
                            SEQNR documentation
                                      
   

CONTENTS

   1.0 SUMMARY 
   2.0 INPUTS & OUTPUTS 
   3.0 INPUT FILE FORMAT 
   4.0 OUTPUT FILE FORMAT 
   5.0 DATA FILES 
   6.0 USAGE 
   7.0 KNOWN BUGS & WARNINGS 
   8.0 NOTES 
   9.0 DESCRIPTION 
   10.0 ALGORITHM 
   11.0 RELATED APPLICATIONS 
   12.0 DIAGNOSTIC ERROR MESSAGES 
   13.0 AUTHORS 
   14.0 REFERENCES 

1.0 SUMMARY

   Removes redundancy from DHF files

2.0 INPUTS & OUTPUTS

   SEQNR removes redundancy from DHF files (domain hits files) or other
   files of sequences. A directory of DHF files (all sequences) is read
   and a directory of new DHF files (non-redundant sequences) plus
   (optionally) a second directory of DHF files (redundant sequences) is
   written. Optionally, up to two further directories of filter sequences
   may be read: these are considered in the redundancy calculation but
   never appear in the output files. Typically, one of the further
   directories contains DHF files each with a single sequence and the
   other DAF files (domain alignment files) each containing a sequence
   alignment, but any sequence(s) may be given. Each filter directory
   must contain a file for each file in main input directory and the
   files must have the same base name. For example, sequences from
   "family.dhf" and "family.daf" are considered for the input DHF file
   "family.hits".
   Redundancy is removed at either (i) a user-defined threshold of
   sequence similarity or (ii) a user-defined range of threshold sequence
   similarity. Files of sequences in any supported format may be read and
   written (not just DHF or DAF files). A log file is also written.
   The path for all files (input and output) are specified by the user.
   The file extensions are set in the ACD file. The name of the log file
   is set by the user.

3.0 INPUT FILE FORMAT

   The format of the domain hits file is described in SEQSEARCH
   documentation.
   The format of the domain alignment file is described in DOMAINALIGN
   documentation.
   If other sequences or sequence sets (aligned or unaligned) are used as
   input, all of the common file formats are supported.

4.0 OUTPUT FILE FORMAT

   The format of the domain hits file is described in SEQSEARCH
   documentation.

  Output files for usage example

  File: seqnr.log

//
/homes/user/test/qa/seqfraggle-keep/54894.dhf
//
/homes/user/test/qa/seqfraggle-keep/55074.dhf

  Directory: hitsnr

   This directory contains output files, for example 54894.dhf and
   55074.dhf.

  File: hitsnr/54894.dhf

> Q9YBD5^.^1^95^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate c
arbamoyltransferase, Regulatory-chain, N-terminal domain^.^55.30^0.000e+00^2.00
0e-11
VRKIRSGVVIDHIPPGRAFTMLKALGLLPPRGYRWRIAVVINAESSKLGRKDILKIEGYKPRQRDLEVLGIIAPGATFN
VIEDYKVVEKVKLKLP
> Q97FS4^.^1^90^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate c
arbamoyltransferase, Regulatory-chain, N-terminal domain^.^42.60^0.000e+00^1.00
0e-07
INSIKNGIVIDHIKAGHGIKIYNYLKLGEAEFPTALIMNAISKKNKAKDIIKIENVMDLDLAVLGFLDPNITVNIIEDE
KIRQKIQLKLP
> Q7MX57^.^1^92^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate c
arbamoyltransferase, Regulatory-chain, N-terminal domain^.^72.70^0.000e+00^1.00
0e-16
VAAIRNGIVIDHIPPTKLFKVATLLQLDDLDKRITIGNNLRSRSHGSKGVIKIEDKTFEEEELNRIALIAPNVRLNIIR
DYEVVEKRQVEVP
> P96111^.^1^98^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate c
arbamoyltransferase, Regulatory-chain, N-terminal domain^.^42.20^0.000e+00^1.00
0e-07
GIKPIENGTVIDHIAKGKTPEEIYSTILKIRKILRLYDVDSADGIFRSSDGSFKGYISLPDRYLSKKEIKKLSAISPNT
TVNIIKNSTVVEKYRIKLP

  File: hitsnr/55074.dhf

> Q08462^.^1^167^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase c
atalytic domain^.^49.70^0.000e+00^3.000e-09
DCVCVMFASIPDFKEFYTESDVNKEGLECLRLLNEIIADFDDLLSKPKFSGVEKIKTIGSTYMAATGLSAVPSQEHSQE
PERQYMHIGTMVEFAFALVGKLDAINKHSFNDFKLRVGINHGPVIAGVIGAQKPQYDIWGNTVNVASRMDSTGVLDKIQ
VTEETSLVL
> Q03101^.^1^149^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase c
atalytic domain^.^70.90^0.000e+00^1.000e-15
NNACVFFLDIAGFTRFSSIHSPEQVIQVLIKIFNSMDLLCAKHGIEKIKTIGDAYMATCGIFPKCDDIRHNTYKMLGFA
MDVLEFIPKEMSFHLGLQVRVGIHCGPVISGVISGYAKPHFDVWGDTVNVASRMESTGIAGQIHVSDRVY
> Q02153^.^1^165^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase c
atalytic domain^.^75.90^0.000e+00^4.000e-17
HKRPVPAKRYDNVTILFSGIVGFNAFCSKHASGEGAMKIVNLLNDLYTRFDTLTDSRKNPFVYKVETVGDKYMTVSGLP
EPCIHHARSICHLALDMMEIAGQVQVDGESVQITIGIHTGEVVTGVIGQRMPRYCLFGNTVNLTSRTETTGEKGKINVS
EYTYRCL
> P46197^.^1^168^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase c
atalytic domain^.^84.40^0.000e+00^1.000e-19
VQAEAFDSVTIYFSDIVGFTALSAESTPMQVVTLLNDLYTCFDAIIDNFDVYKVETIGDAYMVVSGLPGRNGQRHAPEI
ARMALALLDAVSSFRIRHRPHDQLRLRIGVHTGPVCAGVVGLKMPRYCLFGDTVNTASRMESNGQALKIHVSSTTKDAL
DELGCFQLEL
> P40137^.^1^139^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase c
atalytic domain^.^50.90^0.000e+00^1.000e-09
VTLLFADIRDFTSLSERLRPEQVVTLLNEYYGRMVEVVFRHGGTLDKFIGDALMVYFGAPIADPAHARRGVQCALDMVQ
ELETVNALRSARGEPCLRIGVGVHTGPAVLGNIGSATRRLEYTAIGDTVNLASRIESLTK
> P23466^.^1^154^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase c
atalytic domain^.^55.90^0.000e+00^4.000e-11
PTGNVAIVFTDIKNSTFLWELFPDAMRAAIKTHNDIMRRQLRIYGGYEVKTEGDAFMVAFPTPTSALVWCLSVQLKLLE
AEWPEEITSIQDGCLITDNSGTKVYLGLSVRMGVHWGCPVPEIDLVTQRMDYLGPVVNKAARVSGVADGGQITLS
> O30820^.^1^149^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase c
atalytic domain^.^80.20^0.000e+00^2.000e-18
DEASVLFADIVGFTERASSTAPADLVRFLDRLYSAFDELVDQHGLEKIKVSGDSYMVVSGVPRPRPDHTQALADFALDM
TNVAAQLKDPRGNPVPLRVGLATGPVVAGVVGSRRFFYDVWGDAVNVASRMESTDSVGQIQVPDEVYERL

