Here is the final ugly code.

#!/usr/bin/perl -w
use strict;
use Data::Dumper;

my %info = (); 
my ($gi, $humangi, $accession);

my $data = '/DATA/proteinfile.txt'; 
open INFILE, '<', $data or die "Failed at opening $data!\n";

# Construct the hash with GIs as keys and sequences as values
while ( <INFILE> ) {
my $line = $_;
chomp($line);
    last if m!END!;
    
    if($line=~m/HUMAN/){
        
        ($humangi) = ($line=~m/^\S+\|(\d+)/);
        
       ($accession) = ($line=~m/^\S+\|\d+\|\w+\|(\S{6}?)/);
       
          }
    
    if($line=~m/^\S+\|(\d+)/)
       {
        if(defined($1))
         { 
          $gi=$1;
         }    
       }
    else
       {
        $info{$gi} = $line;
        }
}
    #print Dumper (\%info);

    print "$humangi\n";
    print "$accession\n";

close(INFILE);

my $data2 = '/DATA/variantlist.txt'; 
open INFILE2, '<', $data2 or die "Failed at opening $data2!\n";

my $data3 = '/DATA/VariantOutput.txt'; 
open OUTFILE, '>', $data3 or die "Failed at opening $data3!\n";

print OUTFILE "This is [GI: $humangi] and [Accession: $accession]\nVAR
+IANT\t\tPOTENTIAL\t\tPD\n";

while ( <INFILE2>){
# Grab a variant from the file (in this example: P82L)
my $line2 = $_;
chomp($line2);
my $Variant = $line2;

# Split the variant into three parts
my ($source, $position, $sink) = split(/(\d+)(\w)/, $Variant);

#print "$source\t$position\t$sink\n";
# Check whether HS has the source (i.e., P) at the given position (i.e
+., 82)
my $temp = $info{$humangi};

    #print "Temp contains $temp" . "\n";
    
my @char = split //, $temp;    

    #print "Now \@char contains: @char";

    #print "Inside the temp: $char[0] and $char[1]\n";

my $target = $char[$position-1];
    
    #print "This is the target: $target" . "\n";

if ( $target eq $source) {
    
     print "Yep!\n";
    }
    
my @VariantList = ();
my @PDList = ();
    
# Scan the rest of the sequences to check what amino acid they have at
+ the given position
for my $gi ( keys %info ) {
        my $value = $info{$gi};
        
        my @char2 = split //, $value;
        
        my $potential = $char2[$position-1];
        
        push (@VariantList, $potential); 
        
        
        if ($potential eq $sink){ # Note the cases where we observe th
+e sink (i.e., L) at this position
            
            my $pd = "$potential" . "{" . "$gi" . "}";
            
            push (@PDList, $pd)             
            #print "A pathogenic deviation has been found at site $pos
+ition - from $source to $sink !\n" . " And the corresponding gi for t
+his deviation is: $gi\n";
            
            }
            }

print OUTFILE "$Variant\t\t@VariantList\t\t@PDList\n";
}
close(INFILE2);
[download]

Instead of -w use warnings. The command line flag applies to any modules you include as well as your own code so you may get warnings from code you essentially have no control over using -w.

Use the special variable $! in file i/o error handling messages to give a little more information about the nature of the failure.

You don't need to set arrays or hashes empty when you declare them. They are sold without batteries.

Don't declare variables in a lump: my ($foo, $baa, $baz). It makes it harder to see where they are declared and precludes providing a usage comment (although that shouldn't often be required).

It's not clear from the input loop whether you expect more than one gi. Your use of $accession implies that there should only be one (else the accession value isn't related to the gi value even though they come from the same line of data). You still haven't addressed the possibility that you get a well formatted sequence line before you get a gi line. These are related issues.

Use statement modifiers where you have a trivial statement controlled by a condition. For example $gi = $1 if defined $1;.

Avoid a proliferation of temporary variables and assignments. For example, see the change I made to your second while loop.

