEGTVIFTNSEARLRQRFKDLIMKVFGIPCKDVLQSGKTPSVAVFST +TLVCIFEAMGMAGNSKHKSVPPVIMRSSDKALAAFLRGYYLGDGSFSEGEIEFSTA +SPRLQIAVSYALTRLGIFHTMANSGRRHRIFVRGRDNLRAFYEFTAGGFADHLKF +NAIMEYVNSKKTTYTAHDIVPVGPELIERVYEAAGRPYARLKKAGIEITNYTRNGERMSA +DKFKKFVEITGDPTGELEQLCLYLDDFFCDEIVAIDEMEGPFDVYDVTVPE +THNFIGGTGALVLHNTVVQHQLAKWADADIIVYVGCGERGNEMTDVLMEFPELKDPRSG +QPLMKRTVLIANTSDMPVAAREASIYTGITIAEYFRDMGYSVALMADSTSRWAEALREMS +GRLEEMPGEEGYPAYLSSRLAEFYERTGYVKCMGSQEREGTLTAVGAVSPPGGDISEPVT +QATLRIVKVFWSLDAQLARARHFPAINWLLSYSLYIDNIRDWMNENVAPDWMDLRMQAMR +LLQEESSLEEIVRLVGIDAISIRDRWVLEAARSIREDFLHQVAFDEVDTYTSMNKQYRML +KIIMDYYKRGQQALDEGVELDAITNLPVRERIDRAKYIKEENMNQFDDIEKQMAEQFAQ +LLESSKA +>gi|312137461|ref|YP_004004798.1| h(+)transporting twosector atpase [Methanothermus fervidus DSM 2088] +MTGEKRIIRVSGPVVVAEGMKGSQMYEMVRVGEEKLIGEIIELEGDKATIQVYED +TTGLKPGEKVETTGGPLSVELGPGVLGEIFDGIQRPLDKIKAMTGEFIRRGVDVPSLPRE +KKWKFKPTVDVGDEVVGGDIIGEVQETKSIVHKIMVPPNISGSIENIEEGKFKVDEKI +AEIKTDDSVEELKMMQKWPVRKSRPYKKKLDPDVPLITGQRVQDTFFPIAKGGTAAIPG +PFGSGKCVSGDTPILLGDGSLITMEELYKKSLENGKVIEENEHEEIIKLDKPITVYSFD +GSKIIKTKTDIFYKGKSDSLIHIKTKSGREVKVTPIHILFKINENGEIVETMAKDLN +EGDYIVAARKIDINNEDEK +IDLSKFNEKEIKKLPDKMSPELAE +FLGLLFAAGQLDENKLILKIENGNKDILERFSELSLKLFGVECKILENKAIIENK +LIVKFVKTLGILESKIPKIILKSKNKCIARFIDGYINASASNNVLSIE +DKDLKVQLSYLLTRAGIYHEISHDGIFLHLDNSLLTSVEYGDEVVSVAISSCGETNYPN +E +IFADQIVEIREITGPFDVYDISIPG +IENFFGGFGAILLHNTVTQQQLAKWADADIVIYVGCGERGNEMTEVLEEFPKLEDPRTG +RPLMERTVLIANTSNMPVAAREACVYTGITIAEYFRDMGYDVALMADSTSRWAEAMREIS +GRLEEMPGEEGYPAYLASRLAQFYERAGRVITLGSEDKVASVSVIGAVSPPGGDFSEPVT +QNTLRICKVFWALDSSLADRRHFPAIDWLQSYSLYVDSVKDWWKKKIGKDWKAVRDEAMA +LLQKEAELQEIVQLVGPDALPDIERLTLETARMIREDFLQQNAYHEIDTYCPPEKQFKML +ETILLFNRETKKALKKGAPIDKLTQLPVKEDIARMKYIPPDEFEEKVKEIQDKIIKQCEE +VLK +>gi|339757395|gb|EGQ40976.1| archaeal/vacuolartype H+ ATPase subunit A [Candidatus Nanosalinarum sp. J07AB56] +MTQETIESEGEIYKITGPVVVAEDLDCQMNDVVYVGGEELLGEVIQIEGGQAYIQVYEE +TTGVSPGEPVKNTGEPLSVELGPGLLGSIYDGLQRPLPELEEQMGSFIQRGEDAPGINPE +EEYSFEPAVEEGDHVEPGDVIGTVQVSYGEHKVLLPPHSDGGEVEEVREGNYTVTDHV +AELDTGEKVSMRQEVPIRDQRPAEEQLPPEVPLITGQRVFDGLFPLAKGGTAAVPG +GFGTGKCVVGDTPVALADGSKRAIEDIYHDYEGRGDQTQRENERWTDLDNGPRVLSRK +KGEIVEKQVSTVYKGKTDSTVSVGTRSGREVELTPVHRLFVLTPEMEIEEREAQNLQ +KGDTLLVPRNLPVDSSNVEIEVAEALPEKRVVGNGFEAVREAITVLEENHGTRKAAAEHL +GIDDHRMDAYATGRNRPRVADATAILEEAGKTHKLRCVKGEKQSKPTRIPEEVDEDFAE +LLGLLLGDGTVKPRSVQFYNNNERLLDRVEHLAEKLFGLKSARTTANTVESVRVDSK +VLRDLLVYLGFPETEKSLNCSVPETVMKGSEDVVAAFVRGYFLADGHFSEYEAELSTS +SRRMQEDLAYALTRIGITPRVSEKQTDKNPHFRVRFSGDQLIEFHRKLEADYDKFEQI +EEYLDRVEDHFRGTESVDIAPETVRSAFESSEATRADLKSAGAKLSNYETQEERISV +PALQNFADVTKNKHLAEMAGNHLEHFHPDRVASIETHQETKEVYDLTVPD +THNFVGGNAPMLLHNTVTQQSLAKFSDADVIVYIGCGERGNEMTEVLEEFPELEDPQTG +EKLIDRTVLIANTSNMPVAAREASIYTGVTIAEYFRDQGLDVALMADSTSRWAEAMREVS +ARLEEMPGERGYPAYLASRLAEFYERGGRVRPLGPEEPGSVSIIGAVSPPGGDFSEPVT +QNTLRVVKNFFALDKDLAEKRHFPSINWNDSYSGYSETLSDYWQEEVDEDWNQNVQRLRD +LLQESDDLEETVQLVGKDALPDRDRLTLEIGDMLKEFYLQQNAFHPVDQYSSPQKTFDML +EVILEYADHAYEALDEGALVEDIVSLNSRAEIGRIKTAEDHREKLEEVREQMQDEFGE +VAEQ +>gi|332158477|ref|YP_004423756.1| Vtype ATP synthase subunit A [Pyrococcus sp. NA2] +MPVKGEIIRVTGPLVVAKGMKGAKMYEVVRVGELGLIGEIIRLEGDKAVIQVYEE +TAGVRPGEPVIGTGSSLSVELGPGLLTSIYDGIQRPLEVIREKTGDFITRGVTAPALPRD +KKWHFIPKVKVGDKVVGGDIIGEVPETSIIVHKIMVPPGIEGEIVEIAEEGDYTIEEVI +AKVKTPSGEIKELKMYQRWPVRVKRPYKEKLPPEVPLITGQRVIDTFFPQAKGGTAAIPG +PFGSGKCVDGDTLVLTKEFGLIKIRDLYKILDGKGKKTINGNEEWTELDNPITLYGYK +NGKIVEIKATHIYKGFSAGMIEIKTRTGRKIRVTPIHKLFTGRVTKNGLEIKEVMAMDLK +KGDRIIVAKKIDGGER +VKLNIKVDQKRGKKIKIPEVLDEKLAE +FLGYLIADGTLKPRTVAIYNNDESILKRANELAKDLFNVEGKIIKEKTVKALLIHSK +ALVEFFSMLGVPRSKKARTWKVPKELLISEPEVVKAFIKAYIMCDGHYHEKKGEIEIVTA +SEEAAYGLSYLLAKLGIYAIIREKVIKDRTYYRVIISGKSNLEKLGIARMGRGYTSFDV +VPMDVEELYDAIGRSYAELKKAGIEIHNYLSGENMSY +EMFKRFAKFVGMEEIAENHLSHVLFDEIVEIRYIEMGQEVYDVTTET +HNFVGGNMPTLLHNTVTQHQLAKWSDAQVVVYIGCGERGNEMTDVLEEFPKLKDPKTG +KPLMERTVLIANTSNMPVAAREASIYTGITIAEYFRDMGYDVALMADSTSRWAEALREIS +GRLEEMPGEEGYPAYLASKLAEFYERAGRVITLGSDNRVGSVSVIGAVSPPGGDFSEPVV +QNTLRVVKVFWALDADLARRRHFPAINWLTSYSLYTDAVKDWWHKNVDPEWKKMRDEAMA +LLQKEAELQEIVRIVGPDALPERERAILLVARMLREDYLQQDAFDEVDTYCPPEKQVTMM +RVLLNFYHKTMEAINRGIPLEEIAKLPVREEIGRMKFERDIEKIRELIDKTNEQFEE +LFKKYGA +>gi|18976554|ref|NP_577911.1| Vtype ATP synthase subunit A [Pyrococcus furiosus DSM 3638] +MPAKGRIIRVTGPLVIADGMKGAKMYEVVRVGELGLIGEIIRLEGDKAVIQVYEE +TAGLKPGEPVEGTGSSLSVELGPGLLTSIYDGIQRPLEVLREKSGHFIARGISAPALPRD +KKWHFTPKVKVGDKVVGGDIIGEVPETSIIVHKIMVPPGIEGEIVEIADEGEYTIEEVI +AKVKTPSGEIKELKMYQRWPVRVKRPYKEKLPPEVPLVTGQRVIDTFFPQAKGGTAAIPG +PFGSGKCVDGDTLILTKEFGLIKIKDLYEKLDGKGRKTVEGNEEWTELEEPITVYGYK +NGKIVEIKATHVYKGASSGMIEIKTRTGRKIKVTPIHKLFTGRVTKDGLVLEEVMAMHIK +PGDRIAVVKKIDGGEY +VKLDTSSVTKIKVPEVLNEELAE +FLGYVIGDGTLKPRTVAIYNNDESLLKRANFLAMKLFGVSGKIVQERTVKALLIHSK +YLVDFLKKLGIPGNKKARTWKVPKELLLSPPSVVKAFINAYIACDGYYNKEKGEIEIVTA +SEEGAYGLTYLLAKLGIYATIRRKTINGREYYRVVISGKANLEKLGVKREARGYTSIDV +VPVDVESIYEALGRPYSELKKEGIEIHNYLSGENMSY +ETFRKFAKVVGLEEIAENHLQHILFDEVVEVNYISEPQEVYDITTET +HNFVGGNMPTLLHNTVTQHQLAKWSDAQVVVYIGCGERGNEMTDVLEEFPKLKDPNTG +KPLMERTVLIANTSNMPVAAREASIYTGITIAEYFRDMGYDVALMADSTSRWAEALREIS +GRLEEMPGEEGYPAYLASRLAEFYERAGRVVTLGSDYRVGSVSVIGAVSPPGGDFSEPVV +QNTLRVVKVFWALDADLARRRHFPAINWLTSYSLYVDAVQDWWHKNVDPEWRRMRDKAME +LLQKEAELQEIVRIVGPDALPERERAILLVARMLREDYLQQDAFDEVDTYCPPQKQVTMM +RVLMTFYERTMDAISRGVPLEEIAKLPVREEIGRMKFEPDIEKIRALIDKTNEQFDE +LLKKYGA +>gi|14591712|ref|NP_143800.1| Vtype ATP synthase subunit A [Pyrococcus horikoshii OT3] +MVAKGRIIRVTGPLVVADGMKGAKMYEVVRVGELGLIGEIIRLEGDKAVIQVYEE +TAGVRPGEPVVGTGASLSVELGPGLLTSIYDGIQRPLEVIREKTGDFIARGVTAPALPRD +KKWHFIPKAKVGDKVVGGDIIGEVPETSIIVHKIMVPPGIEGEIVEIAEEGDYTIEEVI +AKVKTPSGEIKELKMYQRWPVRVKRPYKEKLPPEVPLITGQRVIDTFFPQAKGGTAAIPG +PFGSGKCVDGDTLVLTKEFGLIKIKELYEKLDGKGRKIVEGNEEWTELEKPITVYGYK +DGKIVEIKATHVYKGVSSGMVEIRTRTGRKIKVTPIHRLFTGRVTKDGLILKEVMAMHVK +PGDRIAVVKKIDGGEY +IKLDSSNVGEIKVPEILNEELAE +FLGYLMANGTLKSGIIEIYCDDESLLERVNSLSLKLFGVGGRIVQKVDGKALVIQSK +PLVDVLRRLGVPEDKKVENWKVPRELLLSPSNVVRAFVNAYIKGKEEVEITLA +SEEGAYELSYLFAKLGIYVTISKSGEYYKVRVSRRGNLDTIPVEVNG +MPKVLPY +EDFRKFAKSIGLEEVAENHLQHIIFDEVIDVRYIPEPQEVYDVTTET +HNFVGGNMPTLLHNTVTQHQLAKWSDAQVVIYIGCGERGNEMTDVLEEFPKLKDPKTG +KPLMERTVLIANTSNMPVAAREASIYTGITIAEYFRDMGYDVALMADSTSRWAEALREIS +GRLEEMPGEEGYPAYLASKLAEFYERAGRVVTLGSDYRVGSVSVIGAVSPPGGDFSEPVV +QNTLRVVKVFWALDADLARRRHFPAINWLTSYSLYVDAVKDWWHKNIDPEWKAMRDKAMA +LLQKESELQEIVRIVGPDALPERERAILLVARMLREDYLQQDAFDEVDTYCPPEKQVTMM +RVLLNFYDKTMEAINRGVPLEEIAKLPVREEIGRMKFERDVSKIRSLIDKTNEQFEE +LFKKYGA +>gi|16081190|ref|NP_393482.1| Vtype ATP synthase subunit A [Thermoplasma acidophilum DSM 1728] +MGKIIRISGPVVVAEDVEDAKMYDVVKVGEMGLIGEIIKIEGNRSTIQVYED +TAGIRPDEKVENTRRPLSVELGPGILKSIYDGIQRPLDVIKITSGDFIARGLNPPALDRQ +KKWEFVPAVKKGETVFPGQILGTVQETSLITHRIMVPEGISGKVTMIADGEHRVEDVI +ATVSGNGKSYDIQMMTTWPVRKARRVQRKLPPEIPLVTGQRVIDALFPVAKGGTAAVPG +PFGSGKCVSGDTPVLLDAGERRIGDLFMEAIQDQKNAVEIGQNEEIVRLHDPLRIYSMV +GSEIVESVSHAIYHGKSNAIVTVRTENGREVRVTPVHKLFVKIGNSVIERPASEVN +EGDEIACASVSENGDS + + + + + +QTVTTTLVLTFDRVVSKEMHSGVFDVYDLMVPD +YGYNFIGGNGLIVLHNTVIQHQLAKWSDANIVVYIGCGERGNEMTEILTTFPELKDPNTG +QPLMDRTVLIANTSNMPVAAREASIYTGITIAEYYRDMGYDVALMADSTSRWAEALREIS +GRLEEMPGEEGYPAYLGRRVSEFYERSGRARLVSPDERYGSITVIGAVSPPGGDISEPVS +QNTLRVTRVFWALDAALANRRHFPSINWLNSYSLYTEDLRSWYDKNVSSEWSALRERAME +ILQRESELQEVAQLVGYDAMPEKEKSILDVARIIREDFLQQSAFDEIDAYCSLKKQYLML +KAIMEIDTYQNKALDSGATMDNLASLAVREKLSRMKIVPEAQVESYYNDLVEEIHKEYGN +FIGEKNAEASL +>gi|13540883|ref|NP_110571.1| Vtype ATP synthase subunit A [Thermoplasma volcanium GSS1] +MGKIVRISGPVVVAEDIENAKMYDVVKVGEMGLIGEIIRIEGNRSTIQVYED +TAGIRPDEKVENTMRPLSVELGPGLLKSIYDGIQRPLDVIKETSGDFIARGLNPPPLDRK +KEWDFVPAVKKNDIVYPGQVIGTVQETSLITHRIIVPDGVSGKIKSIYEGKRTVEDVV +CTISTEHGDVDVNLMTTWPVRKARRVVRKLPPEIPLVTGQRVIDALFPVAKGGTAAVPG +PFGSGKCVSGETPVYLADGKTIKIKDLYSSERKKEDNIVEAGSGEEIIHLKDPIQIYSYV +DGTIVRSRSRLLYKGKSSYLVRIETIGGRSVSVTPVHKLFVLTEKGIEEVMASNLK +VGDMIAAVAESESEAR + + + + + +DCGMSEECVMEAEVYTSLEATFDRVKSIAYEKGDFDVYDLSVPE +YGRNFIGGEGLLVLHNTVIQHQLAKWSDANIVVYIGCGERGNEMTEILTTFPELKDPVSG +QPLMDRTVLIANTSNMPVAAREASIYTGITIAEYYRDMGYDVALMADSTSRWAEALREIS +GRLEEMPGEEGYPAYLGRRISEFYERSGRARLVSPEDRFGSITVIGAVSPPGGDISEPVS +QNTLRVTRVFWALDASLANRRHFPSINWLNSYSLYTEDLRHWYDENVAKDWGSLRSQAMD +ILQRESELQEVAQLVGYDAMPEKEKSILDVARIIREDFLQQSAFDEIDSYCSLRKQYLML +KAIMELNSYQSMAIDHGVTMDNLSSLPVREKLSRMKIVPEDQVESYYSSIIKEIHKEYTS +FIGEKNAEANI +>gi|9369338|emb|CAB99208.1| AATPase Asubunit [Thermoplasma acidophilum] +MGKIIRISGPVVVAEDVEDAKMYDVVKVGEMGLIGEIIKIEGNRSTIQVYED +TAGIRPDEKVENTRRPLSVELGPGILKSIYDGIQRPLDVIKITSGDFIARGLNPPALDRQ +KKWEFVPAVKKGETVFPGQILGTVQETSLITHRIMVPEGISGKVTMIADGEHRVEDVI +ATVSGNGKSYDIQMMTTWPVRKARRVQRKLLSRDPLVTAQSGNRCAFPVAEAANCRVPG +PFGSGKCVSGDTPVLLDAGERRIGDLFMEAIRPKERGEIGQNEEIVRLHDSWRIYSMV +GSEIVETVSHAIYHGKSNAIVNVRTENGREVRVTPVHKLFVKIGNSVIERPASEVN +EGDEIAWPSVSENGDS + + + + + +QTVTTTLVLTFDRVVSKEMHSGVFDVYDLMVPD +YGYNFIGGNGLIVLHNTVIQHQLAKWSDANIVVYIGCGERGNEMTEILTTFPELKDPNTG +QPLMTGLSFIANTSNMPVAAREASIYTGITIAEYYRDMGYDVALMADSTSRWAEALREIS +GRLEEMPGEEGYPAYLGRRVSEFYERSGRARLVSPDERYGSITVIGAVSPPGGDISEPVS +QNTLRVTRVFWALDAALANRRHFPSINWLNSYSLYTEDLRSWYDKNVSSEWSALRERAME +ILQRESELQEVAQLVGYDAMPEKEKSILDVARIIREDFLQQSAFDEIDAYCSLKKQYLML +KAIMEIDTYQNKALDSGATMDNLASLAVREKLSRMKIVPEAQVESYYNDLVEEIHKEYGN +FIGEKNAEASL +>gi|14521960|ref|NP_127437.1| Vtype ATP synthase subunit A [Pyrococcus abyssi GE5] +MVAKGRIIRVTGPLVVADGMKGAKMYEVVRVGELGLIGEIIRLEGDKAVIQVYEE +TAGVRPGEPVIGTGSSLSVELGPGLLTSIYDGIQRPLEVIREKTGDFIARGVTAPALPRD +KKWHFIPKVKVGDKVVGGDIIGEVPETSIITHKIMVPPGIEGEIVEIAEEGEYTIEEVI +AKVKTPSGEIKELKMYQRWPVRVKRPYKEKLPPEVPLITGQRVIDTFFPQAKGGTAAIPG +PFGSGKCVDGDTLVLTKEFGLIKIKDLYKILDGKGKKTVNGNEEWTELERPITLYGYK +DGKIVEIKATHVYKGFSAGMIEIRTRTGRKIKVTPIHKLFTGRVTKNGLEIREVMAKDLK +KGDRIIVAKKIDGGER +VKLNIRVEQKRGKKIRIPDVLDEKLAE +FLGYLIADGTLKPRTVAIYNNDESLLRRANELANELFNIEGKIVKGRTVKALLIHSK +ALVEFFSKLGVPRNKKARTWKVPKELLISEPEVVKAFIKAYIMCDGYYDENKGEIEIVTA +SEEAAYGFSYLLAKLGIYAIIREKIIGDKVYYRVVISGESNLEKLGIERVGRGYTSYDI +VPVEVEELYNALGRPYAELKRAGIEIHNYLSGENMSY +EMFRKFAKFVGMEEIAENHLTHVLFDEIVEIRYISEGQEVYDVTTET +HNFIGGNMPTLLHNTVTQHQLAKWSDAQVVIYIGCGERGNEMTDVLEEFPKLKDPKTG +KPLMERTVLIANTSNMPVAAREASIYTGITIAEYFRDMGYDVALMADSTSRWAEALREIS +GRLEEMPGEEGYPAYLASKLAEFYERAGRVVTLGSDYRVGSVSVIGAVSPPGGDFSEPVV +QNTLRVVKVFWALDADLARRRHFPAINWLTSYSLYVDAVKDWWHKNVDPEWKAMRDKAME +LLQKESELQEIVRIVGPDALPERERAILLVARMLREDYLQQDAFDEVDTYCPPEKQVTMM +RVLLNFYDKTMEAISRGVPLEEIAKLPVREEIGRMKFEPDVGKIKALIDKTNEQFEE +LFKKYGA +:::::::::::::: +vma.ina +:::::::::::::: +>SexIFO1128_VMA +GCFAKGTQVMMADGSDKSIEDIQLGENVMGKDGTPRTVISLPRGKETMYEVCHSSTKGTT +KDTLMNYVCSGNHKIVMQTPQQIGITEHGIDGKTYTSVSYFALRDS +QHGYPIVKKLTKSFEHQQHGGKEQTLITVNNFVSSLKSEPINWDVEAKHY +ESLGHYVKKCSYQLINPVFHQSGKLAQEIASLNYSKDKAPLLAWLIGFWVGNGAMRH +SQFVVESQDIELVNRIQDIAGLLNLSATTACYYSGSKDDEAKLAKLN +SSSAEGFEDDLEGNPSVKELADMDRLSESKTATLPTAFGVENIDE +LIISLGEGRGNGNVFAQVIGSFGIDLADKDTLVTKIAHELAGDAFEVREQ +FVAGLVDAAGYVRKDVYDHASEATISTESKSTVLGLVKIARSLGIKITVTSDDSDDSDE +HDHAHCGHDHGSSSSYTAVMTGDALTNSMRFCAIGRNRVAAKEFMRQAVPFYF +SLEKKSEDDYYGITVPDNTDKQYLLSSMALVHNC + + +>Pst_VMA +GCFAKGTKVLMANGDDKNIEDIAVGEEVLGKDGLPREVVALPRGRETMYEVSEKTQHRAE +TVFGTASYTCNATHKLVLQTNQRVNITNHVLRGESQTSVTYFQMKTA +VADGREIELPKLCTKSFQHSSHGRENAWKKAEVFASTISRDPIDWTAEARDI +SRLGYHVRRATRQLWSPVLVEKEVLAPMIAKRGFDESIAPYMAYLVGLWVGDGYSDR +ATFSIDIQDVEIHERIKDFASHAGLTPRIA +CYKKSRDATISLHNSET +RGKNVRQNLNTGNLLWSLLAEICGKKENEMLFKLVPSFLRSESIAVREY +FISGLVDSDGHVKRDEADKCYSATVKTIYPAVRDGLVSVARSLGIQTSVSVEEAKEVNS +VKHQESYAIYMANSSALDSVLSKCAAPRKRAEEPVCVNREPHPYTF +HMVEKEEDDFYGITLSEDSDHQFLLSNLALVHNC + + +>Zba_VMA +GCFAKGTEVMMHDGSVKAIETIEAGEAVMGTDGQPRKVVGLPRGREVMYKVSQKTAHRVH +KTDETRAAPVALFEYNCNATHKLVVRTPRSCRSITRKMQGVDYNEVIFFDLKKK +KLEDGREIEIVKEVSRSYPAAEGAEKAAQMVKDYYDAARGKEFFEWTIEARDV +XELGAHVRKATHQVYAPVLYESDFFFHYVKNSKFALRSEASTALAYLLGLWVGDGLSDR +AVLSVDSEDSSLLERITGYADILDLSAEYK +DREIPKRAKTVCLYPKTI +RGNDIRRNLNTDNPVWNAIVDLGYLKDGVKNVPSYLFSDSICHREV +FLAGLIDSDGHVRGDDGLSVTIKTIHKTVMEGTVAVARSLGLIVSVNTEEAKIDKND +VNHRFVYAIYISGGDALLSVLAHCAAAKKFRAPPSNEVVRGLKKVFF +EMEELKEDDYYGITLAKESDHQFLLANQLVVHNC + + +>SceDH11A_VMA +GCFAKGTNVLMADGSIECIENIEVGNKVMGKDGRPREVIKLPRGSETMYSVVQKSQHRAH +KSDSSREMPELLKFTCNATHELVVRTPRSVRRLSRTIKGVEYFEVITFEMGQK +KAPDGRIVELVKEVSKSYPVSEGPERANELVESYRKASNKAYFEWTIEARDL +SLLGSHVRKATYQTYAPILYENDHFFDYMQKSKFHLTIEGPKVLAYLLGLWIGDGLSDR +ATFSVDSRDTSLMERVTEYAEKLNLCAEYK +DRKEPQVAKTVNLYSKVV +RGNGVRNNLNTENPLWDAIIGLGFLKDGVKNIPSFLSTDNIGTRET +FLAGLIDSDGYVTDEHGIKATIKTIHTSVRDGLVSLARSLGLVASVNAEPAKVDMNG +TKHKISYAIYMSGGDVLLNVLSKCAGSKKFRPAPVATFVRECQGFYF +ELQELKENDYYGITLSDDSDHQFLLANQVVVHNC + + +>SceOUT7112_VMA +GCFAKGTNVLMADGSIECIENIEVGNKVMGKDGRPREVIKLPRGSETMYSVVQKSQHRAH +KSDSSREMPELLKFTCNATHELVVRTPRSVRRLSRTIKGVEYFEVITFEMGQK +KAPDGRIVELVKEVSKSYPVSEGPERANELVESYRKASNKAYFEWTIEARDL +SLLGSHVRKATYQTYAPILYENDHFFDYMQKSKFHLTIEGPKVLAYLLGLWIGDGLSDR +ATFSVDSRDTSLMERVTEYAEKLNLCAEYK +DRKEPQVAKTVNLYSKVV +RGNGVRNNLNTENPLWDAIIGLGFLKDGVKNIPSFLSTDNIGTRET +FLAGLIDSDGYVTDEHGIKATIKTIHTSVRDGLVSLARSLGLVASVNAEPAKVDMNG +TKHKISYAIYMSGGDVLLNVLSKCAGSKKFRPAPVATFVRECQGFYF +ELQELKENDYYGITLSDDSDHQFLLANQVVVHNC + + +>ScaCBS4309_VMA +GCFAKGTEVLMADGSDKAIEAIEVGEQVMGKDGAPRTVIALPRGTETMYEVCHTTQHRNG +NEKFGLMNYVCSGNHKLVLRTPQLIRTTIHELRGKHYTSVTFFVTEKS +ANGTIVKQRTKTFQHEFHGGEEAATKLAADFASTIDPKHIDWDIEAKDY +KQLDHYVKKSSYQMINPVFKESGNLANILGDAGIEKTLAAKMAWLLGFWVGNGHMET +AQFPVDSWDTQLVDRISEYGKHFNLTTTTENHYRSNHVESNKDIEIFEMNEAQIEEAE +QTGVVAFDSNRKGDPSETELIEAEIFNESRPSTAGLFTPAAISPASLVTDLSVTLRGTGI +GGAGVSKERNLNNIFWDIVTSFGVRTNGQGSTYEKSVPLHLSYDDIEVREQ +FIAGLIDSDGYVKSADNRFSATVTTIYKGVSEGLIRLARSLGIRVSVSTEKEHVDKNN +VKHKSCYRVFLSGEALIGVLRFCALDRKRTAFKEFTREAVPFYF +TLQEKDQDEYYGITLPDETDKQYLLSSLALVHNC + + +>KlaNRRLY1140_VMA +GCFSKGTEVMMGDGKDELIENIQVGDEVMGRDGLPRQVVGLPRGHDDMYQVTEKSEDNET +AKISFQCNSSHKLVLVTPQDIRLTESKEKVTVAFNRLADISVGNG +TESRTVRLVERAEKSFANAESNQAIINAAEFVTTIDTTSIEWTLEARDM +LLVDSSIREVTQQLINPVLLEKEHLAGVLKSNDFQSSLAPQFSYLLGAFVGSS +GKDNSEYLQQLSAQFDKKIVAEKSID +VQSNGKTVGTASIVISQE +PVQENKRRKVAQVSLVSKIVQESFSSGIPSFMMSENINVRES +FLAGIVDSQNQKLDDTVALKTLSVKTHDGIARLARSLGIRVSG +KKQNQEYTLTLSGDALKSVSNWTSTSNIEKVDVIHKAQPISF +DLEKIESADYFGVTLAEESDHKFLLSNMTLVHNC + + +>Vpo_VMA +GCFAKGTEVMMADSSIKNIEDIEIGDLVMGQDGQPREVTQLPRGSDKMYKVNEINENSTS +ELFSFVCNATHQLIVRTPRNIKVQTRIIDGIECNEIVYTDLFKE +ITEDARIIELIKEVSKIYPVSEGMDDVQEFVSQYNKSLEDYFQWTVEPRDI +NRLTESIREATYQVYAPVLYECENLLQYLKNTKYNLNEKSPTALAYLLGLWTGSGMTRR +AGLSVSTTDESLMNNIVAAADLLNLKSEFK +QERTTTRVGNVNFY +GNSTSTNQNVDNLLWDAIQELGFIQDGNKTVPSFLSSDLIEIRET +FLAGLIDSNGSVDNNKQDISCTIELEDNKVMSGIVSLIRSLGLKADVTQSSGKLN +DVCYNVTVKGGELLKSVLSRCSAINYTKCESRDLLREPVEFYF +ELQELEEAEYYGITLPEYSDHQFMLSNQVVVHNC + + +>SceOUT7091_VMA +GCFAKGTNVLMADGSIECIENIEVGNKVMGKDGRPREVIKLPRGRETMYSVVQKSQHRAH +KSDSSREVPELLKFTCNATHELVVRTPRSVRRLSRTIKGVEYFEVITFEMGQK +KAPDGRIVELVKEVSKSYPISEGPERANELVESYRKASNKAYFEWTIEARDL +SLLGSHVRKATYQTYAPILYENDHFFDYMQKSKFHLTIEGPKVLAYLLGLWIGDGLSDR +ATFSVDSRDTSLMERVTEYAEKLNLCAEYK +DRKEPQVAKTVNLYSKVV +RGNGIRNNLNTENPLWDAIVGLGFLKDGVKNIPSFLSTDNIGTRET +FLAGLIDSDGYVTDEHGIKATIKTIHTSVRDGLVSLARSLGLVVSVNAEPAKVDMNG +TKHKISYAIYMSGGDVLLNVLSKCAGSKKFRPAPAAAFARECPGFYF +ELQELKEDDYYGITLSDDSDHQFLLANQVVVHNC + + +>Tpr_VMA +GCFAKGTKVLLHDGSLRAIESIEVGEDVMGVDGERRKVVGLPRGREVMYKVSQKTTNRAH +ETAETRSEPLGLFEYTCNATHKLVVRTPRSCRLLTRNENGADYYDVAFFDLVKT +KLKDGREIEIVKEMSNSYLATEGPEKAAQMVKEYQEASEGKEFFEWTIEARDV +AVLGADVREATYQVYSPVLYESDFFSQYVKDSKFGLTSEAPLALAYLLGLWAGDVSSEE +TVFSVNSEDGSLYERITQFADILGLSAEFK +DREAPKQGKTVYLHPKAI +GGNDIQENSNNDNPLRNAIVDLGYLTDGVKNVPTYLLSDAIPHREI +FLAGLIDSDGFVRSEDGCSATIKTTLKTVMAGTVAVARSLGLNVSVNTEEAKVDNG +VDQRLSYAISISVSDALLSVLAKCAGAEMFRELPASEVVRKMNKVYF +EMEELEEDDYYGLTLANGTDHQFMLANQLVVHNC + + +>Ctr_VMA +GCFTKGTQVMMADGADKSIESIEVGDKVMGKDGMPREVVGLPRGYDDMYKVRQLSSTRRN +AKSEGLMDFTVSADHKLILKTKQDVKIATRKIGGNTYTGVTFYVLEKT +KTGIELVKAKTKVFGHHIHGQNGAEEKAATFAAGIDSKEYIDWIIEARDY +VQVDEIVKTSTTQMINPVHFESGKLGNWLHEHKQNKSLAPQLGYLLGTWAGIGNVKS +SAFTMNSKDDVKLATRIMNYSSKLGMTCSST +ESGELNVAENEEEFFNNLGAEKDEAGDFTFDEFTDAMDELTI +NVHGAAASKKNNLLWNALKSLGFRAKSTDIVKSIPQHIAVDDIVVRES +LIAGLVDAAGNVETKSNGSIEAVVRTSFRHVARGLVKIAHSLGIESSINIKDTHIDAAG +VRQEFACIVNLTGAPLAGVLSKCALARNQTPVVKFTRDPVLFNF +DLIKSAKENYYGITLAEETDHQFLLSNMALVHNC + + +>Spa_VMA +GCFAKGTNVLMADGSIECIENIEVGNKVMGKDGRPREVIKLPRGSETMYSVVQKSQHRAH +KSDSSREMPELLKFTCNATHELVVRTPRSVRRLSRTIKGVEYFEVITFEMGQK +KAPDGRIVELVKEVSKSYPVSEGPERANELVESYRKASNKAYFEWTIEARDL +SLLGSHVRKATYQTYAPILYENDHFFDYMQKSKFHLTIEGPKVLAYLLGLWIGDGLSDR +ATFSVDSRDTSLMERVTEYAEKLNLCAEYK +DRKEPQVAKTVNLYSKVV +RGNGVRNNLNTENPLWDAIIGLGFLKDGVKNIPSFLSTDNIGTRET +FLAGLIDSDGYVTDEHGIKATIKTIHTSVRDGLVSLARSLGLVASVNAEPAKVDMNG +TKHKISYAIYMSGGDVLLNVLSKCAGSKKFRPAPVATFVRECQGFYF +ELQELKENDYYGITLSDDSDHQFLLANQVVVHNC + + +>Cgl_VMA +GCFAKGTQVLMADGSNQSIENIKIGDKVMGQDGKPRNVTALPRGYDDMYNVELDGETD +LSYTCNSNHTLVLKTEQNVLLAGNTVSYFALGAL +IDETNGRAVEIVQEVQETFESNISASDFAANINREPISWTLEIRDI +DYLSERVRMFTKQSVNPVLLETPTLAKQLESNESTATNLAYLLGTWIASKATTA +GTISVPTTKADLLSKVKSALSSLSIDYSSE +SINSVSTYRRTQSIPLMENGKHVGNANI +TAEQEIEETMEVLSLNVTNHSSKLFHDLALSMINQDGSRSIPSAFTHEQLCVRES +FVAGILDMQGCNIENGVEIDSSINGLAKLSRSLGLRCN +KSSNLLKLSGNMSNISAQSTNNWTSTEDNSSAYKAQLMDF +SVQKLPKDNYYGVTLDDDSDHQFLLSNLVLVHNC + + +>Scar_VMA +GCFAKGTTVLMADGSIECIENIKIGDKVMGKDGKPREVIKLPRGNETMYSVVQKSQHRAH +KTDSSREVPDLLKFTCNSTHELVVRTPRSVRRVSRTMKGVEYFEVISFEMVQK +KVPDGRIIELVKEVSKSYPASEGPERADELVESYRKASTKPYFEWTVEARDL +SLLGSHVRKATYQTYAPILYENDYFFNYMENSKFHPTIEAPKVLAYFLGLWIGDGLTDR +TTFSIDSRDTSLMERVTEYAEKLDLCAEYK +DRKEPKVAKTVNLYSKSV +RXNGIRNNLNTENPLWDAIVGLGFLKDGVKNIPSFLSTDNIGTRET +FLAGLIDSDGYVTDEHGITATVKTIHTSVRDGLVSVARSLGLVISVNAEPAKIDMSG +TSHKMCYAIYMSGGDILLNVLSKCASFKKFRPAPVAPPVRECRGFYF +ELQELEEDDYYGITLSDDSDHQFLLANQVVVHNC + + +>Zro_VMA +GCFAKGTEVMMSDGSIKEVEGIEVGQEVMGKDGKPREVVGTPSGREKMYKVSHKTAHRAH +KSDSTSERFGLFEYTCNATHKLVVRTSRSCRPLVRNIQGTDYVEVCLFNMTKK +TLEDGRVIDIVEETSDFYPAVEGPEKALRILKEYAEADGGKEYFEWTIEARDV +ALLSAQVRKATYQLSAPVLLENNHFSHYLKDSNSAVGNDTVRALSYFLGLWIGDGMLNNA +ATFSVDSQNASLLNRINEFAEVLGLSAEYK +DSQEPKRAKTVNLYAKAI +RDEGVRKNLDTHNLLWDAIVDLGYLKDDSKNVPGYICSDSFQHREV +FLAGIIDSTGYVSDETATVKTIDQSVMTGTVAVARSLGINVSVDVEVDEDG +VDRSFVYAIYMDRSDALLAVLANCASNNKQIEAPPHGVIREFNKAYF +EMEELEEDEYYGLTLSNESDHQFLLANQLVVHNC + + +>Lel_VMA +GCFTKGTQVMMADGKDKSIEDVQLGELVMGKDGDARKVVGLPRGFDTMYKVEQIGHDD +SLNFTVSADHKLVLKTEQRIEVTTRKFAGKNYAAVNYFAMGKT +KKSAGGKDGVEIVRVKSKVFAHHIHGKEVAESKALEFAASVDMSAIEWVVEAKDYY +EQVEDTVKQNSTQLINPVFYESNAIGKWLADNGETKPSSASELAYLMGAAFNESR +ESISDAATNTKRTLENVEFDDLKSVDSSLD +LSMDDGYETDNTSIHSV +NEKESVNVARLLKQALDHFGFSTGSNKVIPSSIAVENIEVRES +FLAGFVDASQTELKQDSAIINIGASNKSIIANIVKLARSLGIKAACKDDG +LNRITLEGPALAGVLSKCSSSSVDAKSFARDAVPFNF +NLLRSAKEDYYGITLSETSDHMFLLSNLALVHNC + + +>Dhan_VMA +GCFAKGTEVLMADGSNKNIEEVQIGESVLGKDGEARNVVALPRGNETMYEINESTPEEEA +DLARIAFTCNAKHELVVNTKQDIAVEQNCVTYFALESV +TDEANGREFSVVKSQTKTFEESSMAKEFASTISKNSIDWTIEARDV +GHMSDDVRCATQQSWAPVLASKEVLAPVVQEAGFDATIAPYVSYLLGLWIGNGYSDR +VQYLIDGKNTELINRVREYDEAI +ENNNQTSAKTV +DFLWDVINSMSFKVEGKSGKAIPSFLRTESFEVREQ +FLAGLIDSDGIVTKNPLSASVRTNSSKVGEGVIAVSRSLGICTSVKAENE +SYIISMTRNSALESVLSKCALAEKTTSVPSHITRTGQNFDF +SVKKIEAADYYGVTLPDNSDHQFMLANQAVVHNC + + +>Sce_VMA +GCFAKGTNVLMADGSIECIENIEVGNKVMGKDGRPREVIKLPRGRETMYSVVQKSQHRAH +KSDSSREVPELLKFTCNATHELVVRTPRSVRRLSRTIKGVEYFEVITFEMGQK +KAPDGRIVELVKEVSKSYPISEGPERANELVESYRKASNKAYFEWTIEARDL +SLLGSHVRKATYQTYAPILYENDHFFDYMQKSKFHLTIEGPKVLAYLLGLWIGDGLSDR +ATFSVDSRDTSLMERVTEYAEKLNLCAEYK +DRKEPQVAKTVNLYSKVV +RGNGIRNNLNTENPLWDAIVGLGFLKDGVKNIPSFLSTDNIGTRET +FLAGLIDSDGYVTDEHGIKATIKTIHTSVRDGLVSLARSLGLVVSVNAEPAKVDMNG +TKHKISYAIYMSGGDVLLNVLSKCAGSKKFRPAPAAAFARECRGFYF +ELQELKEDDYYGITLSDDSDHQFLLANQVVVHNC + + +>Sja_VMA +GCFAKGTEVLMANGADKKIEDVVIGDKVMGKDGRPRDVVALPRGFDTMYTVSQKISRKGA +KSSNNLSYTCNATHKLVLKTPQQISLVEQVVRGKKQSSVSFLRLADVVVGSS +RGGDRRRIQIVKKVTKSFQHEPRGVEKARELAMEFLSTIGDDDIYWTIEARDY +TLVSQEVRELTQQMISPVLFEKADLQNRLVKRGISAKYASEAAYLLGVWVGAGFSRS +SAFSLYEEDSELVSRIISFGKALGLKAVTA +EHNPRTVKIVRGELGVDGTFTSEVEDLVEVVDFQEGSEIPAWEQ +RGNLSVSFEGNTDNVFWKLISDLGFSGAVKSIPSHFAYESFPVREA +FLAGLIDADGSVKHGDLSSAHLSTTSPKVRDGTVRIARSLGISAYVSTKSEQIVDG +VYYPETYTIELEGNEALQSVLSKSALSSNVAPAPGSFERKAVPMYF +DLGITTPANYYGVTLAEDSDHQFLLSNLTLVHNC + + +>KexCBS379_VMA +GCFAKGTQVMMADGTDKSIEDIQLGENVMGKDGTPRTVISLPRGKETMYEVCHSSIKGTT +NETLMNYVCSGNHKIVMQTPQQIGITEHAIDGKTYTSVSYFALRDS +QDGYPIVKKLTKSFEHQQNGGKEQTLITVNNFVASLKSEPINWDVEAKHY +ESLGHYVKKCSYQLINPVFHQSGKLAQEIASLNYSKDKAPLLAWLIGFWVGNGAMRH +SQFVIDSQDIELVNRIQEIATLLNLSATTACYYSGSVDDQDKLAKLN +TATGEGFEDDLQSNPTAKELADMDILSESKTATLPTAFGVEKIDE +LIISLGEGRGNGNVFAQVIGSFGIDLADKDTLVSKIAHELAGDAFEVREQ +FVAGLVDATGYVRKDVYDHASEATVSIESKSTVLGLVKIARSLGIKIVVTSNDYQDPED +HDHGHDHGSCGHDEVATGYTAVMTGDALTNSMRFCAIGRNRVTAKQFMRQAIPFYF +SLEKKSEDDYYGITVPDNTDKQYLLSSMALVHNC + + +>CtrMYA3404_VMA +GCFTKGTQVMMADGADKSIESIEVGDKVMGKDGMPREVVGLPRGYDDMYKVRQLSSTRRN +AKSEGLMDFTVSADHKLILKTKQDVKIATRKIGGNTYTGVTFYVLEKT +KTGIELVKAKTKVFGHHIHGQNGAEEKAATFAAGIDSKEYIDWIIEARDY +VQVDEIVKTSTTQMINPVHFESGKLGNWLHEHKQNKSLAPQLGYLLGTWAGIGNVKS +SAFTMNSKDDVKLATRIMNYSSKLGMTCSST +ESGELNVAENEEEFFNNLGAEKDEAGDFTFDEFTDAMDELTI +NVHGAAASKKNNLLWNALKSLGFRAKSTDIVKSIPQHIAVDDIVVRES +LIAGLVDAAGNVETKSNGSIEAVVRTSFRHVARGLAKIAHSLGIESSINIKDTHIDAAG +VRQEFACIVNLTGAPLAGVLSKCALARNQTPVVKFTRDPVLFNF +DLIKSAKENYYGITLAEETDHQFLLSNMALVHNC + + +>KlaIFO1267_VMA +GCFSKGTEVMMGDGKDELIENIQVGDEVMGRDGLPRQVVGLPRGHDDMYQVTEKSEDNET +AKISFQCNSSHKLVLVTPQDIRLTESKEKVTVAFNRLADISVGNG +TESRTVRLVERAEKSFANAESNQAIINAAEFVTTIDTTSIEWTLEARDM +LLVDSSIREVTQQLINPVLLEKEHLAGVLKSNDFQSSLAPQFSYLLGAFVGSS +GKDNSEYLQQLSAQFDKKIVAEKSID +VQSNGKTVGTASIVISQE +PVQENKRRKVAQVSLVSKIVQESFSSGIPSFMMSENINVRES +FLAGIVDSQNQKLDDTVALKTLSVKTHDGIARLARSLGIRVSG +KKQNQEYTLTLSGDALKSVSNWTSTSNIEKVDVIHKAQPISF +DLEKIESADYFGVTLAEESDHKFLLSNMTLVHNC + + +>KlaCBS683_VMA +CFSKGTEVMMGDGKDELIENIQVGDEVMGRDGLPRQVVGLPRGHDDMYQVTEKSEDNET +AKISFQCNSSHKLVLVTPQDIRLTESKEKVTVAFNRLADISVGNG +TESRTVRLVERAEKSFANAESNQAIINAAEFVTTIDTTSIEWTLEARDM +LLVHSSIREVTQQLINPVLLEKEHLAGVLKSNDFQSSLAPQFSYLLGAFVGSS +GKDNSKYLQQLSAQFDKKIVAEKSID +VQSNGKTVGTASIVISQE +PVQENKRRKVAQVSLVSKIVQESFSSGIPSFMMSENINVRES +FLAGIVDSQNQKLDDTVALKTLSVKTHDGIARLARSLGIRVSG +KKQNQEYTLTLSGDALKSVSNWTSTSNIEKVDVIHKAQPISF +DLEKIESADYFGVTLAEESDHKFLLSNMTLVHNC + + +>Sda_VMA +GCFAKGTQVMMADGSDKSIEEIQIGEQVMGKDGNPRTVIALPRGKETMYEVCHITPHRTT +SGENFGVMDYVCSGNHKLVLRTPQNVTLTTHELDGQTYTNVSYFALEES +AYGQIVXKKTKSYQHQRHGGKQETEKKVNEFLATINPDSIEWDVEAKDY +KKLGYNVKKSSHQMINPVFKESGNLIAKLNELGFSKEIAPQMGWLLGFWVGNGSITT +SSFSIDSLDTQLLDRITEYGKLFALTTTSATNHCRNYSGSGNQDIELSKINNGKVE +TDGTITFDDDTEREPSEQELIDMESSGCKASSEMTVALGAPLV +RGNAIRQLLTENNVFLKLIESFGVRKENGSEYVKAIPMHLSYDDIEVREQ +FIAGLVDSIGHVKRTSNGTIECAAISTAYKSVSEGLIRLARSLGIKVSVTTKRECLDKHN +VKHQICYSICLSGATLSGALRFCALDKNNANSKKPFVRGPVPFYF +TLKEKDEDNYYGITLPDSTDKQYLLSSLALVHNC + + +>SceJay291_VMA +GCFAKGTNVLMADGSIECIENIEVGNKVMGKDGRPREVIKLPRGRETMYSVVQKSQHRAH +KSDSSREVPELLKFTCNATHELVVRTPRSVRRLSRTIKGVEYFEVITFEMGQK +KAPDGRIVELVKEVSKSYPVSEGPERANELVESYRKASNKAYFEWTIEARDL +SLLGSHVRKATYQTYAPILYENDHFFDYMQKSKFHLTIEGPKVLAYLLGLWIGDGLSDR +ATFSVDSRDTSLMERVTEYAEKLNLCAEYK +DRKEPQVAKTVNLYSKVV +RGNGVRNNLNTENPLWDAIIGLGFLKDGVKNIPSFLSTDNIGTRET +FLAGLIDSDGYVTDEHGIKATIKTIHTSVRDGLVSLARSLGLVASVNAEPAKVDMNG +TKHKISYAIYMSGGDVLLNVLSKCAGSKKFRPAPVATFVRECQGFYF +ELQELKENDYYGITLSDDSDHQFLLANQVVVHNC + + +>Tgl_VMA +GCFAKGTPVMMHDGSVKAIETINVGEEVMGADGLGRKIVGLPRGREVMYKVSQKTEHRAY +ETDETRSAPVGLFEYTCNATHKLVVRTPRSCRTLNRTMKGVEYYEVVFFDLAKE +KLKDGREIEVVKEISRSYPVTEGPERAAEIMKEYQEAGAGKQFFEWTIEARDV +GALGAHVRKATHQVYAPVLYESDFFFHYVKDSKFCLKSEAPFALAYLLGLWVGDGLSDR +AVFSVDSEDTTLFDRIIDFADILDLSAEYK +DREIPKRAKTVGLFPKTI +RGNDIGRNLNTDNPLWNAIVDLGYLKGGVKHVPSYLLTDSIPHREV +FLAGLIDSDGYVRGEEAPAATIKTIHKTVMEGTVAVARSLGLTVSVNIEEAKVDKDG +VNHRPAYAIYISGGDALLSVLANCASAKKHRAAPTKEVVRGLNEVYF +EMKELQEDDYYGITLSENSDHQFMLANQLVVHNC + + +>SceYJM789_VMA +GCFAKGTNVLMADGSIECIENIEVGNKVMGKDGRPREVIKLPRGSETMYSVVQKSQHRAH +KSDSSREMPELLKFTCNATHELVVRTPRSVRRLSRTIKGVEYFEVITFEMGQK +KAPDGRIVELVKEVSKSYPVSEGPERANELVESYRKASNKAYFEWTIEARDL +SLLGSHVRKATYQTYAPILYENDHFFDYMQKSKFHLTIEGPKVLAYLLGLWIGDGLSDR +ATFSVDSRDTSLMERVTEYAEKLNLCAEYK +DRKEPQVAKTVNLYSKVV +RGNGVRNNLNTENPLWDAIIGLGFLKDGVKNIPSFLSTDNIGTRET +FLAGLIDSDGYVTDEHGIKATIKTIHTSVRDGLVSLARSLGLVASVNAEPAKFDMNG +TKHKISYAIYMSGGDVLLNVLSKCAGSKKFRPAPVATFVRECQGFYF +ELQELKENDYYGITLSDDSDHQFLLANQVVVHNCLVSLARSLGLVVSVNAEPAKFDMNGT +KHKISYAIYMSGGDVLLNVLSKCAGSKKFRPAPAAAFARECRGFYFELQELKEDDYYGIT +LSDDSDHQFLLANQVVVHNC +>ScaIFO1992_VMA +GCFAKGTEVLMADGSDKAIEAIEVGEQVMGKDGAPRTVIALPRGTETMYEVCHTTQHRNG +NEKFGLMNYVCSGNHKLVLRTPQLIRTTIHELRGKHYTSVTFFVTEKS +ANGTIVKQRTKTFQHEFHGGEEAATKLAADFASTIDPKHIDWDIEAKDY +KQLDHYVKKSSYQMINPVFKESGNLANILGDAGIEKTLAAKMAWLLGFWVGNGHMET +AQFPVDSWDTQLVDRISEYGKHFNLTTTTENHYRSNHVESNKDIEIFEMNEAQIEEAE +QTGVVAFDSNRKGDPSETELIEAEIFNESRPSTAGLFTPAAISPASLVTDLSVTLRGTGI +GGAGVSKERNLNNIFWDIVTSFGVRTNGQGSTYEKSVPLHLSYDDIEVREQ +FIAGLIDSDGYVKSADNRFSATVTTIYKGVSEGLIRLARSLGIRVSVSTEKEHVDKNN +VKHKSCYRVFLSGEALIGVLRFCALDRKRTAFKEFTREAVPFYF +TLQEKDQDEYYGITLPDETDKQYLLSSLALVHNC + + +>Zbi_VMA +GCFAKGTEVMMSDASVKTVESVKVGEQVMGKDGKPRKVVATPSGCEKMYKVTQKVAHKRT +HTLNEPRGLSEYTCNATHKLVVRTPRICRSVIRKFKGTNYIDVIFFNKVKG +SVEDGRVIDIVQEASMSYPAVEGPERALRAIKEYAEADGAREFFEWTIEARDI +SLLDENVRAATYQLRAPVLLQNDFFSQYVSNSKFASGTEATRALSYFLGLWIGGGLTDK +TTLSVDSEDTSLFDRINQFAEILGLSAEQE +AKEESKRAKKVNLHPKTN +GAEDADRSLNIGNPLWNAIVDLEYLKDGSKNVPAYLSSDCFENREM +FLAGLVDSEGHVRGEVATINTCHHSVMTGVVAVARSLGITVTVNTKGEKFGNIG +ANQDSGYVIQLSSCDALLSVLANCGAVDKRREAPAHGVIRELNKVYF +EMRELGEDEYYGLTLSNDSDHQFLLANQLVVHNC + + +>Sun_VMA +GCFEKGTEVLMADGTDKVIEDITIGEQVMGKDGQPREVVGLPRGKMTMYQVCHKATEQNE +IALMDYVCSGNHKFVLVTPQNVKITEHMLRGKMYTSVNYFVANDF +ENGQVVKLRTKTFQHDIHGGADGAKVEAQKFASTIDLSPISWEIEASKY +VELDVNVRNATTQLINPVFYESGKLASRLQTKNIDQTSADKLAYVMGSWVGAGSMDQ +PTFAGNQLDEEFVSRLTEYGSGLDLTK + +NNSVWDIINESGLRTLNANGEATKTIPKELVSDSISVREH +FIAGLVDTQGNVKRASTGAVETASISTVYERISNDLVKLARSLGIKASVSQQEEHVDAKG +VDQQQTYNIKLTGSALNGVVRLSALSKNRDEPVSFERLPVPFHF +TLLEKAEDNYYGVTLPDATDKQYLLSSLALVHNC + + +>gi|257076363|ref|ZP_05570724.1| A1A0 ATP synthase, subunit A [Ferroplasma acidarmanus fer1] +MENKGSIYSISGPVVIATDLDGKMFDVVRVGEMGLVGEVIKIVGDKFTIQVYEDTSGLKPGEPVYSTGKP +LSVELGPGLLKSIYDGIQRPLDIIQSETGDFIVRGATAPPLDEKKEWDFVPLLKEGDEVEQGYILGTVQE +TNIITHKIMVPYGIRGIIKSISKGKFKVSDTVCMIDTGTSKYDIKLKQIWPVRQARKVFLKFAPEIPLIT +GQRVIDSFFPVAKGGTVAVPGPFGSGKTVIQHQLSKWSDADITVYVGCGERGNEMTEILSTFPELQDPKS +GKPLMEKTILIANTSNMPVAAREASIYTGVTIAEYYRDMGYDVALMADSTSRWAEALREISGRLEEMPGE +EGYPAYLGRRISEFYERSGNAQIIAQDERTGSITLIGAVSPPGGDLSDPVVQNTLRVTRAFWALDASLAS +RRHFPSINWLNSYSLYLDSLSGWFKSNVNPEWPQMHSLMMGILQKESELQEIVQLVGYDSLPENQKNVLD +IAKIIREDFLQQNAFDDTDTYCSIKKQYEMLTIIKTLNEMQEKSIASGLKLTQTATLPVRMKISRMKEIP +ENDFEKFYNDVIKEINNEYDNIMEGVESV +>gi|255514086|gb|EET90349.1| H+transporting twosector ATPase alpha/beta subunit central region [Candidatus Micrarchaeum acidiphilum ARMAN2] +MIDMAGIIYRISGPVVIAQGLDDPNMYDVVRVGETKLVGEIIKLDGDKAIIQVYEDTSGLKPGEPVENTG +TQLSVDLGPGLLGSIYDGIQRPLDKIKEMTGDFIARGINVPPLDLKKKWHFVPKLKAGDEANGGTVIGEL +DETSLIRHRVMVPPKLSGKIKSIKEGDYTVDEAVAVLSTESGDVEIKLMQKWPVRIPRPVKDKLPPEIPL +ITGQRVIDSLFPVAKGGTAAVPGPFGSGKTVIQHQLAKWSDSEIVVYVGCGERGNEMTEILTTFPELKDP +KSGKPIMDRTILIANTSNMPVAAREASIYTGITIAEYYRDMGYSVALMADSTSRWAEALREISGRLEEMP +GEEGYPAYLGRKIAEFYERAGRVHILAGGVGSVTAIGAVSPPGGDISEPVSQNTLRVTRVFWALDAALAN +SKHFPSINWLNSYSLYFEDMKKWYVENVSKDWPELYLRAMQTLQKEAEINEIVQLVGYDALPEADKLTLD +VAKSIREDYLQQSAFDDVDTYTSMHKQYLMLSSIMELAAEQAKSLERGVTLEQLSKLDVRQKIARMKYVK +DGDIDAYYKDVMDSIAKIKGMQPAVK +>gi|167045267|gb|ABZ09926.1| putative ATP synthase alpha/beta family, nucleotidebinding domain protein [uncultured marine crenarchaeote HF4000_APKG9M20] +MADAIISRISGPVAVAKDIEGAHMFDVVRIGEMGLMGEIIRLEGNTAQIQVYEDTTGLRPGEKVVNTNRP +LSLQLGPGLLTSIYDGIQRPLDVLAAESGDFISRGKIIPALDQKKKWEFIPVKKNGDQVSPGEIIAEVQE +TPLIKHKIMVPYNVSGELVDISEGQFTVNDKIAAVKNSKTTDIGLSSWWTVRTPRPVLRKLAPDQPLLTG +QRVLDTFFPVAKGGSAAIPGPFGSGKTVTQQQLAKWADSEIIVYIGCGERGNEMCEVLTQFPELIDPKSK +RPLMERTILVANTSNMPVAAREASIYTGITMGEYYRDMGYGVALMADSTSRWAEALREISGRLEEMPGEE +GYPAYLGRRLAEFYERGGRCIVISPEEREGSLSIVGAVSPPGGDFSEPVSQNTLRVTRVFWGLDANLANR +RHFPAINWLTSYSLYMDDMADWYKSNVSKDWIDQRKEALEILQKESELQEIVQLVGYDALPEPEKGILDT +ARSIREDYLQQSAFDEVDTYTSIQKQHKMLSTILEFGRKEADVIKKGSTSAKVGALESRGMIPKMKWTKE +EELEKLLNDINSKMKQEFDSLSKESSN +>gi|167042305|gb|ABZ07034.1| putative ATP synthase alpha/beta family, nucleotidebinding domain protein [uncultured marine crenarchaeote HF4000_ANIW97J3] +MADAIISRITGPVVVAKDIEGAHMFDVVRIGEMGLMGEIIRLEGNTAQIQVYEDTTGLKPGEKVINTNRP +LSLQLGPGLLTSIYDGIQRPLDVLAAESGDFISRGKIIPALDQKKKWEFIPVKKNGDQVSPGEIIAEVQE +TPLIKHKIMVPYNVSGELVDISEGQFTVNDKIAAVKNSKTTDIGLSSWWTVRIPRPVLRKLPPDQPLLTG +QRVLDTFFPVAKGGSAAIPGPFGSGKTVTQQQLAKWADSEIIVYIGCGERGNEMCEVLTQFPKLIDPKSK +RPLMERTILVANTSNMPVAAREASIYTGITMGEYYRDMGYGVALMADSTSRWAEALREISGRLEEMPGEE +GYPAYLGRRLAEFYERGGRCIVISPEEREGSLSIVGAVSPPGGDFSEPVSQNTLRVTRVFWGLDANLANR +RHFPAINWLTSYSLYMDDMADWYKSNVSKDWIDQRKEALEILQKESELQEIVQLVGYDALPEPEKGILDT +ARSIREDYLQQSAFDEVDTYTSIQKQHKMLSTILEFGRKEADVIKKGSTSAKVGALESRGMIPKMKWTKE +EELEKLLNDINSKMKQEFDSLSKESSN +>gi|288932643|ref|YP_003436703.1| ATP synthase, subunit alpha [Ferroglobus placidus DSM 10642] +MEVGEVYRVSGPLVVAEGLKARMYDVCRVGEERLMGEVVGLVGNRVLIQVYEDTSGIKPGDKVENTGMPL +SVELGPGLLKSIYDGVQRPLPALKEASGDFIGRGIDAPALDRKKQWEFNPVVKKGDKVSGGDILGTVQET +ELIEHKILVPPNVEGVITEIYEGKFTVEETVAVLDNGVELKLYHKWPVRQPRPYREKLPPQIPLITGQRI +LDTLFPVAKGGTAAIPGPFGSGKTVTQHQLAKWSDTHVVVYIGCGERGNEMTEVLEEFPELEDPRTGKPL +MERTVLIANTSNMPVAAREASVYTGITIAEYFRDMGYDVGLMADSTSRWAEAMREISGRLEEMPGEEGYP +AYLASRLAEFYERAGRVRTLNGNIGSVTIIGAVSPPGGDFSEPVTQNTLRIVKVFWALDAKLAARRHFPA +INWLQSYSLYADTLAEWFNKNVAEDWSELRRWAMEVLQEEANLQEIVQLVGSDALPESQRILLEVARLIR +EVYLQQYAYHPVDTYCDLKKQYDLLKAIKQVADMFYKALEAGKLVEEIINVPGKDEFARAKFEENYKEAL +EAAMKKMKEALGV +>gi|298674214|ref|YP_003725964.1| ATP synthase subunit A [Methanohalobium evestigatum Z7303] +MEVKGEIYRVSGPVVIATGIRPKMYDVVKVGHEGLMGEVIKIEGDKSTIQVYEDTSGIKPGEPVENTGLP +LSVELGPGLLESIYDGIQRPLQVLQDKMGDFIARGATANGIDREKQWEFKPIVDKGDKVEPGDIIGVVQE +TPNLEHQIMVPPNMQGGTVSDIYSGKFTVDETVCVLSNGKELSMLQKWPVRTPRPTKRKLKPDKPLLTGQ +RILDGMFPVAKGGTAAIPGPFGSGKTVTQQQLAKWSDTDIVVYVGCGERGNEMADVLDEFPELEDPKAGR +PLMERTVLIANTSNMPVAAREASVYTGITISEYYRDMGYDVALMADSTSRWAEAMREISSRLEEMPGEEG +YPAYLAARLSEFYERAGYVKSNSGYDGSITVIGAVSPPGGDFSEPVTQNTLRIVKVFWALDAKLSQRRHF +PAINWLTSYSLYTESLSDWLSENVASDWIDLRNYAMDILEEESELQEIVQLVGSDALPESQQLKLEVARM +FREYFLQQNAFHEIDRYCPFYKQYKLVQAIHKFSETANSKLEAGYSINDIMAMESKDELAKVRYEEDFDG +ALNKVLSKMDDEFSQIGG +>gi|219853232|ref|YP_002467664.1| Vtype ATP synthase subunit A [Methanosphaerula palustris E19c] +MEVKAKEGKIEGKGVLKRIAGPVVTAVDLDAHMYDVVKVGNEELMGEVIKIEGNNTIIQVYENTSGIKPG +EPVSNTGLSLAVELGPGLLTSIYDGIQRPLEVLMDKMGNFIERGVSAPGISREKKWEFKPLARVGDQVSP +GAIIGEVQETNIVHKIMVPPNTKAGVITTITPGTFTVEEVVCVLDNGAELTMMQRWPVRIPRPVAEKMNP +TIPLITGQRILDGLFPIAKGGTAAIPGPFGSGKTVTQQQLAKWSDAEIVVYIGCGERGNEMTEVLTEFPE +LEDPKTGKPLMERTILIANTSNMPVAAREASVYTGITIAEYFRDMGYDVSLMADSTSRWAEAMREISSRL +EEMPGEEGYPAYLAARLSEFYERAGLVKTLNGQEGSVSVIGAVSPPGGDFSEPVTQNTLRIVKVFWALDA +KLSQRRHFPAINWLDSYSLYLDTLHDWYDREVSPEWNKIRSWAMEILQKEAELQEIVQLVGSDALPEAEQ +ITIEVARMIREIFLQQNAYDAVDTFCSMKKQYDMLKSIKTFSDLSYAAQTVGVSPQQIIAVKSKNELSQV +KFTADYEPLLEKILKDMEAEFNALRAGA +>gi|302390562|ref|YP_003826383.1| ATP synthase, A subunit [Thermosediminibacter oceani DSM 16646] +MSQGVIAKVSGPLVVATGLPEAKMFDVVKVGTQGLIGEIIEIRNDKVSIQVYEETSGLGPGDPVVSTGEP +LSVELGPGMIEGIFDGIQRPLDVIEKKVGSFITRGIDVPALNREKKWGFTPRVRPGDRVTGGDIIGTVQE +TVIVEHRIMVPPGVSGVVEDIKEGEFTVTEPVARIKTDSGQVVKVTMMQKWPVRKTRPYKEKLPPEIPMS +TGQRVIDTLFPVTKGGTACIPGPFGSGKTVVQHQLAKWADAEIVVYIGCGERGNEMTDVLLEFPELKDPK +TGEPLMKRTVLIANTSNMPVAAREASIYTGITIAEYFRDMGYSVALMADSTSRWAEALREMSGRLEEMPG +EEGYPAYLARRLAEFYERAGRVICLGSDNREGALTVVGAVSPPGGDLSEPVTQATLRVVKVFWALDSQLA +YARHFPAINWLTSYSLYSDVVENYMNKNVSSDWGELRSEAMKLLQEEASLQEIVRLVGIDALSTRDRLVL +EVARSIREDFLHQNAFHEVDTYSSMNKQYRMLKLILMFYEEAQKALEKGALFSEIEKHPVRERIARAKFI +EESNLAEFDEIEKEIKKAMQDLAEGGGADA + diff --git a/submissionscripts/metagenomepipeline/intein.db.phr b/submissionscripts/metagenomepipeline/intein.db.phr new file mode 100644 index 0000000..af8005f Binary files /dev/null and b/submissionscripts/metagenomepipeline/intein.db.phr differ diff --git a/submissionscripts/metagenomepipeline/intein.db.pin b/submissionscripts/metagenomepipeline/intein.db.pin new file mode 100644 index 0000000..6b54d9f Binary files /dev/null and b/submissionscripts/metagenomepipeline/intein.db.pin differ diff --git a/submissionscripts/metagenomepipeline/intein.db.psq b/submissionscripts/metagenomepipeline/intein.db.psq new file mode 100644 index 0000000..8cef316 Binary files /dev/null and b/submissionscripts/metagenomepipeline/intein.db.psq differ diff --git a/submissionscripts/metagenomepipeline/inteinseq.sh b/submissionscripts/metagenomepipeline/inteinseq.sh new file mode 100644 index 0000000..52dd7cc --- /dev/null +++ b/submissionscripts/metagenomepipeline/inteinseq.sh @@ -0,0 +1,16 @@ +#!/bin/bash +#SBATCH --job-name=nrblast +#SBATCH -N 1 +#SBATCH -n 1 +#SBATCH -c 9 +#SBATCH --partition=amd +#SBATCH --mail-type=END +#SBATCH --mem=40G +#SBATCH --mail-user=yutian.feng@uconn.edu +#SBATCH -o nrblast_%j.out +#SBATCH -e nrblast_%j.err + + + +module load blast/2.7.1 +for filn in *.seqfile; do blastx -query $filn -db /home/CAM/yfeng/inteindb/intein.db -outfmt "6 qaccver qstart qstop qseq" -max_target_seqs 1 >> seqs.tsbh ;done \ No newline at end of file diff --git a/submissionscripts/metagenomepipeline/metagenomepipeline.sh b/submissionscripts/metagenomepipeline/metagenomepipeline.sh new file mode 100644 index 0000000..11527ec --- /dev/null +++ b/submissionscripts/metagenomepipeline/metagenomepipeline.sh @@ -0,0 +1,170 @@ + +####set up psi blast to get pssms +#### *.fa = amino acid sequences of inteins +#### transcont.fasta = aminoacid sequence of metagenome (use emboss transeq on assembled reads) +for b in *.fa; do psiblast -query "$b" -db transcont.fasta -out ${b%.fa}.blast -outfmt 6 -num_iterations 5 -out_pssm ${b%.fa}.pssm -save_pssm_after_last_round; done +# this takes a while, recommend doin git in a script +#to get rid of converged sequences/pssm +for file in $(grep -l CONVERGED *.blast); do rm -i ${file%.blast}.pssm; done + + +###################### search an AA metagenome with all intein pssms ################### + + +######### +######### *.pssm= pssm +######### contigs.fastaa = nucleotide sequence from assembled reads + +for b in *.pssm; do tblastn -in_pssm "$b" -db contigs.fasta -out "$b".search -outfmt 6 -evalue 1e-10; done + +#use each pssm to blast a metagenome (-d) this command will only work for aa metagenomes +#this must be done in a directory containing all the pssms, an infile for each pssm, and the +#metagenome that the user intends to search which has been previously formated into a db, +#and a list of the names of each pssm in a file called pssm.list + +###########extract all the hits from a metagenome using all PSSMs ####################### + ################ remove redundant sequences hit in multiple PSSMs ##################### + + +cat *.search |cut -f 2 >all.bout +#list all of the hits from a psiblast using all intein PSSMs + +sort all.hits >sort.hits +#sort all of the hits alphabetically by contig name from metagenome file + +uniq sort.hits >mg_name.hits +#extract only unique hits mg_name.hits is a list of contigs which were found by PSSMs +#can also do in excel, data -> remove duplicates + + +####need to remove \n in contigs so each sequence is all in one line +#linebreak inbetween multifasta +awk '!/^>/ { printf "%s", $0; n = "\n" } +/^>/ { print n $0; n = "" } +END { printf "%s", n } +' contigs.fasta >> contigs.eol + + + +##### mg.fas = fasta of metagenome assembly, usually contigs.eol from above +for filn in `cat all.hits`; do grep -A 1 $filn contigs.eol> $filn.seqfile;done +#makes a list of all of the contigs and searches for the corresponding fasta sequence in the metagenome .fas file + +#### *.seqfile = fasta sequences of contigs identified by pssms +#### intein.db == multifasta of intein sequences containing all inteins from inteins.com (AA) +for filn in `cat all.hits`; do blastx -query $filn.seqfile -db /home/CAM/yfeng/inteindb/intein.db -outfmt 6 -out $filn.blast ;done +#new blast + + + +for f in `cat all.hits`; do head -1 $f.blast >> all.tsbh; done +#works for all +#extract tsbh for each contig, identifies hit as being BIL, HNT, HE, mid, or intein + +cat *.tsbh > all.tsbh +#make one file of all the tsbh for all contigs + +for filn in *.seqfile; do blastx -query $filn -db /home/CAM/yfeng/inteindb/intein.db -outfmt "6 qaccver qstart qstop qseq" -max_target_seqs 1 >> seqs.tsbh ;done + +#sort all.tsbh by bitscore in excel or equivalent (highlight all -> data -> sort ) + +# at this point the user needs to determine how many of the hits should be extracts I have +#determined that bits of 100 or more are actually inteins anything under that cannot be reliably aligned +# to the identified intein hit, once the user has determined how many of the hits are above 100 +#use tail to grab _ hits from the bottom of the list for instance if the last 20 hits are +#above 100: tail -n 20 mg.int.sorted >mg.int.significant + + + + +############ NR blast is optional: used to identify gene/species + + +################ once hits are extracted they need to be blasted against the ############# +################ nr db to identify the extein the intein may be inserted into ############ + +cut -f 1 mg.int.significant > contigs.list +#makes a list of the contigs in the list which have hits over 100 +for filn in `cat contigs.list`; do blastall -p blastp -i $filn.seqfile -d nr -m 8 -o $filn.outfile; done +#blasts nr db with significant contigs + +for filn in `cat contigs.list`; do grep -m 1 "gi" $filn.outfile > $filn.nr.tsbh;done +#extracts tsbh from nr db + +for filn in `cat contigs.list`; do cut -f 2 $filn.nr.tsbh >$filn.nr.gi;done +#extracts gi # from the tsbh of each contig + +for filn in *.fa; do blastx -query $filn -db /isg/shared/databases/blast/nr -outfmt 6 -out $filn.outfile -evalue 1e-10 -max_target_seqs 1 -num_threads 10; done + +#extract sequences from nr which correspond to the contigs used to search nr + + + + + +########################################################## +######################################################### +######################################################## +##################################################### + + +#mapping + + + +#for mapping you need to prepare two sets of nucl sequences +#1) contigs as is: which contains extein/intein/extein +#2) contigs with intein removed: extein/extein +#sometimes the contig seqs might be very large so you have to cut them down to size +#attached is