  Directory: hitsred

   This directory contains output files, for example 54894.dhf and
   55074.dhf.

  File: hitsred/54894.dhf

> Q9UX07^.^1^93^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate c
arbamoyltransferase, Regulatory-chain, N-terminal domain^.^59.20^0.000e+00^1.00
0e-12
VSKIRNGTVIDHIPAGRALAVLRILGIRGSEGYRVALVMNVESKKIGRKDIVKIEDRVIDEKEASLITLIAPSATINII
RDYVVTEKRHLEVP
> Q9KP65^.^1^92^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate c
arbamoyltransferase, Regulatory-chain, N-terminal domain^.^119.00^0.000e+00^9.0
00e-31
VEAIKNGTVIDHIPAKVGIKVLKLFDMHNSAQRVTIGLNLPSSALGSKDLLKIENVFISEAQANKLALYAPHATVNQIE
NYEVVKKLALQLP
> Q9K1K9^.^1^92^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate c
arbamoyltransferase, Regulatory-chain, N-terminal domain^.^91.90^0.000e+00^2.00
0e-22
VEAIEKGTVIDHIPAGRGLTILRQFKLLHYGNAVTVGFNLPSKTQGSKDIIKIKGVCLDDKAADRLALFAPEAVVNTID
NFKVVQKRHLNLP
> Q9JWY6^.^1^92^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate c
arbamoyltransferase, Regulatory-chain, N-terminal domain^.^90.40^0.000e+00^5.00
0e-22
VEAIEKGTVIDHIPAGRGLTILRQFKLLHYGNAVTVGFNLPSKTQGSKDIIKIKGVCLDDKAADRLALFAPEAVVNTID
HFKVVQKRHLNLP
> Q9HKM3^.^1^93^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate c
arbamoyltransferase, Regulatory-chain, N-terminal domain^.^71.90^0.000e+00^2.00
0e-16
ISKIRDGTVIDHVPSGKGIRVIGVLGVHEDVNYTVSLAIHVPSNKMGFKDVIKIENRFLDRNELDMISLIAPNATISII
KNYEISEKFQVELP
> Q9HHN3^.^1^93^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate c
arbamoyltransferase, Regulatory-chain, N-terminal domain^.^70.40^0.000e+00^4.00
0e-16
VSKIQAGTVIDHIPAGQALQVLQILGTNGASDDQITVGMNVTSERHHRKDIVKIEGRELSQDEVDVLSLIAPDATINIV
RDYEVDEKRRVDRP
> Q97B28^.^1^93^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate c
arbamoyltransferase, Regulatory-chain, N-terminal domain^.^71.90^0.000e+00^2.00
0e-16
ISKIKDGTVIDHIPSGKALRVLSILGIRDDVDYTVSVGMHVPSSKMEYKDVIKIENRSLDKNELDMISLTAPNATISII
KNYEISEKFKVELP
> Q970X3^.^1^91^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate c
arbamoyltransferase, Regulatory-chain, N-terminal domain^.^71.10^0.000e+00^3.00
0e-16
VSKIKNGTVIDHIPAGRALAVLRILKIAEGYRIALVMNVESKKMGKKDIVKIENKEVDEKEANLITLIAPTATINIIRD
YEVVEKKKLKIP
> Q8ZTG2^.^1^93^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate c
arbamoyltransferase, Regulatory-chain, N-terminal domain^.^58.00^0.000e+00^3.00
0e-12
VSKIENGTVIDHIPAGRALTVLRILGISGKEGLRVALVMNVESKKLGKKDIVKIEGRELTPEEVNIISAVAPTATINII
RNFAVVKKFKVTPP
> Q8ZB38^.^1^92^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate c
arbamoyltransferase, Regulatory-chain, N-terminal domain^.^143.00^0.000e+00^3.0
00e-38
VEAIKCGTVIDHIPAQIGFKLLSLFKLTATDQRITIGLNLPSKRSGRKDLIKIENTFLTEQQANQLAMYAPDATVNRID
NYEVVKKLTLSLP
> Q8Z130^.^1^92^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate c
arbamoyltransferase, Regulatory-chain, N-terminal domain^.^167.00^0.000e+00^4.2
04e-45
VEAIKCGTVIDHIPAQVGFKLLSLFKLTETDQRITIGLNLPSGEMGRKDLIKIENTFLTDEQVNQLALYAPQATVNRID
NYDVVGKSRPSLP
> Q8U374^.^1^94^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate c
arbamoyltransferase, Regulatory-chain, N-terminal domain^.^82.70^0.000e+00^1.00
0e-19
VSAIKEGTVIDHIPAGKGLKVIQILGLGELKNGGAVLLAMNVPSKKLGRKDIVKVEGKFLSEEEVNKIALVAPTATVNI
IREYKVVEKFKVEIP
> Q8TVB1^.^1^92^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate c
arbamoyltransferase, Regulatory-chain, N-terminal domain^.^65.40^0.000e+00^2.00
0e-14
VKRIEMGTVLDHLPPGTAPQIMRILDIDPTETTLLVAINVESSKMGRKDILKIEGKILSEEEANKVALVAPNATVNIVR
DYSVAEKFQVKPP
> Q8THL3^.^1^92^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate c
arbamoyltransferase, Regulatory-chain, N-terminal domain^.^66.50^0.000e+00^7.00
0e-15
IQAIENGTVIDHITAGQALNVLRILRISSAFRATVSFVMNAPGARGKKDVVKIEGKELSVEELNRIALISPKATINIIR
DFEVVQKNKVVLP
> Q8PXK6^.^1^92^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate c
arbamoyltransferase, Regulatory-chain, N-terminal domain^.^60.70^0.000e+00^4.00
0e-13
VQAIESGTVIDHIKSGQALNVLRILGISSAFRATISFVMNAPGAGGKKDVVKIEGKELSVEELNRIALISPKATINIIR
DFVVVQKNNVVLP
> Q8K9H8^.^1^92^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate c
arbamoyltransferase, Regulatory-chain, N-terminal domain^.^135.00^0.000e+00^1.0
00e-35
VEAIKSGSVIDHIPAHIGFKLLSLFRFTETEKRITIGLNLPSQKLDKKDIIKIENTFLSDDQINQLAIYAPCATVNYIE
KYNLVGKIFPSLP
> Q8DCF7^.^1^92^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate c
arbamoyltransferase, Regulatory-chain, N-terminal domain^.^116.00^0.000e+00^5.0
00e-30
VEAIKNGTVIDHIPAQVGIKVLKLFDMHNSSQRVTIGLNLPSSALGNKDLLKIENVFINEEQASKLALYAPHATVNQIE
DYQVVKKLALELP
> Q8D1W6^.^1^92^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate c
arbamoyltransferase, Regulatory-chain, N-terminal domain^.^113.00^0.000e+00^5.0
00e-29