Avoid comments that say the same thing as the code. 'split into three parts' adds no extra information that a trivial inspection of the code doesn't tell you. The data format related comments ('... P82L ...') however are good!

You can use {} to ensure a variable is interpolated correctly in a string. For example you can write "${potential}{$gi}" instead of concatenating a bunch of substrings together.

My reworked version with the changes implied is:

#!/usr/bin/perl
use strict;
use warnings;
use Data::Dumper;

my $data = '/DATA/proteinfile.txt';
open my $inFile, '<', $data or die "Failed at opening $data: $!\n";

# Populate the info hash with GIs as keys and sequences as values
my $humanGi;
my $accession;
my $gi;    # Current gi while reading sequences
my %info;

while (<$inFile>) {
    my $line = $_;
    chomp $line;
    last if m!END!;

    if ($line =~ m/HUMAN/) {
        ($humanGi, $accession) = $line =~ m/^\S+\|(\d+)\|\w+\|(\S{6}?)
+/;
    }

    if ($line =~ m/^\S+\|(\d+)/) {
        $gi = $1 if defined $1;
    } else {
        $info{$gi} = $line;
    }
}
close $inFile;

my $data2 = '/DATA/variantlist.txt';
open $inFile, '<', $data2 or die "Failed at opening $data2: $!\n";

my $data3 = '/DATA/VariantOutput.txt';
open my $outfile, '>', $data3 or die "Failed at opening $data3: $!\n";

print $outFile
    "This is [GI: $humanGi] and [Accession: $accession]\nVARIANT\t\tPO
+TENTIAL\t\tPD\n";

while (defined (my $Variant = <$inFile>)) {
    # Grab a variant from the file (in this example: P82L)
    chomp $Variant;

    my ($source, $position, $sink) = split /(\d+)(\w)/, $Variant;

    # Check whether HS has the source (i.e., P) at the given position 
+(i.e., 82)
    my @char = split //, $info{$humanGi};
    my $target = $char[$position - 1];
    my @VariantList;
    my @PDList;

    # Scan the rest of the sequences to check what amino acid they hav
+e at
    # the given position
    for my $gi (keys %info) {
        my @char2 = split //, $info{$gi};
        my $potential = $char2[$position - 1];

        push @VariantList, $potential;

        if ($potential eq $sink) {
            # Note the cases where we observe the sink (i.e., L) at th
+is position

            push @PDList, "${potential}{$gi}";
        }
    }

    print $outFile "$Variant\t\t@VariantList\t\t@PDList\n";
}
close $inFile;
close $outFile;
[download]

This is still rather unsatisfactory code because there are many ways it can fail due to unexpected data. Sanity checking helps ensure the code and the data format conform to the same expectations and make it much easier to diagnose problems when expectations aren't met.

There are no obvious inefficiencies in the current code. Initially efficiency shouldn't be an major consideration in any case. Generally if you avoid nested loops to the extent reasonable and avoid re-reading input files code of this sort will perform well enough for most purposes.

True laziness is hard work

Thank you very much, GrandFather. I'll pay close attention to all points you mentioned.

Redundant comments are result of my code writing process. I first write down the comments to have them as instructions to myself when implementing the algorithm. I should have removed or modified them as such they are used appropriately.

Thank you once again. I have just begun writing small scripts to help me with my research. And I do enjoy a lot writing codes. I hope to improve my programming skills for the sake of both increasing productivity and fun! :)

Ah, ah, I should not have shouted "victory" so early! That was only the battle, I seem to have lost the war here.

The code works for some input and not for the rest! I have manipulated the input file to have an insight into what might cause the problem, yet I have nothing. I'll post it to here hoping that someone might have an idea.

Essentially, the problem is that the script takes the first 22 input items (of two lines each) and ignores the rest. All these items have the same format. I could not figure out why there is such limitation on the input while there is no difference at all between various input items.

I hope the files do not violate any space limitation (if there is one).

The code -- revised version by GrandFather. 