contigtrimmer.pl which does that. usage: perl contigtrimmer.pl all.tsbh + #you may need to adjust or look at script + #if you trim contigs then you need to blastx again to find location of the intein in the sequence +#to artificially remove inteins from the exteins to get the second set of sequences use extein.pl + #similar to contigtrimmer.pl, except it takes theflanking region instead of the intein + #usage: perl extein.pl all.tsbh + #again may need to adjust script + +############After you have both sets of sequences you can map them to the reads##### + + +###do this for both sets of sequences, make sure you change the names of output and input files#### + +##i would do all of this with a submission script unless the reads file is small#### + +###build bowtie index +bowtie2-build extonly.txt extonly +#extonly.txt = multifasta with second set of sequences from above +#extonly name of bowtie index (can be anything) + + + +#map reads back to sequences +bowtie2 -x exind -1 /home/CAM/yfeng/metagenomes/lakevida/trimmedf.fastq -2 /home/CAM/yfeng/metagenomes/lakevida/trimmr.fastq -S exmap.sam -p 10 +# -x: base name of the bowtie index +# -1 and -2 path to forward and reveerse reads, can also work for unpaired reads +# -S sam file to output to +# -p number of threads + + +#makes your sam file much smaller so its downloadable, and also convert sam to bam +samtools view -b -F 4 combmap.sam > combmapped.bam +#only thing you should chabge is the .sam and .bam file name +#these other parameters are required for filtering to work + +#sort bam file by genome position so it actually makes sense +samtools sort exmapped.bam -o exsort.bam +#change .bam to output file name of previous step + +#you can then load the files into IGV and see the mapped reads and coverage or use them in bedtools +#for Integrated genome viewer(IGV) you need to generate a bam index for your map file and a fasta index for your sequences + + +#bam index +samtools index -b name.bam + +#fasta index +samtools faidx name.fasta + + + + diff --git a/submissionscripts/metagenomepipeline/mg.int.sorted b/submissionscripts/metagenomepipeline/mg.int.sorted new file mode 100644 index 0000000..d89f518 --- /dev/null +++ b/submissionscripts/metagenomepipeline/mg.int.sorted @@ -0,0 +1,102 @@ + 102 L_17763 CZIV_RIR1 43.36 143 73 3 1132 1536 1 141 2e-23 102 + 112 L_86122 Nph_CDC21 62.07 87 33 0 261 1 1 87 1e-27 112 + 122 L_60537 FacFer1_RIR1 45.90 122 65 2 363 1 1 121 7e-30 122 + 127 L_144221 Hvo_PolB 68.52 108 34 0 91 414 1 108 8e-32 127 + 134 L_86123 Nph_CDC21 57.60 125 51 1 378 10 130 254 3e-34 134 + 138 L_87109 FacFer1_RIR1 48.91 137 67 3 402 1 1 136 8e-35 138 + 162 L_38519 APAPSE2_dpola 33.96 318 206 6 979 1920 2 309 2e-41 162 + 170 L_17527 MspMCS_DnaB 37.39 345 196 9 244 1218 3 324 8e-44 170 + 173 L_39776 Punc_DnaB 33.61 363 208 12 274 1263 1 354 9e-45 173 + 189 L_92998 FacFer1_RIR1 44.87 234 129 1 747 46 143 368 4e-50 189 + 191 L_54356 IIV6_RIR1 48.86 176 90 0 31 558 166 341 1e-50 191 + 194 L_53997 HspNRC1_PolII 54.04 198 79 6 1075 1632 1 197 3e-51 194 + 197 L_102087 Hut_MCM1 56.57 175 76 0 76 600 211 385 4e-57 197 +21.9 L_101897 AfuAf293_PRP8 36.84 19 12 0 72 16 657 675 5.3 21.9 +23.5 L_129760 MvuM7_Pol2 45.83 24 13 0 4 75 109 132 1.5 23.5 + 237 L_114422 Nph_rPol_A'' 72.61 157 43 0 482 12 219 375 5e-65 237 + 241 L_19013 Punc_DnaB 35.89 365 218 8 433 1479 1 354 3e-65 241 +24.3 L_166074 DprMLMS1_RIR1 52.63 19 9 0 112 56 139 157 0.30 24.3 +25.0 L_157546 Pab_CDC211 31.15 61 41 2 169 348 8 65 0.33 25.0 +25.4 L_101769 Nph_CDC21 52.17 23 11 0 223 291 289 311 0.18 25.4 +25.4 L_132593 CbuRSA493_DnaB 31.71 41 28 1 270 148 73 111 0.38 25.4 +26.2 L_143975 HmuDSM12286_PolB 31.11 45 31 0 52 186 52 96 0.22 26.2 +26.6 L_137742 TspGT_Pol2 34.88 43 24 1 384 268 27 69 0.20 26.6 +26.9 L_143311 CneAD_prp8 33.93 56 36 2 237 401 74 126 0.17 26.9 +27.7 L_52764 TthHB8_RIR12 57.14 21 9 0 472 534 2 22 0.26 27.7 +28.1 L_71722 She_RPB2 35.14 37 24 0 115 225 63 99 0.066 28.1 +28.9 L_69052 NspPCC7120_RIR1 36.96 46 29 0 298 161 203 248 0.045 28.9 +29.6 L_85897 Ter_RIR1 46.88 32 17 0 151 246 3 34 0.039 29.6 +30.0 L_22477 AaveAAC001_RIR1 30.00 100 67 4 181 471 286 380 0.047 30.0 +30.0 L_57815 Pfl_Fha 66.67 18 6 0 40 93 1 18 0.031 30.0 +30.4 L_22149 NmaATCC43099_PolB2 28.41 88 59 3 220 471 2 75 0.024 30.4 + 310 L_41817 Cwa_RIR1 49.57 351 156 5 688 1677 1 349 7e-86 310 +31.2 L_34728 Mja_GF6P 27.27 44 32 0 220 351 1 44 0.014 31.2 +31.2 L_81829 TaqY51MC23_DnaE 56.00 25 11 0 553 627 74 98 0.022 31.2 +32.0 L_96053 gi|339757395|gb|EGQ40976.1| 28.57 119 81 3 432 88 446 563 0.006 32.0 +32.7 L_16058 Tko_Helicase 30.12 83 58 3 376 624 1 68 0.007 32.7 +33.1 L_47922 PsspA11_Fha 65.22 23 8 0 1 69 7 29 0.003 33.1 +33.5 L_108500 Mja_GF6P 29.55 44 31 0 46 177 1 44 0.002 33.5 +33.9 L_114344 Nfa_RIR1 39.47 38 23 0 103 216 4 41 0.002 33.9 +34.3 L_42365 PsspA11_Fha 47.22 36 18 1 288 184 1 36 0.008 34.3 +34.3 L_74996 PsspA11_Fha 47.22 36 18 1 475 579 1 36 0.002 34.3 +34.7 L_22150 Sru_PolBc_ 28.92 83 59 1 1888 2136 2 73 0.005 34.7 +34.7 L_93555 Sja_VMA 41.18 34 20 0 363 262 3 36 6e-04 34.7 +35.4 L_106234 Nfa_RIR1 29.33 75 53 1 315 91 2 70 3e-04 35.4 +36.6 L_17427 Sas_RPB2 55.56 27 12 0 130 210 9 35 3e-04 36.6 +36.6 L_40213 Naz0708_RIR11 27.91 129 80 4 205 552 3 131 3e-04 36.6 +37.0 L_51906 PsspA11_Fha 53.57 28 13 0 472 555 1 28 4e-04 37.0 +37.0 L_65117 HmuDSM12286_PolB 33.77 77 51 1 313 543 2 76 3e-04 37.0 +37.4 L_109007 Sda_VMA 29.49 78 53 1 139 366 1 78 2e-04 37.4 +37.4 L_62853 Nfa_RIR1 42.11 38 22 0 490 603 5 42 3e-04 37.4 +37.4 L_74553 NmaATCC43099_PolB2 27.62 105 76 2 484 798 2 96 3e-04 37.4 +37.7 L_104337 PsspA11_Fha 60.71 28 11 0 175 258 1 28 2e-04 37.7 +37.7 L_27042 Psy_Fha 26.19 84 62 1 469 720 1 81 2e-04 37.7 +37.7 L_31868 Mex_helicase 57.69 26 11 0 355 432 1 26 2e-04 37.7 +38.1 L_28966 Nph_PolB2 24.65 142 97 4 1102 1497 2 131 3e-04 38.1 +38.1 L_38652 Nfa_RIR1 51.61 31 15 0 502 594 1 31 2e-04 38.1 +38.1 L_86280 HmuDSM12286_PolB 27.73 119 86 3 390 34 2 110 2e-04 38.1 +38.9 L_21786 Nfa_RIR1 44.19 43 24 0 424 552 5 47 1e-04 38.9 +39.3 L_104372 Nfa_RIR1 51.61 31 15 0 133 225 2 32 5e-05 39.3 +39.7 L_22148 Psy_Fha 33.33 84 50 4 754 987 1 77 8e-05 39.7 +40.0 L_92753 Pfl_Fha 29.55 88 58 2 154 405 1 81 3e-05 40.0 +40.4 L_112559 Pfl_Fha 61.54 26 10 0 387 310 1 26 2e-05 40.4 + 404 L_113176 NmaATCC43099_PolB2 77.14 245 54 1 729 1 104 348 4e-115 404 +40.4 L_119276 CtrMYA3404_VMA 27.91 86 57 2 181 423 3 84 2e-05 40.4 +40.4 L_82747 PsspA11_Fha 60.71 28 11 0 472 555 1 28 4e-05 40.4 +41.6 L_34727 PsspA11_Fha 58.62 29 12 0 1291 1377 1 29 3e-05 41.6 +41.6 L_52443 CtrMYA3404_VMA 30.43 92 59 2 1866 1606 3 90 4e-05 41.6 +42.7 L_138419 PsspA11_Fha 30.43 92 59 2 405 145 1 92 2e-06 42.7 +42.7 L_71997 CtrMYA3404_VMA 29.55 88 62 2 331 594 2 82 7e-06 42.7 +42.7 L_99004 Sru_PolBc_ 34.48 87 55 3 352 606 2 75 6e-06 42.7 +43.1 L_65635 NmaATCC43099_PolB2 29.91 107 73 3 475 789 2 96 5e-06 43.1 +43.5 L_26408 PsspA11_Fha 30.68 88 60 2 390 130 1 84 3e-06 43.5 +43.5 L_38653 Nfa_RIR1 34.21 76 50 2 1111 1338 2 71 7e-06 43.5 +43.5 L_39745 Hma_PolB 26.79 112 75 2 3007 3321 2 96 2e-05 43.5 +43.5 L_74720 HmuDSM12286_PolB 31.43 105 72 3 67 381 2 96 2e-06 43.5 +44.3 L_23622 PsspA11_Fha 37.04 81 46 2 445 672 1 81 2e-06 44.3 +44.3 L_34726 Hma_PolB 30.91 110 71 2 808 1122 2 96 3e-06 44.3 +44.3 L_50918 Mja_GF6P 25.23 107 80 2 931 1251 1 91 4e-06 44.3 +44.7 L_98728 PsspA11_Fha 64.52 31 11 0 363 271 1 31 2e-06 44.7 +45.4 L_76122 gi|312137461|ref|YP_004004798.1| 26.88 93 68 0 279 1 501 593 3e-07 45.4 +46.2 L_86319 CtrMYA3404_VMA 30.21 