VEAIFGGTVIDHIPAQVGLKLLSLFKWLHTKERITMGLNLPSNQQKKKDLIKLENVLLNEDQANQLSIYAPLATVNQIK
NYIVIKKQKLKLP
> Q8A9S4^.^1^92^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate c
arbamoyltransferase, Regulatory-chain, N-terminal domain^.^57.30^0.000e+00^4.00
0e-12
VAALKNGTVIDHIPSEKLFTVVQLLGVEQMKCNITIGFNLDSKKLGKKGIIKIADKFFCDEEINRISVVAPYVKLNIIR
DYEVVEKKEVRMP
> Q891I9^.^1^91^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate c
arbamoyltransferase, Regulatory-chain, N-terminal domain^.^46.10^0.000e+00^1.00
0e-08
ITSIKDGIVIDHIKSGYGIKIFNYLNLKNVEYSVALIMNVFSSKLGKKDIIKIANKEIDIDFTVLGLIDPTITINIIED
EKIKEKLNLELP
> Q87LF7^.^1^92^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate c
arbamoyltransferase, Regulatory-chain, N-terminal domain^.^121.00^0.000e+00^2.0
00e-31
VEAIKNGTVIDHIPAQIGIKVLKLFDMHNSSQRVTIGLNLPSSALGHKDLLKIENVFINEEQASKLALYAPHATVNQIE
NYEVVKKLALELP
> Q83IL8^.^1^92^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate c
arbamoyltransferase, Regulatory-chain, N-terminal domain^.^174.00^0.000e+00^0.0
00e+00
VEAIKRGTVIDHIPAQIGFKLLSLFKLTETDQRITIGLNLPSGEMGRKDLIKIENTFLSEEQVDQLALYAPQATVNRID
NYEVVGKSRPSLP
> Q7P144^.^1^92^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate c
arbamoyltransferase, Regulatory-chain, N-terminal domain^.^117.00^0.000e+00^3.0
00e-30
VEALKQGTVIDHIPAGEGVKILRLFKLTETGERVTVGLNLVSRHMGSKDLIKVENVALTEEQANELALFAPKATVNVID
NFEVVKKHKLTLP
> Q7MZ14^.^1^92^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate c
arbamoyltransferase, Regulatory-chain, N-terminal domain^.^139.00^0.000e+00^6.0
00e-37
VEAIRCGTVIDHIPAQVGFKLLSLFKLTETDQRITIGLNLPSNRLGKKDLIKIENTFLTEQQANQLAMYAPNATVNCIE
NYEVVKKLPINLP
> Q7MHF0^.^1^92^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate c
arbamoyltransferase, Regulatory-chain, N-terminal domain^.^116.00^0.000e+00^5.0
00e-30
VEAIKNGTVIDHIPAQVGIKVLKLFDMHNSSQRVTIGLNLPSSALGNKDLLKIENVFINEEQASKLALYAPHATVNQIE
DYQVVKKLALELP
> Q58801^.^1^91^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate c
arbamoyltransferase, Regulatory-chain, N-terminal domain^.^53.40^0.000e+00^6.00
0e-11
VKKITNGTVIDHIDAGKALMVFKVLNVPKETSVMIAINVPSKKKGKKDILKIEGIELKKEDVDKISLISPDVTINIIRN
GKVVEKLKPQIP
> P96175^.^1^92^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate c
arbamoyltransferase, Regulatory-chain, N-terminal domain^.^98.10^0.000e+00^2.00
0e-24
VEAICNGYVIDHIPSGQGVKILRLFSLTDTKQRVTVGFNLPSHDGTTKDLIKVENTEITKSQANQLALLAPNATVNIIE
NFKVTDKHSLALP
> P77919^.^1^94^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate c
arbamoyltransferase, Regulatory-chain, N-terminal domain^.^83.80^0.000e+00^4.00
0e-20
VSAIKEGTVIDHIPAGKGLKVIEILKLGKLTNGGAVLLAMNVPSKKLGRKDIVKVEGRFLSEEEVNKIALVAPNATVNI
IRDYKVVEKFKVEVP
> P74766^.^1^93^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate c
arbamoyltransferase, Regulatory-chain, N-terminal domain^.^67.30^0.000e+00^4.00
0e-15
VSKIKNGTVIDHIPAGRAFAVLNVLGIKGHEGFRIALVINVDSKKMGKKDIVKIEDKEISDTEANLITLIAPTATINIV
REYEVVKKTKLEVP
> P57451^.^1^92^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate c
arbamoyltransferase, Regulatory-chain, N-terminal domain^.^131.00^0.000e+00^2.0
00e-34
VEAIKSGSVIDHIPEYIGFKLLSLFRFTETEKRITIGLNLPSKKLGRKDIIKIENTFLSDEQINQLAIYAPHATVNYIN
EYNLVRKVFPTLP
> P19936^.^1^92^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate c
arbamoyltransferase, Regulatory-chain, N-terminal domain^.^147.00^0.000e+00^4.0
00e-39
VEAIKCGTVIDHIPAQIGFKLLTLFKLTATDQRITIGLNLPSNELGRKDLIKIENTFLTEQQANQLAMYAPKATVNRID
NYEVVRKLTLSLP
> P08421^.^1^92^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate c
arbamoyltransferase, Regulatory-chain, N-terminal domain^.^168.00^0.000e+00^1.4
01e-45
VEAIKCGTVIDHIPAQVGFKLLSLFKLTETDQRITIGLNLPSGEMGRKDLIKIENTFLTEEQVNQLALYAPQATVNRID
NYDVVGKSRPSLP
> P00478^.^1^92^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate c
arbamoyltransferase, Regulatory-chain, N-terminal domain^.^175.00^0.000e+00^0.0
00e+00
VEAIKRGTVIDHIPAQIGFKLLSLFKLTETDQRITIGLNLPSGEMGRKDLIKIENTFLSEDQVDQLALYAPQATVNRID
NYEVVGKSRPSLP
> O58452^.^1^94^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate c
arbamoyltransferase, Regulatory-chain, N-terminal domain^.^85.40^0.000e+00^2.00
0e-20
VSAIKEGTVIDHIPAGKGLKVIEILGLSKLSNGGSVLLAMNVPSKKLGRKDIVKVEGKFLSEEEVNKIALVAPTATVNI
IRNYKVVEKFKVEVP
> O30129^.^1^93^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate c
arbamoyltransferase, Regulatory-chain, N-terminal domain^.^70.40^0.000e+00^5.00
0e-16
VSKIKEGTVIDHINAGKALLVLKILKIQPGTDLTVSMAMNVPSSKMGKKDIVKVEGMFIRDEELNKIALISPNATINLI
RDYEIERKFKVSPP
> O26938^.^1^91^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate c
arbamoyltransferase, Regulatory-chain, N-terminal domain^.^73.80^0.000e+00^4.00
0e-17
VKPIKNGTVIDHITANRSLNVLNILGLPDGRSKVTVAMNMDSSQLGSKDIVKIENRELKPSEVDQIALIAPRATINIVR
DYKIVEKAKVRL

  File: hitsred/55074.dhf

> Q9WVI4^.^1^149^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase c
atalytic domain^.^84.40^0.000e+00^1.000e-19
DDVTMLFSDIVGFTAICAQCTPMQVISMLNELYTRFDHQCGFLDIYKVETIGDAYCVASGLHRKSLCHAKPIALMALKM
MELSEEVLTPDGRPIQMRIGIHSGSVLAGVVGVRMPRYCLFGNNVTLASKFESGSHPRRINISPTTYQLL
> Q9ERL9^.^1^152^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase c
atalytic domain^.^72.10^0.000e+00^5.000e-16
VTMLFSDIVGFTAICSQCSPLQVITMLNALYTRFDQQCGELDVYKVETIGDAYCVAGGLHRESDTHAVQIALMALKMME
LSNEVMSPHGEPIKMRIGLHSGSVFAGVVGVKMPRYCLFGNNVTLANKFESCSVPRKINVSPTTYRLLKDCPG
> Q9DGG6^.^1^181^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase c
atalytic domain^.^142.00^0.000e+00^4.000e-37
EQVSILFADIVGFTKMSANKSAHALVGLLNDLFGRFDRLCEDTKCEKISTLGDCYYCVAGCPEPRADHAYCCIEMGLGM
IKAIEQFCQEKKEMVNMRVGVHTGTVLCGILGMRRFKFDVWSNDVNLANLMEQLGVAGKVHISEATAKYLDDRYEMEDG
KVTERVGQSAVADQLKGLKTYLI
> Q99396^.^1^212^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase c
atalytic domain^.^192.00^0.000e+00^0.000e+00
KELADPVTLIFTDIESSTAQWATQPELMPDAVATHHSMVRSLIENYDCYEVKTVGDSFMIACKSPFAAVQLAQELQLRF
LRLDWGTTVFDEFYREFEERHAEEGDGKYKPPTARLDPEVYRQLWNGLRVRVGIHTGLCDIRYDEVTKGYDYYGQTANT
AARTESVGNGGQVLMTCETYHSLSTAERSQFDVTPLGGVPLRGVSEPVEVYQLN
> Q99280^.^1^216^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase c
atalytic domain^.^218.00^0.000e+00^0.000e+00
NDSAPKEPTGPVTLIFTDIESSTALWAAHPDLMPDAVATHHRLIRSLITRYECYEVKTVGDSFMIASKSPFAAVQLAQE
LQLRFLRLDWETNALDESYREFEEQRAEGECEYTPPTAHMDPEVYSRLWNGLRVRVGIHTGLCDIRYDEVTKGYDYYGR
TSNMAARTESVANGGQVLMTHAAYMSLSGEDRNQLDVTTLGATVLRGVPEPVRMYQLN
> Q99279^.^1^218^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase c
atalytic domain^.^258.00^0.000e+00^0.000e+00
NNNRAPKEPTDPVTLIFTDIESSTALWAAHPDLMPDAVAAHHRMVRSLIGRYKCYEVKTVGDSFMIASKSPFAAVQLAQ
ELQLCFLHHDWGTNALDDSYREFEEQRAEGECEYTPPTAHMDPEVYSRLWNGLRVRVGIHTGLCDIIRHDEVTKGYDYY
GRTPNMAARTESVANGGQVLMTHAAYMSLSAEDRKQIDVTALGDVALRGVSDPVKMYQLN
> Q91WF3^.^1^165^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase c
atalytic domain^.^54.30^0.000e+00^1.000e-10
VCVLFASVPDFKEFYSESNINHEGLECLRLLNEIIADFDELLSKPKFSGVEKIKTIGSTYMAATGLNATSGQDTQQDSE
RSCSHLGTMVEFAVALGSKLGVINKHSFNNFRLRVGLNHGPVVAGVIGAQKPQYDIWGNTVNVASRMESTGVLGKIQVT
EETARAL
> Q91WF3^.^1^158^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase c
atalytic domain^.^160.00^0.000e+00^1.001e-42
FHSLYVKRHQGVSVLYADIVGFTRLASECSPKELVLMLNELFGKFDQIAKEHECMRIKILGDCYYCVSGLPLSLPDHAI
NCVRMGLDMCRAIRKLRVATGVDINMRVGVHSGSVLCGVIGLQKWQYDVWSHDVTLANHMEAGGVPGRVHITGATLALL
> Q8VHH7^.^1^186^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase c
atalytic domain^.^178.00^0.000e+00^0.000e+00
FNTMYMYRHENVSILFADIVGFTQLSSACSAQELVKLLNELFARFDKLAAKYHQLRIKILGDCYYCICGLPDYREDHAV
CSILMGLAMVEAISYVREKTKTGVDMRVGVHTGTVLGGVLGQKRWQYDVWSTDVTVANKMEAGGIPGRVHISQSTMDCL
KGEFDVEPGDGGSRCDYLDEKGIETYLI
> Q8NFM4^.^1^161^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase c
atalytic domain^.^54.70^0.000e+00^9.000e-11
VCVLFASVPDFKEFYSESNINHEGLECLRLLNEIIADFDELLSKPKFSGVEKIKTIGSTYMAATGLNATSGQDAQQDAE
RSCSHLGTMVEFAVALGSKLDVINKHSFNNFRLRVGLNHGPVVAGVIGAQKPQYDIWGNTVNVASRMESTGVLGKIQVT
EET
> Q8NFM4^.^1^158^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase c
atalytic domain^.^160.00^0.000e+00^1.001e-42
FHSLYVKRHQGVSVLYADIVGFTRLASECSPKELVLMLNELFGKFDQIAKEHECMRIKILGDCYYCVSGLPLSLPDHAI
NCVRMGLDMCRAIRKLRAATGVDINMRVGVHSGSVLCGVIGLQKWQYDVWSHDVTLANHMEAGGVPGRVHITGATLALL
> Q29450^.^1^186^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase c
atalytic domain^.^179.00^0.000e+00^0.000e+00
FHNLYVKRHQNVSILYADIVGFTRLASDCSPKELVVVLNELFGKFDQIAKANECMRIKILGDCYYCVSGLPVSLPNHAR
NCVKMGLDMCEAIKQVREATGVDISMRVGIHSGNVLCGVIGLRKWQYDVWSHDVSLANRMEAAGVPGRVHITEATLKHL
DKAYEVEDGHGQQRDPYLKEMNIRTYLV
> Q27675^.^1^217^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase c
atalytic domain^.^167.00^0.000e+00^5.605e-45
NNDAAPKDGDEPVTLLFTDIESSTALWAALPQLMSDAIAAHHRVIRQLVKKYGCYEVKTIGDSFMIACRSAHSAVSLAC