#!/usr/bin/perl
use strict;
use warnings;
use Data::Dumper;

my $data = '/DATA/alignment.fas';
open my $inFile, '<', $data or die "Failed at opening $data: $!\n";

# Populate the info hash with GIs as keys and sequences as values
my $humanGi;
my $accession;
my $gi;    # Current gi while reading sequences
my %info;

while (<$inFile>) {
    my $line = $_;
    chomp $line;
    last if m!END!;

    if ($line =~ m/(HUMAN|Homo)/) {
        ($humanGi, $accession) = $line =~ m/^\S+\|(\d+)\|\w+\|(\S{6}?)
+/;
    }

    if ($line =~ m/^\S+\|(\d+)/) {
        $gi = $1 if defined $1;
    } else {
        $info{$gi} = $line;
    }
}
print Dumper (\%info);
close $inFile;

my $data2 = '/DATA/variantList.txt';
open $inFile, '<', $data2 or die "Failed at opening $data2: $!\n";

my $data3 = '/DATA/pathogenList.txt';
open my $outFile, '>', $data3 or die "Failed at opening $data3: $!\n";

print $outFile
    "This is [GI: $humanGi] and [Accession: $accession]\nVARIANT\t\tPO
+TENTIAL\t\tPD\n";

while (defined (my $Variant = <$inFile>)) {
    # Grab a variant from the file (in this example: P82L)
    chomp $Variant;

    my ($source, $position, $sink) = split /(\d+)(\w)/, $Variant;

    # Check whether HS has the source (i.e., P) at the given position 
+(i.e., 82)
    #my @char = split //, $info{$humanGi};
    #my $target = $char[$position - 1];
    my @VariantList;
    my @PDList;

    # Scan the rest of the sequences to check what amino acid they hav
+e at
    # the given position
    foreach my $gi (keys %info) {
        my @char2 = split //, $info{$gi};
        my $potential = $char2[$position - 1];

        push @VariantList, "${potential}{$gi}";

        if ($potential eq $sink) {
            # Note the cases where we observe the sink (i.e., L) at th
+is position

            push @PDList, "${potential}{$gi}";
        }
    }

    print $outFile "$Variant\t@VariantList\t@PDList\n";
}
close $inFile;
close $outFile;
[download]

First input. Variant list. 

A5V
A5S
A5T
C7F
V8E
L9Q
L9V
G13R
V15G
V15M
G17S
F21C
E22K
E22G
Q23L
G38R
L39R
L39V
G42D
G42S
H44R
F46C
H47R
H49R
H49Q
E50K
T55R
N66S
L68R
G73S
D77Y
H81A
L85F
L85V
G86R
N87S
V88A
A90T
A90V
D91A
D91V
G94A
G94C
G94D
G94R
G94V
V98M
E101G
E101K
D102N
D102G
I105F
S106L
L107V
G109V
I113M
I113T
I114T
G115A
R116G
V119L
D125V
D125G
D126H
L127S
S135N
N140K
L145F
L145S
A146T
C147R
G148R
V149G
V149I
I150T
I152T
[download]

and the second input file. 