96 62 3 448 720 1 90 6e-07 46.2 +46.6 L_76123 Pfu_IF2 26.89 119 87 2 447 91 1 114 2e-07 46.6 +48.5 L_59537 Pab_RtcB_(Pab_Hyp2) 30.91 110 74 3 375 52 336 438 7e-08 48.5 +50.1 L_147322 Tko_RadA 37.84 74 46 1 18 239 203 272 1e-08 50.1 +50.8 L_125470 TspOGLP20_Pol 31.62 117 78 3 402 58 32 147 1e-08 50.8 +51.2 L_93385 PsspA11_Fha 39.24 79 44 3 211 435 1 79 1e-08 51.2 +52.4 L_108494 Hwa_RCF 73.33 30 8 0 492 403 296 325 5e-09 52.4 +52.8 L_31363 MspFS40622_LHR 29.75 121 82 3 784 1137 2 117 4e-08 52.8 +53.5 L_143447 TthHB8_RIR12 37.35 83 52 2 249 1 328 407 5e-10 53.5 +54.3 L_17762 Cmo_ClpP 35.00 80 52 1 1642 1881 1 79 6e-09 54.3 + 545 L_02848 Aeh_DnaB2 63.81 420 152 0 1171 2430 1 420 1e-156 545 +54.7 L_26248 Mex_helicase 35.29 85 55 3 1096 1350 1 82 5e-09 54.7 +58.9 L_63035 Mja_rPol_A&quo> 28.77 146 88 5 1221 832 337 473 1e-10 58.9 +62.4 L_107385 Mja_RNR2 30.71 127 81 3 402 43 6 130 2e-12 62.4 +70.5 L_63034 Mja_rPol_A&quo> 32.60 181 102 7 534 52 130 306 1e-14 70.5 +80.5 L_108940 Hut_MCM2 43.12 109 57 2 312 1 93 195 5e-18 80.5 +80.9 L_105951 Hwa_MCM4 64.81 54 19 0 606 445 521 574 2e-17 80.9 +82.8 L_31207 Memar_MCM2 50.00 70 35 0 1243 1452 2 71 2e-17 82.8 +87.0 L_46868 Hwa_RCF 42.45 106 58 2 1 309 10 115 9e-19 87.0 +88.2 L_112325 SelPC7942_RIR1 53.41 88 41 0 264 1 283 370 2e-20 88.2 +95.9 L_51394 Hwa_RCF 46.73 107 55 1 690 376 1 107 6e-22 95.9 +99.4 L_30700 Hwa_RCF 29.39 262 177 5 178 939 1 256 1e-22 99.4 diff --git a/submissionscripts/metagenomepipeline/pipeline.sh b/submissionscripts/metagenomepipeline/pipeline.sh new file mode 100644 index 0000000..0161ad4 --- /dev/null +++ b/submissionscripts/metagenomepipeline/pipeline.sh @@ -0,0 +1,88 @@ + + +###################### search an AA metagenome with all intein pssms ################### + + +######### *.out = sequence used to make pssm +######### *.chk= pssm +######### *.psiout= hits from pssm + +for filn in `cat pssm.list`;do blastpgp -i $filn.out -R $filn.chk -d **** -j 1 -o $filn.psiout -m 8; +done +#use each pssm to blast a metagenome (-d) this command will only work for aa metagenomes +#this must be done in a directory containing all the pssms, an infile for each pssm, and the +#metagenome that the user intends to search which has been previously formated into a db, +#and a list of the names of each pssm in a file called pssm.list + +###########extract all the hits from a metagenome using all PSSMs ####################### + ################ remove redundant sequences hit in multiple PSSMs ##################### + + +cat *.psiout |cut -f 2 >all.hits +#list all of the hits from a psiblast using all intein PSSMs + +sort all.hits >sort.hits +#sort all of the hits alphabetically by contig name from metagenome file + +uniq sort.hits >mg_name.hits +#extract only unique hits mg_name.hits is a list of contigs which were found by PSSMs + + +for filn in `cat mg_name.hits`; do grep -A 1 $filn mg.fas> $filn.seqfile;done +#makes a list of all of the contigs and searches for the corresponding fasta sequence in the metagenome .fas file + +ls *.seqfile|cut -d "." -f 1 >seqfile.list +#for filn in `cat seqfile.list`; do blastall -p blastp -i $filn.seqfile -o $filn.blastout -m 8 -d first_db;done + +for filn in `cat yellow.hits`; do blastx -query $filn.seqfile -db intein.db -outfmt 6 -out $filn.blast ;done +#new blast +#blast each contig against a db of inteins, hnt, bil, he, mid domains + +#for filn in `cat seqfile.list`;do grep -m 1 "_" $filn.blastout >$filn.tsbh;done +for f in `cat yellow.hits`; do head -1 $f.blast > $f.tsbh; done +#works for all +#extract tsbh for each contig, identifies hit as being BIL, HNT, HE, mid, or intein + +cat *.tsbh > all.tsbh +#make one file of all the tsbh for all contigs + +grep ":HE" all.tsbh > mg.he +#extract contigs idetified as HEs and put them in file +grep ":mid" all.tsbh >mg.mid +#extract all contigs identified as mid domains +grep "BIL:" all.tsbh > mg.bil +#extract all contigs identified as BIL domains +grep "|*:" all.tsbh > mg.HNT +#extract all contigs identified as HNT domains +grep -v ":HE" all.tsbh | grep -v ":mid" | grep -v "BIL:" |grep -v "|*:" > mg.intein +#extract all contigs identified as inteins + +cut -f 12 mg.intein > mg.intein.bits +#makes a file of only the bit scores for each intein hit +paste mg.intein.bits mg.intein > mg.bit.inteins +#makes a file where the bit score is the first column so it can be sorted by bit score +sort mg.bit.inteins >mg.int.sorted +#sorts the file based on the bit score + +# at this point the user needs to determine how many of the hits should be extracts I have +#determined that bits of 100 or more are actually inteins anything under that cannot be reliably aligned +# to the identified intein hit, once the user has determined how many of the hits are above 100 +#use tail to grab _ hits from the bottom of the list for instance if the last 20 hits are +#above 100: tail -n 20 mg.int.sorted >mg.int.significant + +################ once hits are extracted they need to be blasted against the ############# +################ nr db to identify the extein the intein may be inserted into ############ + +cut -f 1 mg.int.significant > contigs.list +#makes a list of the contigs in the list which have hits over 100 +for filn in `cat contigs.list`; do blastall -p blastp -i $filn.seqfile -d nr -m 8 -o $filn.outfile; done +#blasts nr db with significant contigs + +for filn in `cat contigs.list`; do grep -m 1 "gi" $filn.outfile > $filn.nr.tsbh;done +#extracts tsbh from nr db + +for filn in `cat contigs.list`; do cut -f 2 $filn.nr.tsbh >$filn.nr.gi;done +#extracts gi # from the tsbh of each contig + +for filn in `cat contig.list`; do fastacmd -i $filn.nr.gi -o $filn.nr.hit ;done +#extract sequences from nr which correspond to the contigs used to search nr \ No newline at end of file diff --git a/submissionscripts/metagenomepipeline/short.tsbh b/submissionscripts/metagenomepipeline/short.tsbh new file mode 100644 index 0000000..e8c987f --- /dev/null +++ b/submissionscripts/metagenomepipeline/short.tsbh @@ -0,0 +1,26 @@ +NODE_3_length_57712_cov_4.792167 Sru_RIR1 71.467 375 106 1 42832 43956 1 374 1.36E-172 +NODE_11_length_47111_cov_27.354535 Hma_PolB 44.769 411 208 4 23367 24542 1 411 1.28E-108 +NODE_71_length_28382_cov_3.773220 Hut_MCM1 26.654 544 357 16 17762 16215 1 530 1.98E-34 +NODE_282_length_16063_cov_3.037794 Sru_RIR1 73.191 235 62 1 15906 15202 141 374 1.35E-113 +NODE_236_length_17314_cov_3.595342 Hma_PolII 48.108 185 86 7 15533 15000 1 182 7.50E-38 +NODE_74_length_27964_cov_3.536279 Mka_RtcB 36.162 495 289 15 15894 14458 1 484 7.58E-66 +NODE_444_length_13286_cov_3.827904 gi|298674214|ref|YP_003725964.1| 61.131 283 97 3 12449 13285 4 277 2.92E-105 +NODE_294_length_15787_cov_28.622108 gi|339757395|gb|EGQ40976.1| 49.638 1104 518 15 15246 11992 1 1085 0 +NODE_573_length_11668_cov_12.855335 Hwa_RCF 47.619 126 64 1 10580 10951 1 126 2.92E-26 +NODE_535_length_12123_cov_29.480030 HspNRC1_PolII 54.04 198 78 6 9663 10220 1 197 7.79E-55 +NODE_103_length_24836_cov_4.744441 Mka_RtcB 32.998 497 299 17 8380 9807 1 484 2.44E-61 +NODE_314_length_15288_cov_4.066369 S42459__Tli_Pol1 24.212 603 333 19 7792 9456 14 540 8.67E-30 +NODE_895_length_9454_cov_8.660177 Mka_RtcB 30.667 450 282 11 7343 8641 1 437 1.49E-49 +NODE_485_length_12653_cov_5.693761 Hwa_MCM4 34.179 591 305 15 6303 7874 1 574 9.35E-81 +NODE_1626_length_7057_cov_3.598686 Hma_PolB 71.671 413 115 2 5658 6896 1 411 0 +NODE_354_length_14577_cov_6.546412 Mja_RFC1 23.89 473 299 18 7985 6612 124 550 1.02E-23 +NODE_1619_length_7074_cov_4.551788 Mja_RFC1 