EIQTKLLKHDWGTEALDRAYREFELARVDTLDDYEPPTARLSEEEYAALWCGLRVRVGIHTGLTDIRYDEVTKGYDYYG
DTSNMAARTEAVANGGQVVATEAAWWALSNDERAGIAHTAMGPQGLRGVPFAVEMFQLN
> Q26896^.^1^216^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase c
atalytic domain^.^195.00^0.000e+00^0.000e+00
NDSAPKEFTDPVTLIFTDIESSTALWAAHPGMMADAVATHHRLIRSLIALYGAYEVKTVGDSFMIACRSAFAAVELARD
LQLTLVHHDWGTVAIDESYRKFEEERAVEDSDYAPPTARLDSAVYCKLWNGLRVRAGIHTGLCDIAHDEVTKGYDYYGR
TPNLAARTESAANGGQVLVTGATYYSLSVAERARLDATPIGPVPLRGVPEPVEMYQLN
> Q26721^.^1^206^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase c
atalytic domain^.^223.00^0.000e+00^0.000e+00
PVTLIFTDIESSTALWAAHPEVMPDAVATHHRLIRTLISKYECYEVKTVGDSFMIASKSPFAAVQLAQELQLCFLHHDW
GTNAIDESYQQFEQQRAEDDSDYTPPTARLDPKVYSRLWNGLRVRVGIHTGLCDIRRDEVTKGYDYYGRTSNMAARTES
VANGGQVLMTHAAYMSLSAEERQQIDVTALGDVPLRGVPKPVEMYRLN
> Q25263^.^1^217^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase c
atalytic domain^.^166.00^0.000e+00^1.962e-44
NNDAAPKDGDEPVTLLFTDIESSTALWAALPQLMSDAIAAHHRVIRQLVKKYGCYEVKTIGDSFMIACRSAHSAVSLAC
EIQTKLLKHDWGTEALDRAYREFELARVDTLDDYEPPTARLSEEEYAALWCGLRVRVGIHTGLTDIRYDEVTRGYDYYG
DTSNMAARTEAVANGGQVVATEAAWWALSNDERAGIAHTAMGPQGLRGVPFAVEMFQLN
> Q09435^.^1^161^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase c
atalytic domain^.^79.80^0.000e+00^2.000e-18
DSVTVFFSDVVKFTILASKCSPFQTVNLLNDLYSNFDTIIEQHGVYKVESIGDGYLCVSGLPTRNGYAHIKQIVDMSLK
FMEYCKSFNIPHLPRENVELRIGVNSGPCVAGVVGLSMPRYCLFGDTVNTASRMESNGKPSLIHLTNDAHSLLTTHYPN
QYE
> Q08828^.^1^186^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase c
atalytic domain^.^217.00^0.000e+00^0.000e+00
FHKIYIQRHDNVSILFADIVGFTGLASQCTAQELVKLLNELFGKFDELATENHCRRIKILGDCYYCVSGLTQPKTDHAH
CCVEMGLDMIDTITSVAEATEVDLNMRVGLHTGRVLCGVLGLRKWQYDVWSNDVTLANVMEAAGLPGKVHITKTTLACL
NGDYEVEPGYGHERNSFLKTHNIETFFI
> Q08462^.^1^186^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase c
atalytic domain^.^180.00^0.000e+00^0.000e+00
FHNLYVKRHTNVSILYADIVGFTRLASDCSPGELVHMLNELFGKFDQIAKENECMRIKILGDCYYCVSGLPISLPNHAK
NCVKMGLDMCEAIKKVRDATGVDINMRVGVHSGNVLCGVIGLQKWQYDVWSHDVTLANHMEAGGVPGRVHISSVTLEHL
NGAYKVEEGDGDIRDPYLKQHLVKTYFV
> Q07553^.^1^152^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase c
atalytic domain^.^82.50^0.000e+00^4.000e-19
DCVTILFSDIVGFTELCTTSTPFEVVEMLNDWYTCCDSIISNYDVYKVETIGDAYMVVSGLPLQNGSRHAGEIASLALH
LLETVGNLKIRHKPTETVQLRIGVHSGPCAAGVVGQKMPRYCLFGDTVNTASRMESTGDSMRIHISEATYQLL
> Q07093^.^1^158^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase c
atalytic domain^.^65.50^0.000e+00^5.000e-14
VTILFSDIVGFTSICSRATPFMVISMLEGLYKDFDEFCDFFDVYKVETIGDAYCVASGLHRASIYDAHRCLDGLKMIDA
CSKHITHDGEQIKMRIGLHTGTVLAGVVGRKMPRYCLFGHSVTIANKFESGSEALKINVSPTTKDWLTKHEGFEFELQP
> Q04400^.^1^189^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase c
atalytic domain^.^299.00^0.000e+00^0.000e+00
MMFHKIYIQKHDNVSILFADIEGFTSLASQCTAQELVMTLNELFARFDKLAAENHCLRIKILGDCYYCVSGLPEARADH
AHCCVEMGMDMIEAISSVREVTGVNVNMRVGIHSGRVHCGVLGLRKWQFDVWSNDVTLANHMEAGGKAGRIHITKATLN
YLNGDYEVEPGCGGERNAYLKEHSIETFLIL
> Q04400^.^1^159^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase c
atalytic domain^.^55.10^0.000e+00^7.000e-11
VAVMFASIANFSEFYVELEANNEGVECLRLLNEIIADFDEIISEDRFRQLEKIKTIGSTYMAASGLNDSTYDKAGKTHI
KALADFAMKLMDQMKYINEHSFNNFQMKIGLNIGPVVAGVIGARKPQYDIWGNTVNVASRMDSTGVPDRIQVTTDMYQV
L
> Q03343^.^1^189^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase c
atalytic domain^.^285.00^0.000e+00^0.000e+00
MMFHKIYIQKHDNVSILFADIEGFTSLASQCTAQELVMTLNELFARFDKLAAENHCLRIKILGDCYYCVSGLPEARADH
AHCCVEMGVDMIEAISLVREVTGVNVNMRVGIHSGRVHCGVLGLRKWQFDVWSNDVTLANHMEAGGRAGRIHITRATLQ
YLNGDYEVEPGRGGERNGYLKEQCIETFLIL
> Q03343^.^1^159^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase c
atalytic domain^.^55.90^0.000e+00^3.000e-11
VAVMFASIANFSEFYVELEANNEGVECLRLLNEIIADFDEIISEERFRQLEKIKTIGSTYMAASGLNASTYDQVGRSHI
TALADYAMRLMEQMKHINEHSFNNFQMKIGLNMGPVVAGVIGARKPQYDIWGNTVNVSSRMDSTGVPDRIQVTTDLYQV
L