>gi|134611|sp|P00441.2|_Homo_sapiens
MATKAVCVLKGDGPVQGIINFEQKESNGPVKVWGSIKGLTEGLHGFHVHEFGDNTAGCTSAGPHFNPLSR
+KHGGPKDEERHVGDLGNVTADKDGVADVSIEDSVISLSGDHCIIGRTLVVHEKADDLGKGGNEESTKTG
+NAGSRLACGVIGIAQ
>gi|112419222|Xenopus_laevis
AMVKAVCVLAGSGDVKGVVRFEQQDD-GDVTVEGKIEGLTDGNHGFHIHVFGDNTNGCLSAGPHFNPQNK
+NHGSPKDADRHVGDLGNVTA-EGGVAQFKFTDPQISLKGERSIIGRTAVVHEKQDDLGKGGDDESLKTG
+NAGGRLACGVIGFCP
>gi|62858937|_Xenopus_(Silurana)_tropi...
-MVRAVCVLAGSGDVKGVVHFQQQDE-GPVTVEGKIYGLTDGKHGFHIHEFGDNTNGCISAGPHFNPESK
+THGAPEDAVRHVGDLGNVTA-KDGVAEFKLTDSLISLKGNHSIIGRCAVVHEKEDDLGKGGNDESLKTG
+NAGGRLACGVIGLCQ
>gi|226372562|_Rana_catesbeiana
--MKAICVLKGSSEVTGVVRFEQEED-GPVTVTGQITGLTDGKHGFHIHTYGDNTDGCVSAGPHFNPQGK
+THGGPDDEVRHVGDLGNVTS-AGGVADINIKDKLISLKGEHSIIGRTAVVHEKEDDLGKGGDNESLITG
+NAGGRLACGVIGICQ
>gi|116048074|_Scyliorhinus_torazame
--MKAICVLKGTGEVTGTVQFDQAGG-GPVTVKGSITGLTPGKHGFHVHAFGDNTNGCISAGPHYNPFLK
+THGGPGDEERHVGDLGNVEANGDGVATFEIQDNQLHLSGERSIIGRTLVVHEKEDDLGKGEDEESTRTG
+NAGSRLACGVIGIAK
>gi|216963348|_Ctenopharyngodon_idella
-------------------YFEQEGEKSPVTLSGEITGLTAGKHGFHVHAFGDNTNGCISAGPHFNPYSK
+NHGGPTDSERHVGDLGNVIAGENGVAKIDIVDKMLTLSGPDSIIGRTMVIHEKEDDLGKGGNEESLKTG
+NAGGRLACGVIGITQ
>gi|226232347|_Pimephales_promelas
---------------------------------------------------------------HFNPHTQ
+NHGGPTDSARHVGDLGNVTAGENGVAKIDIVDKMLTLSGQHSIIGRTMVIHEKEDDLGKGGNE------
+---------------
>gi|238801237|_Hemibarbus_mylodon
MAKKAVCVLKGTGEVTGTVFFEQETDGSPVKLSGTISGLTAGKHGFHVHVFGDNTNGCISAGPHFNPHNK
+NHGGPTDGDRHVGDLGNVTAGESGVAKIDIVDKMLTLSGQHSIIGRTMVIHEKEDDLGKGGNEESLKTG
+NAGGRLACGVIGITG
>gi|47227092|_Tetraodon_nigroviridis
MVIKAVCVLKGAGETSGTVYFEQQDEKAPVKLTGEIKGLTAGEHGFHVHAFGDNTNGCISAGPHYNPHNK
+THAGPNDENRHVGDLGNVTAEADQIAKIDITDSVISLHGKFSIIGRTMVIHEKADDLGKGGNEESLKTG
+NAGGRLACGVIGITQ
>gi|225706520|_Osmerus_mordax
MVLKAVCVLKGTGEVTGTVFFEQEGDNGPVKLTGEISGLTPGEHGFHVHAFGDNTNGCISAGPHFNPHSK
+THGGPTDDVRHVGDLGNVTAGQDNVAKISIQDKHLTLNGVHSIIGRTMVIHEKADDLGKGGNEESLKTG
+NAGGRLACGVIGITQ
>gi|185132317|_Oncorhynchus_mykiss