25.949 316 180 11 7071 6151 280 550 3.91E-23 +NODE_2119_length_6098_cov_4.256826 MaeoN3_UDP_GD 29.268 492 302 15 4456 5874 1 465 3.06E-54 +NODE_2030_length_6250_cov_20.856013 Hma_PolII 47.283 184 91 4 6212 5673 1 182 2.03E-45 +NODE_1334_length_7894_cov_16.876132 Mja_rPol_A&quo> 23.952 501 277 18 5934 4489 58 473 1.53E-27 +NODE_3176_length_4798_cov_4.998524 Hwa_GyrB 58.036 224 83 3 3664 4323 1 217 7.16E-73 +NODE_3746_length_4357_cov_17.156671 Hma_PolB 39.659 411 215 9 3046 4179 1 411 2.42E-85 +NODE_3387_length_4618_cov_5.378041 Hwa_PolII1 42.138 159 81 4 4614 4168 374 531 4.38E-26 +NODE_1606_length_7089_cov_5.165624 TsiMM739_Pol1 25.413 484 292 20 2818 4131 1 461 2.63E-28 +NODE_2641_length_5361_cov_12.084056 Mka_RtcB 33.26 454 274 14 5244 3931 44 484 1.60E-59 +NODE_890_length_9480_cov_3.792361 NmaATCC43099_MCM 57.669 652 264 6 1977 3920 1 644 0 diff --git a/submissionscripts/metagenomepipeline/sig.mgcds.txt b/submissionscripts/metagenomepipeline/sig.mgcds.txt new file mode 100644 index 0000000..291a030 --- /dev/null +++ b/submissionscripts/metagenomepipeline/sig.mgcds.txt @@ -0,0 +1,20 @@ +102 L_17763 CZIV_RIR1 43.36 143 73 3 1132 1536 1 141 2.00E-23 102 +545 L_02848 Aeh_DnaB2 63.81 420 152 0 1171 2430 1 420 1.00E-156 545 +404 L_113176 NmaATCC43099_PolB2 77.14 245 54 1 729 1 104 348 4.00E-115 404 +310 L_41817 Cwa_RIR1 49.57 351 156 5 688 1677 1 349 7.00E-86 310 +241 L_19013 Punc_DnaB 35.89 365 218 8 433 1479 1 354 3.00E-65 241 +237 L_114422 Nph_rPol_A'' 72.61 157 43 0 482 12 219 375 5.00E-65 237 +197 L_102087 Hut_MCM1 56.57 175 76 0 76 600 211 385 4.00E-57 197 +194 L_53997 HspNRC1_PolII 54.04 198 79 6 1075 1632 1 197 3.00E-51 194 +191 L_54356 IIV6_RIR1 48.86 176 90 0 31 558 166 341 1.00E-50 191 +189 L_92998 FacFer1_RIR1 44.87 234 129 1 747 46 143 368 4.00E-50 189 +173 L_39776 Punc_DnaB 33.61 363 208 12 274 1263 1 354 9.00E-45 173 +170 L_17527 MspMCS_DnaB 37.39 345 196 9 244 1218 3 324 8.00E-44 170 +162 L_38519 APAPSE2_dpola 33.96 318 206 6 979 1920 2 309 2.00E-41 162 +138 L_87109 FacFer1_RIR1 48.91 137 67 3 402 1 1 136 8.00E-35 138 +134 L_86123 Nph_CDC21 57.6 125 51 1 378 10 130 254 3.00E-34 134 +127 L_144221 Hvo_PolB 68.52 108 34 0 91 414 1 108 8.00E-32 127 +122 L_60537 FacFer1_RIR1 45.9 122 65 2 363 1 1 121 7.00E-30 122 +112 L_86122 Nph_CDC21 62.07 87 33 0 261 1 1 87 1.00E-27 112 +99.4 L_30700 Hwa_RCF 29.39 262 177 5 178 939 1 256 1.00E-22 99.4 +95.9 L_51394 Hwa_RCF 46.73 107 55 1 690 376 1 107 6.00E-22 95.9 diff --git a/submissionscripts/nrblast.sh b/submissionscripts/nrblast.sh new file mode 100644 index 0000000..42c880d --- /dev/null +++ b/submissionscripts/nrblast.sh @@ -0,0 +1,16 @@ +#!/bin/bash +#SBATCH --job-name=nrblast +#SBATCH -N 1 +#SBATCH -n 1 +#SBATCH -c 20 +#SBATCH --partition=himem4 +#SBATCH --mail-type=END +#SBATCH --mem=250G +#SBATCH --mail-user=yutian.feng@uconn.edu +#SBATCH -o nrblast_%j.out +#SBATCH -e nrblast_%j.err + + + +module load blast/2.7.1 +for filn in *.txt; do blastx -query $filn -db /isg/shared/databases/blast/nr -outfmt "6 qaccver sgi sallgi sseqid qseq" -out exteinbackground.tab -max_target_seqs 1 -evalue 1e-10 -num_threads 20; done diff --git a/submissionscripts/nrgiextract.sh b/submissionscripts/nrgiextract.sh new file mode 100644 index 0000000..6c40f3c --- /dev/null +++ b/submissionscripts/nrgiextract.sh @@ -0,0 +1,17 @@ +#!/bin/bash +#SBATCH --job-name=nrblast +#SBATCH -N 1 +#SBATCH -n 1 +#SBATCH -c 20 +#SBATCH --partition=himem4 +#SBATCH --mail-type=END +#SBATCH --mem=250G +#SBATCH --mail-user=yutian.feng@uconn.edu +#SBATCH -o nrblast_%j.out +#SBATCH -e nrblast_%j.err + + + +module load blast/2.7.1 +for f in `cat con503.gi.list`; do blastdbcmd -entry $f -db /isg/shared/databases/blast/nr >> con503.tsbh; done +for f in `cat node503.gi.list`; do blastdbcmd -entry $f -db /isg/shared/databases/blast/nr >> node503.tsbh; done diff --git a/submissionscripts/parse.py b/submissionscripts/parse.py new file mode 100644 index 0000000..ec133ed --- /dev/null +++ b/submissionscripts/parse.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python +f=open("exteinonly.txt","r"); +opened = False +for line in f : + if(line[0] == ">") : + if(opened) : + of.close() + opened = True + of=open("%s" % (line[1:].rstrip()), "w") + print(line[1:].rstrip()) + of.write(line) +of.close() diff --git a/submissionscripts/prokka.sh b/submissionscripts/prokka.sh new file mode 100644 index 0000000..9c57ba1 --- /dev/null +++ b/submissionscripts/prokka.sh @@ -0,0 +1,16 @@ +#!/bin/bash +#SBATCH --job-name=prokka +#SBATCH -N 1 +#SBATCH -n 1 +#SBATCH -c 16 +#SBATCH --partition=amd +#SBATCH --mail-type=END +#SBATCH --mem=50G +#SBATCH --mail-user=yutian.feng@uconn.edu +#SBATCH -o prokka_%j.out +#SBATCH -e prokka_%j.err + + +cd /home/CAM/yfeng/metagenomes/worked/test2ass +module load prokka/1.11 +prokka --outdir annotated --prefix annocontigs contigs.fasta \ No newline at end of file diff --git a/submissionscripts/psiblast.sh b/submissionscripts/psiblast.sh new file mode 100644 index 0000000..45177f0 --- /dev/null +++ b/submissionscripts/psiblast.sh @@ -0,0 +1,16 @@ +#!/bin/bash +#SBATCH --job-name=psi +#SBATCH -N 1 +#SBATCH -n 1 +#SBATCH -c 4 +#SBATCH --partition=amd +#SBATCH --mail-type=END +#SBATCH --mem=100G +#SBATCH --mail-user=yutian.feng@uconn.edu +#SBATCH -o psi_%j.out +#SBATCH -e psi_%j.err + + + +module load blast/2.7.1 +for b in *.fa; do psiblast -query "$b" -db /isg/shared/databases/blast/nr -out ${b%.fa}.blast -outfmt 6 -num_iterations 5 -out_pssm ${b%.fa}.pssm -save_pssm_after_last_round; done \ No newline at end of file diff --git a/submissionscripts/raxml.bash b/submissionscripts/raxml.bash new file mode 100644 index 0000000..504e218 --- /dev/null +++ b/submissionscripts/raxml.bash @@ -0,0 +1,17 @@ +#!/bin/bash +#SBATCH --job-name=raxml +#SBATCH -N 1 +#SBATCH -n 1 +#SBATCH -c 16 +#SBATCH --partition=amd +#SBATCH --mail-type=END +#SBATCH --mem=20G +#SBATCH --mail-user=yutian.feng@uconn.edu +#SBATCH -o racks_%j.out +#SBATCH -e racks_%j.err + + + +module load RAxML/8.2.11 +raxmlHPC ­f i ­t extein.te ­z inteinaa.align.ufboot ­m GTRCAT ­n T4 + \ No newline at end of file diff --git a/submissionscripts/tblastn.sh b/submissionscripts/tblastn.sh new file mode 100644 index 0000000..c75719a --- /dev/null +++ b/submissionscripts/tblastn.sh @@ -0,0 +1,16 @@ +#!/bin/bash +#SBATCH --job-name=tblastn +#SBATCH -N 1 +#SBATCH -n 1 +#SBATCH -c 1 +#SBATCH --partition=amd +#SBATCH --mail-type=END +#SBATCH --mem=50G +#SBATCH --mail-user=yutian.feng@uconn.edu +#SBATCH -o tblastn_%j.out +#SBATCH -e tblastn_%j.err + + + +module load blast/2.7.1 +for b in *.pssm; do tblastn -in_pssm "$b" -db contigs.fasta -out "$b".search -outfmt 6 -evalue 1e-10; done \ No newline at end of file diff --git a/submissionscripts/test.fna b/submissionscripts/test.fna new file mode 100644 index 0000000..1e19675 --- /dev/null +++ b/submissionscripts/test.fna @@ -0,0 +1,3 @@ +>swagger.txt +atgcatagca +ataatttacg \ No newline at end of file diff --git a/submissionscripts/transeq.sh b/submissionscripts/transeq.sh new file mode 100644 index 0000000..fbefac0 --- /dev/null +++ b/submissionscripts/transeq.sh @@ -0,0 +1,16 @@ +#!/bin/bash +#SBATCH --job-name=trans +#SBATCH -N 1 +#SBATCH -n 1 +#SBATCH -c 10 +#SBATCH --partition=amd +#SBATCH --mail-type=END +#SBATCH --mem=50G +#SBATCH --mail-user=yutian.feng@uconn.edu +#SBATCH -o trans_%j.out +#SBATCH -e trans_%j.err + + +cd /home/CAM/yfeng/metagenomes/test1 +module load emboss/6.6.0 +transeq -sequence contigs.fasta -outseq transcont.fasta -frame 6 -clean \ No newline at end of file