  [Part of this file has been deleted for brevity]

DCVCVMFASIPDFKEFYTESDVNKEGLECLRLLNEIIADFDDLLSKPKFSGVEKIKTIGSTYMAATGLSAIPSQEHAQE
PERQYMHIGTMVEFAYALVGKLDAINKHSFNDFKLRVGINHGPVIAGVIGAQKPQYDIWGNTVNVASRMDSTGVLDKIQ
VTEET
> P26338^.^1^216^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase c
atalytic domain^.^233.00^0.000e+00^0.000e+00
NNLAPKELTDPVTLIFTDIESSTALWAAHPELMPDAVATHHRLIRSLIGRYGCYEVKTVGDSFMIASKSPFAAVQLAQE
LQLCFLHHDWGTNAIDESYQQLEQQRAEEDAKYTPPTARLDLKVYSRLWNGLRVRVGIHTGLCDIRRDEVTKGYDYYGR
TSNMAARTESVGNGGQVLMTTAAYMSLSAEEREQIDVTALGDVPLRGVAKPVEMYQLN
> P25092^.^1^150^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase c
atalytic domain^.^71.70^0.000e+00^6.000e-16
VTIYFSDIVGFTTICKYSTPMEVVDMLNDIYKSFDHIVDHHDVYKVETIGDAYMVASGLPKRNGNRHAIDIAKMALEIL
SFMGTFELEHLPGLPIWIRIGVHSGPCAAGVVGIKMPRYCLFGDTVNTASRMESTGLPLRIHVSGSTIAIL
> P23897^.^1^150^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase c
atalytic domain^.^71.70^0.000e+00^8.000e-16
VTIYFSDIVGFTTICKYSTPMEVVDMLNDIYKSFDQIVDHHDVYKVETIGDAYVVASGLPMRNGNRHAVDISKMALDIL
SFMGTFELEHLPGLPVWIRIGVHSGPCAAGVVGIKMPRYCLFGDTVNTASRMESTGLPLRIHMSSSTIAIL
> P22717^.^1^147^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase c
atalytic domain^.^63.20^0.000e+00^3.000e-13
TILFSDVVTFTNICAACEPIQIVNMLNSMYSKFDRLTSVHDVYKVETIGDAYMVVGGVPVPVESHAQRVANFALGMRIS
AKEVMNPVTGEPIQIRVGIHTGPVLAGVVGDKMPRYCLFGDTVNTASRMESHGLPSKVHLSPTAHRAL
> P21932^.^1^186^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase c
atalytic domain^.^178.00^0.000e+00^0.000e+00
FNTMYMYRHENVSILFADIVGFTQLSSACSAQELVKLLNELFARFDKLAAKYHQLRIKILGDCYYCICGLPDYREDHAV
CSILMGLAMVEAISYVREKTKTGVDMRVGVHTGTVLGGVLGQKRWQYDVWSTDVTVANKMEAGGIPGRVHISQSTMDCL
KGEFDVEPGDGGSRCDYLDEKGIETYLI
> P20595^.^1^165^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase c
atalytic domain^.^75.90^0.000e+00^4.000e-17
HKRPVPAKRYDNVTILFSGIVGFNAFCSKHASGEGAMKIVNLLNDLYTRFDTLTDSRKNPFVYKVETVGDKYMTVSGLP
EPCIHHARSICHLALDMMEIAGQVQVDGESVQITIGIHTGEVVTGVIGQRMPRYCLFGNTVNLTSRTETTGEKGKINVS
EYTYRCL
> P20594^.^1^168^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase c
atalytic domain^.^84.40^0.000e+00^1.000e-19
VQAEAFDSVTIYFSDIVGFTALSAESTPMQVVTLLNDLYTCFDAIIDNFDVYKVETIGDAYMVVSGLPGRNGQRHAPEI
ARMALALLDAVSSFRIRHRPHDQLRLRIGVHTGPVCAGVVGLKMPRYCLFGDTVNTASRMESNGQALKIHVSSTTKDAL
DELGCFQLEL
> P19754^.^1^186^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase c
atalytic domain^.^217.00^0.000e+00^0.000e+00
FHKIYIQRHDNVSILFADIVGFTGLASQCTAQELVKLLNELFGKFDELATENHCRRIKILGDCYYCVSGLTQPKTDHAH
CCVEMGLDMIDTITSVAEATEVDLNMRVGLHTGRVLCGVLGLRKWQYDVWSNDVTLANVMEAAGLPGKVHITKTTLACL
NGDYEVEPGHGHERNSFLKTHNIETFFI
> P19687^.^1^161^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase c
atalytic domain^.^77.10^0.000e+00^1.000e-17
AVQAKRFGNVTMLFSDIVGFTAICSQCSPLQVITMLNALYTRFDRQCGELDVYKVETIGDAYCVAGGLHKESDTHAVQI
ALMALKMMELSHEVVSPHGEPIKMRIGLHSGSVFAGVVGVKMPRYCLFGNNVTLANKFESCSVPRKINVSPTTYRLLKD
CPG
> P19686^.^1^160^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase c
atalytic domain^.^72.50^0.000e+00^4.000e-16
VQAKKFNEVTMLFSDIVGFTAICSQCSPLQVITMLNALYTRFDQQCGELDVYKVETIGDAYCVAGGLHRESDTHAVQIA
LMALKMMELSNEVMSPHGEPIKMRIGLHSGSVFAGVVGVKMPRYCLFGNNVTLANKFESCSVPRKINVSPTTYRLLKDC
PG
> P18910^.^1^168^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase c
atalytic domain^.^84.40^0.000e+00^1.000e-19
VQAEAFDSVTIYFSDIVGFTALSAESTPMQVVTLLNDLYTCFDAVIDNFDVYKVETIGDAYMVVSGLPVRNGQLHAREV
ARMALALLDAVRSFRIRHRPQEQLRLRIGIHTGPVCAGVVGLKMPRYCLFGDTVNTASRMESNGEALKIHLSSETKAVL
EEFDGFELEL
> P18293^.^1^168^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase c
atalytic domain^.^85.90^0.000e+00^4.000e-20
VQAEAFDSVTIYFSDIVGFTALSAESTPMQVVTLLNDLYTCFDAVIDNFDVYKVETIGDAYMVVSGLPVRNGQLHAREV
ARMALALLDAVRSFRIRHRPQEQLRLRIGIHTGPVCAGVVGLKMPRYCLFGDTVNTASRMESNGEALRIHLSSETKAVL
EEFDGFELEL