MAMKAVCVLKGTGEVTGTVFFEQEGADGPVKLIGEISGLAPGEHGFHVHAYGDNTNGCMSAGPHFNPHNQ
+THGGPTDAVRHVGDLGNVTAGADNVAKINIQDKMLTLTGPDSIIGRTMVIHEKADDLGKGGNEESLKTG
+NAGGRQACGVIGIAQ
>gi|56790262|_Danio_rerio
MVNKAVCVLKGTGEVTGTVYFNQEGEKKPVKVTGEITGLTPGKHGFHVHAFGDNTNGCISAGPHFNPHDK
+THGGPTDSVRHVGDLGNVTADASGVAKIEIEDAMLTLSGQHSIIGRTMVIHEKEDDLGKGGNEESLKTG
+NAGGRLACGVIGITQ
>gi|185135289|_Salmo_salar
MALKAVCVLKGTGEVTGTVFFEQEGDGAPVKLTGEIAGLTPGEHGFHVHAFGDNTNGCMSAGPHFNPHNH
+THGGPTDTVRHVGDLGNVTAAADSVAKINIQDEILSLAGPHSIIGRTMVIHEKADDLGKGDNEESRKTG
+NAGSRLACGVIGIAQ
>gi|134284932|_Carassius_auratus
---------------------------------------------FHVHAFGDNTNGCTSAGPHYNPHNQ
+THGGPTDSVRHVGDLGNV---------------------------------------------------
+---------------
>gi|110180503|_Oryzias_javanicus
----------------------------------------PGEHGFHVHAFGDNTNGCISAGPHFNPYGK
+DHAGPTDEHRHVGDLGNVTANAENVAKLDFTDKVITLAGPHSIIGRTMVIHEKKDDLGKGGNEESLKTG
+NA-------------
>gi|229365862|_Anoplopoma_fimbria
MVVKAVCVLKGAGETSGVVHFEQEGDTAAVKLTGEIIGLTPGEHGFHVHAFGDNTNGCISAGPHFNPHNN
+THAGPTDEQRHVGDLGNVTAGGDNIAKIDITDKIITLTGQHSIIGRTMVIHEKADDLGKGGNDESLKTG
+NAGARLACGVIGIAQ
>gi|226934254|_Dicentrarchus_labrax
----------------------------------------------------------------------
+---------RHVGDLGDVTAGGDNIAKIDITDKMLTLTGPLFIIGRTMVIHEKADDLGKGGNEESLKTG
+---------------
>gi|54873355|_Sebastes_schlegelii
---------------------------------GEIKGLTPGEHGFHVHAFGDNTNGCISAGPHFNPHGK
+DHAGPTDQERHVGDLGNVTAGAANVAKIDITDKMLTLTGPLSIIRRTMVIHEKKDDLGKGGNEESLKTG
+NAGG-----------
>gi|62550923|_Sparus_aurata
-------------------------------------------------------------------HGK
+NHGGPTDAERHVGDLGNVTAGADNVAKIDITDKMLTLSGPLSIIGRTMVIHEKVDDLGKGGNEE-----
+---------------
>gi|27462182|_Pagrus_major
MVQKAVCVLKGAGETTGVVHFEQESESAPVTLKGEISGLTPDEHGFHVHAFGDNTNGCISAGPHFNPHNK
+NHAGPTDAERHVGDLGNVTAGADNVAKIDITDKMLTLNGPFSIIGRTMVIHEKADDLGKGGNEESLKTG
+NAGGRLACGVIGICQ
>gi|12733941|_Platichthys_flesus
-----------------------------------IAGLAPGEHGFHVHSFGDNTNGCMSAGPHFNPHGK
+NHAGPTDADRHVGDLGNVTAGADNVAEINISDKMLTLNGPNSIIGRTMVIHEKADDLGKGGNDESLKTG
+NA-------------
>gi|151549024|Paralichthys_olivaceus
------------------------------------------EHGFHVHAFGDNTNGCISAGPHFNPHGK
+NHAGPTDAERHVGDLGNVTAGKDNVAEINISDKIITLFGAHSIIGRTMVIHEKADDLGKGGNEESLKTG
+NAGARLACGVIG---
>gi|57908848|_Trematomus_bernacchii
---KAVCVFKGTGEASGTVFFEQENDSAPVKLTGEIKGLTPGEHGFHVHAFGDNTNGCISAGPHFNPHNK
+THAGPTDEDRHVGDLGNVTAAADNVAKLNITDKMITLAGQYSIIGRTMVIHEKADDLGKGGNDESLKTG
+NAGGRLACGVIGIAQ
>gi|57908852|Chionodraco_hamatus
---KAVCVFKGAGEASGTVFFEQETDSCPVKLTGEIKGLTPGEHGFHVHAFGDNTNGCISAGPHFNPHNK
+THAGPTDENRHVGDLGNVTAAADNVAKLDITDKMITLAGQYSIIGRTMVIHEKADDLGKGGNDESLKTG
+NAGGRLACGVIGIAQ
>gi|157152709|_Takifugu_obscurus
MAMKAVCVLKGAGDTSGTVYFEQENESAPVKLTGEIKGLTPGEHGFHVHAFGDNTNGCISAGPHYNPHNK
+THAGPTDADRHVGDLGNVTAGADNIAKIDIKDSMLTLTGPYSIIGRTMVIHEKADDLGKGGNEESLKTG
+NAGGRLACGVIGITQ
>gi|67772081|_Siniperca_chuatsi
--------------------------------------FTPGEHGSHVHVFGDNTNGCISAGPHYNPHGK
+NHAGPNDAERHVGDLGNVTAGADNVAKIDITDKMPSLTGPYSIIGRTMVIHEKADDLGKGGNEESLKTG
+NAGGRLACGVIGITQ
>gi|40218091|_Oreochromis_mossambicus
MVLKAVCVLKGTGDTSGTVYFEQENDSAPVKLTGEIKGLTPGEHGFHVHAFGDNTNGCISAGPHFNPYNK
+NHGGPKDAERHVGDLGNVTAGADNVAKIEITDKVITLTGRDSIIGRTMVIHEKVDDLXKGGNEESLKTG
+NAGGRLACGVIGITQ
>gi|37542151|_Epinephelus_malabaricus
MVLKAVCVLKGAGETSGTVYFEQETDSAPVKLTGEIKGLTPGEHGFQVHAFGDNTNGCISAGPHFNPHNK
+HHAGPTDAERHVGDLGNVTAGGDNVAKIDITDKIITLNGPYSIIGRTMVIHEKADDLGTGGNEESLKTG
+NAGGRLACGVIGISQ
>gi|56785775|Epinephelus_coioides
MDLKAVCVLKGAGETSGTVYFEQESDSAPVKLTGEIKGLTPGEHGFHVHAFGDNTNGCISAGPHFNPHNK
+QHAGPTDADRHVGDLGNVTAGGDNVAKIDITDKMLTLNGPYSIIGRTMVIHEKADDLGRGGNDESLKTG
+NAGGRLACGVIGIAQ
>gi|47607437|_Oplegnathus_fasciatus
MVLKAVCVLKGAGETTGTVYFEQESDSAPVKLTGEIKGLTPGEHGFHVHAFGDNTNGCISAGPHFNPHNK
+NHAGPNDAERHVGDLGNVTAGADNVAKIDIKDHIITLTGPDSIIGRTMVIHEKADDLGKGGNEESLKTG
+NAGGRLACGVIGITQ
>gi|115392225|_Rachycentron_canadum
MVLKAVCVLKGAGETTGTVYFEQESDSAPVKVTGEIKGLTPGEHGFHVHAFGDNTNGCISAGPHFNPHNK
+NHAGPNDEERHIGDLGNVTAGADNVAKVDITDKMLTLNGPYSIIGRTMVIHEKADDLGKGGNEESLKTG
+NAGGRLACGVIGIAQ
>gi|224044145|_Taeniopygia_guttata