> P16068^.^1^165^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase c
atalytic domain^.^75.90^0.000e+00^4.000e-17
HKRPVPAKRYDNVTILFSGIVGFNAFCSKHASGEGAMKIVNLLNDLYTRFDTLTDSRKNPFVYKVETVGDKYMTVSGLP
EPCIHHARSICHLALDMMEIAGQVQVDGESVQITIGIHTGEVVTGVIGQRMPRYCLFGNTVNLTSRTETTGEKGKINVS
EYTYRCL
> P16067^.^1^168^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase c
atalytic domain^.^84.40^0.000e+00^1.000e-19
VQAEAFDSVTIYFSDIVGFTALSAESTPMQVVTLLNDLYTCFDAIIDNFDVYKVETIGDAYMVVSGLPGRNGQRHAPEI
ARMALALLDAVSSFRIRHRPHDQLRLRIGVHTGPVCAGVVGLKMPRYCLFGDTVNTASRMESNGQALKIHVSSTTKDAL
DELGCFQLEL
> P16066^.^1^168^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase c
atalytic domain^.^84.80^0.000e+00^7.000e-20
VQAEAFDSVTIYFSDIVGFTALSAESTPMQVVTLLNDLYTCFDAVIDNFDVYKVETIGDAYMVVSGLPVRNGRLHACEV
ARMALALLDAVRSFRIRHRPQEQLRLRIGIHTGPVCAGVVGLKMPRYCLFGDTVNTASRMESNGEALKIHLSSETKAVL
EEFGGFELEL
> P16065^.^1^143^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase c
atalytic domain^.^82.10^0.000e+00^5.000e-19
VSIFFSDIVGFTALSAASTPIQVVNLLNDLYTLFDAIISNYDVYKVETIGDAYMLVSGLPLRNGDRHAGQIASTAHHLL
ESVKGFIVPHKPEVFLKLRIGIHSGSCVAGVVGLTMPRYCLFGDTVNTASRMESNGLALRIHVS
> O95622^.^1^189^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase c
atalytic domain^.^301.00^0.000e+00^0.000e+00
MMFHKIYIQKHDNVSILFADIEGFTSLASQCTAQELVMTLNELFARFDKLAAENHCLRIKILGDCYYCVSGLPEARADH
AHCCVEMGMDMIEAISLVREVTGVNVNMRVGIHSGRVHCGVLGLRKWQFDVWSNDVTLANHMEAGGKAGRIHITKATLN
YLNGDYEVEPGCGGERNAYLKEHSIETFLIL
> O95622^.^1^159^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase c
atalytic domain^.^55.10^0.000e+00^7.000e-11
VAVMFASIANFSEFYVELEANNEGVECLRLLNEIIADFDEIISEDRFRQLEKIKTIGSTYMAASGLNDSTYDKVGKTHI
KALADFAMKLMDQMKYINEHSFNNFQMKIGLNIGPVVAGVIGARKPQYDIWGNTVNVASRMDSTGVPDRIQVTTDMYQV
L
> O75343^.^1^147^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase c
atalytic domain^.^68.20^0.000e+00^8.000e-15
TILFSDVVTFTNICTACEPIQIVNVLNSMYSKFDRLTSVHAVYKVETIGDAYMVVGGVPVPIGNHAQRVANFALGMRIS
AKEVTNPVTGEPIQLRVGIHTGPVLADVVGDKMPRYCLFGDTVNTASRMESHGLPNKVHLSPTAYRAL
> O60503^.^1^179^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase c
atalytic domain^.^143.00^0.000e+00^2.000e-37
VSILFADIVGFTKMSANKSAHALVGLLNDLFGRFDRLCEETKCEKISTLGDCYYCVAGCPEPRADHAYCCIEMGLGMIK
AIEQFCQEKKEMVNMRVGVHTGTVLCGILGMRRFKFDVWSNDVNLANLMEQLGVAGKVHISEATAKYLDDRYEMEDGKV
IERLGQSVVADQLKGLKTYLI
> O60266^.^1^186^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase c
atalytic domain^.^179.00^0.000e+00^0.000e+00
FNTMYMYRHENVSILFADIVGFTQLSSACSAQELVKLLNELFARFDKLAAKYHQLRIKILGDCYYCICGLPDYREDHAV
CSILMGLAMVEAISYVREKTKTGVDMRVGVHTGTVLGGVLGQKRWQYDVWSTDVTVANKMEAGGIPGRVHISQSTMDCL
KGEFDVEPGDGGSRCDYLEEKGIETYLI
> O43306^.^1^189^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase c
atalytic domain^.^287.00^0.000e+00^0.000e+00
MMFHKIYIQKHDNVSILFADIEGFTSLASQCTAQELVMTLNELFARFDKLAAENHCLRIKILGDCYYCVSGLPEARADH
AHCCVEMGVDMIEAISLVREVTGVNVNMRVGIHSGRVHCGVLGLRKWQFDVWSNDVTLANHMEAGGRAGRIHITRATLQ
YLNGDYEVEPGRGGERNAYLKEQHIETFLIL
> O43306^.^1^159^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase c
atalytic domain^.^55.90^0.000e+00^3.000e-11
VAVMFASIANFSEFYVELEANNEGVECLRLLNEIIADFDEIISEERFRQLEKIKTIGSTYMAASGLNASTYDQVGRSHI
TALADYAMRLMEQMKHINEHSFNNFQMKIGLNMGPVVAGVIGARKPQYDIWGNTVNVSSRMDSTGVPDRIQVTTDLYQV
L
> O19179^.^1^161^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase c
atalytic domain^.^82.50^0.000e+00^4.000e-19
VTLYFSDIVGFTTISAMSEPIEVVDLLNDLYTLFDAIIGSHDVYKVETIGDAYMVASGLPQRNGQRHAAEIANMALDIL
SAVGSFRMRHMPEVPVRIRIGLHSGPCVAGVVGLTMPRYCLFGDTVNTASRMESTGLPYRIHVNMSTVRILHALDEGFQ
TEV
> O02740^.^1^162^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase c
atalytic domain^.^85.20^0.000e+00^7.000e-20
DLVTLYFSDIVGFTTISAMSEPIEVVDLLNDLYTLFDAIIGSHDVYKVETIGDAYMVASGLPKRNGMRHAAEIANMSLD
ILSSVGTFKMRHMPEVPVRIRIGLHSGPVVAGVVGLTMPRYCLFGDTVNTASRMESTGLPYRIHVSHSTVTILRTLGEG
YEVE