AAMRAVCVMQGEGAVKGVIHFEQQGT-GPVKVTGEITGLADGEHGFHVHEFGDNTNGCTSAGPHFNPEQK
+KHGGPSDAERHVGDLGNVTA-KGGVAQVSIQDSVISLSGPHCIIGRTMVVHERRDDLGRGGNDESLLTG
+NAGPRLACGVIGIAK
>gi|45384218|_Gallus_gallus
ATLKAVCVMKGDAPVEGVIHFQQQGS-GPVKVTGKITGLSDGDHGFHVHEFGDNTNGCTSAGAHFNPEGK
+QHGGPKDADRHVGDLGNVTA-KGGVAEVEIEDSVISLTGPHCIIGRTMVVHAKSDDLGRGGDNESKLTG
+NAGPRLACGVIGIAK
>gi|29373121|_Melopsittacus_undulatus
ATLKAVCVMKGEGPVQGVIHFQQQGN-GPVKVTGKISGLADGDHGFHVHEFGDNTNGCTSAGPHFNPEGK
+QHGGPSDAERHVGDLGNVTA-KGGVAEVAIEDSIISLSGPHSIVGRTMVVHEKCDDLGRGGDNESKLTG
+NAGPRLACGVIGIAK
>gi|89515076|_Bufo_gargarizans
-MVKAICVLKGNGPVHGIVGFNQDG--GEVTVKGTINGLTDGLHGFHIHVYGDNTNGCMSAGPHFNPHGK
+SHGAPEDEERHVGDLGNITS-KDGVAEFEFKDKIISLEGEHNIIGRTAVVHEKADDLGKGGDNESKVTG
+NAGGRLACGVIGICQ
>gi|226844835|_Trachemys_scripta_elegans
---------------------------------------------------------CTSAGAHFNPNGK
+NHGGPQDKERHVGDLGNVIANKDGVAEVSIKDSLISLTGPLSIIGRTMVVHEKEDDLGKGNN-------
+---------------
>gi|265797|_Caretta_caretta
---------------------------ATVKAVCVLKGEDPVKEPVKGPVKEPVKGIIYFEQQGN-GPVT
+LSGSITGLTEGKHGFHVHEFGDNTNGCTSAGAHFNPPGKNHGGPQDNERHVGDLGNVIANKEGVAEVCI
+KDSLISLTGSQSIIG
>gi|126352669|_Equus_caballus
MALKAVCVLKGDGPVHGVIHFEQQQEGGPVVLKGFIEGLTKGDHGFHVHEFGDNTQGCTTAGAHFNPLSK
+KHGGPKDEERHVGDLGNVTADENGKADVDMKDSVISLSGKHSIIGRTMVVHEKQDDLGKGGNEESTKTG
+NAGSRLACGVIGIAP
>gi|126325231|_Monodelphis_domestica
MVLKAVCVLKGDGPVQGTIFFEQKQVGEPVELSGSIKGLAEGDHGFHVHEFGDNTQGCTSAGAHFNPHSK
+KHGGPTDEERHVGDLGNVTANKDGVATVSIKDSHIELSGPMSIIGRTMVVHEKADDLGKGGNAESEKTG
+NAGPRLACGVIGIAK
>gi|130497065|_Oryctolagus_cuniculus
MATKAVCVLKGDGPVEATIHFEQKGT-GPVVVKGRITGLTEGLHEFHVHQFGDNRQGCTSAGPHFNPLSK
+KHGGPKDEERHVGDLGNVTAGSNGVADVLIEDSVISLSGDMSVIGRTLVVHEKEDDLGKGGNDESTKTG
+NAGSRLACGVIGISP
>gi|74136167|_Macaca_mulatta
MAMKAVCVLKGDSPVQGTINFEQKESNGPVKVWGSITGLTEGLHGFHVHQFGDNTQGCTSAGPHFNPLSR
+QHGGPKDEERHVGDLGNVTAGKDGVAKVSFEDSVISLSGDHSIIGRTLVVHEKADDLGKGGNEESKKTG
+NAGGRLACGVIGIAQ
>gi|84579183|_Macaca_fascicularis
MAMKAVCVLKGDSPVQGTINFEQKESNGPVKVWGSITGLTEGLHGYHVHQFGDNTQGCTSAGPHFNPLSR
+QHGGPKDEERHVGDLGNVTAGKDGVAKVSFEDSVISLSGDHSIIGRTLVVHEKADDLGKGGNEESKKTG
+NAGGRLACGVIGIAH
>gi|197102620|_Pongo_abelii
MATKAVCVLKGDSPVKGIINFEQKERNGPVKVWGSIEGLTEGLHGFHVHEFGDNTVGCTSAGPHFNPLSR
+KHGGPKDEERHVGDLGNVTADKDGVVSVSIEDSVISLSGDHCIIGRTLVVHEKADDLGKGGNEESTKTG
+NAGSRLACGVIGIAQ
>gi|223633904|_Ovis_aries
MATKAVCVLKGDGPVQGTIRFEAKGD--KVVVTGSITGLTEGDHGFHVHQFGDNTQGCTSAGPHFNPLSK
+KHGGPKDEERHVGDLGNVKADKNGVAIVDIVDPLISLSGEYSIIGRTMVVHERPDDLGRGGNEESTKTG
+NAGGRLACGVIGIAP
>gi|194672519|_Bos_taurus
MATKAVCVLKGDGPVQGTIHFEAKGN--TVVVTGSITGLTEGDHGFHVHQFGDNTQGCTSAGPHFNPLSK
+KHSGPKDEERHVGDLGNVTADKNGVAVVDIVDSLISLSGEYSIIGRTMVVHEKPDDLGRGGNEESTKTG
+NAGSRLACGVIGIAK
>gi|2660692|_Cervus_elaphus
MATKAVCVMKGDGPVQGTIRFEAKGN--TVVVTGSITGLTEGDHGFHVHQFGDNTQGCTSAGPHFNPLSK
+KHGGPKDEERHVGDLGNVTADKNGVAKVDIVDSLISLSGEHSIIGRTMVVHEKPDDLGRGGNEESTKTG
+NARNRLACGVIGIAQ
>gi|39578718|_Cavia_porcellus
-ATKAVCVLKGDGPVQGIIHFEQKAN-GPVVVKGRITGLVEGKHGFHVHEFGDNTQGCTSAGPHFNPLSK
+KHGGPQDEERHVGDLGNVTAGADGVANVSIEDSLISLSGANSIIGRTMVVHEKPDDLGKGGNEESTKTG
+NAGSRLACGVIGIAQ
>gi|15082144|_Sus_scrofa
---KAVCVLKGDGPVQGTIYFELKGE-KTVLVTGTIKGLAEGDHGFHVHQFGDNTQGCTSAGPHFNPESK
+KHGGPKDQERHVGDLGNVTAGKDGVATVYIEDSVIALSGDHSIIGRTMVVHEKPDDLGRGGNEESTKTG
+NAGSRLACGVIG---
>gi|281348263|_Ailuropoda_melanoleuca
--------------------------------------------------------GCTSAGPHFNPLSK
+KHGGPKDEERHVGDLGNVTAGKDGVATVSLEDSLIALSGDHSIIGRTMVVHEKRDDLGKGGNEESTQTG
+NAGSRLACGVIGIAK
>gi|8394328|_Rattus_norvegicus
MAMKAVCVLKGDGPVQGVIHFEQKASGEPVVVSGQITGLTEGEHGFHVHQYGDNTQGCTTAGPHFNPHSK
+KHGGPADEERHVGDLGNVAAGKDGVANVSIEDRVISLSGEHSIIGRTMVVHEKQDDLGKGGNEESTKTG
+NAGSRLACGVIGIAQ
>gi|45597447|_Mus_musculus
MAMKAVCVLKGDGPVQGTIHFEQKASGEPVVLSGQITGLTEGQHGFHVHQYGDNTQGCTSAGPHFNPHSK
+KHGGPADEERHVGDLGNVTAGKDGVANVSIEDRVISLSGEHSIIGRTMVVHEKQDDLGKGGNEESTKTG
+NAGSRLACGVIGIAQ
>gi|55925004|_Mus_spretus
------------------------------------------------HQYGDNTQGCTSAGPHFNPHS-
+---------------------------------------------------------------------
+---------------
END
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