5.0 DATA FILES

   SEQNR requires a residue substitution matrix.

6.0 USAGE

  6.1 COMMAND LINE ARGUMENTS

   Standard (Mandatory) qualifiers (* if not always prompted):
  [-dhfinpath]         dirlist    [./] This option specifies the location of
                                  DHF files (domain hits files) (input). A
                                  'domain hits file' contains database hits
                                  (sequences) with domain classification
                                  information, in the DHF format (FASTA or
                                  EMBL-like). The hits are relatives to a SCOP
                                  or CATH family and are found from a search
                                  of a sequence database. Files containing
                                  hits retrieved by PSIBLAST are generated by
                                  using SEQSEARCH.
   -[no]dosing         toggle     [Y] This option specifies whether to use
                                  singlet sequences (e.g. DHF files) to filter
                                  input. Optionally, up to two further
                                  directories of sequences may be read: these
                                  are considered in the redundancy calculation
                                  but never appear in the output files.
*  -singletsdir        directory  [./] This option specifies the location of
                                  singlet filter sequences (e.g. DHF files)
                                  (input). A 'domain hits file' contains
                                  database hits (sequences) with domain
                                  classification information, in the DHF
                                  format (FASTA or EMBL-like). The hits are
                                  relatives to a SCOP or CATH family and are
                                  found from a search of a sequence database.
                                  Files containing hits retrieved by PSIBLAST
                                  are generated by using SEQSEARCH.
   -[no]dosets         toggle     [Y] This option specifies whether to use
                                  sets of sequences (e.g. DHF files) to filter
                                  input. Optionally, up to two further
                                  directories of sequences may be read: these
                                  are considered in the redundancy calculation
                                  but never appear in the output files.
*  -insetsdir          directory  [./] This option specifies location of sets
                                  of filter sequences (e.g. DAF files)
                                  (input). A 'domain alignment file' contains
                                  a sequence alignment of domains belonging to
                                  the same SCOP or CATH family. The file is
                                  in clustal format annotated with domain
                                  family classification information. The files
                                  generated by using SCOPALIGN will contain a
                                  structure-based sequence alignment of
                                  domains of known structure only. Such
                                  alignments can be extended with sequence
                                  relatives (of unknown structure) by using
                                  SEQALIGN.
   -mode               menu       [1] This option specifies whether to remove
                                  redundancy at a single threshold % sequence
                                  similarity or remove redundancy outside a
                                  range of acceptable threshold % similarity.
                                  All permutations of pair-wise sequence
                                  alignments are calculated for each set of
                                  input sequences in turn using the EMBOSS
                                  implementation of the Needleman and Wunsch
                                  global alignment algorithm. Redundant
                                  sequences are removed in one of two modes as
                                  follows: (i) If a pair of proteins achieve
                                  greater than a threshold percentage sequence
                                  similarity (specified by the user) the
                                  shortest sequence is discarded. (ii) If a
                                  pair of proteins have a percentage sequence
                                  similarity that lies outside an acceptable
                                  range (specified by the user) the shortest
                                  sequence is discarded. (Values: 1 (Remove
                                  redundancy at a single threshold % sequence
                                  similarity); 2 (Remove redundancy outside a
                                  range of acceptable threshold % similarity))
*  -thresh             float      [95.0] This option specifies the % sequence
                                  identity redundancy threshold. The %
                                  sequence identity redundancy threshold
                                  determines the redundancy calculation. If a
                                  pair of proteins achieve greater than this
                                  threshold the shortest sequence is
                                  discarded. (Any numeric value)
*  -threshlow          float      [30.0] This option specifies the % sequence
                                  identity redundancy threshold (lower limit).
                                  The % sequence identity redundancy
                                  threshold determines the redundancy
                                  calculation. If a pair of proteins have a
                                  percentage sequence similarity that lies
                                  outside an acceptable range the shortest
                                  sequence is discarded. (Any numeric value)
*  -threshup           float      [90.0] This option specifies the % sequence
                                  identity redundancy threshold (upper limit).
                                  The % sequence identity redundancy
                                  threshold determines the redundancy
                                  calculation. If a pair of proteins have a
                                  percentage sequence similarity that lies
                                  outside an acceptable range the shortest
                                  sequence is discarded. (Any numeric value)
  [-dhfoutdir]         outdir     [./] This option specifies the location of
                                  DHF files (domain hits files) of
                                  non-redundant sequences (output). A 'domain
                                  hits file' contains database hits
                                  (sequences) with domain classification
                                  information, in the DHF format (FASTA or
                                  EMBL-like). The hits are relatives to a SCOP
                                  or CATH family and are found from a search
                                  of a sequence database. Files containing
                                  hits retrieved by PSIBLAST are generated by
                                  using SEQSEARCH.
   -dored              toggle     [N] This option specifies whether to retain
                                  redundant sequences. If this option is set a
                                  DHF file (domain hits file) of redundant
                                  sequences is written.
*  -redoutdir          outdir     [./] This option specifies the location of
                                  DHF files (domain hits files) of redundant
                                  sequences (output). A 'domain hits file'
                                  contains database hits (sequences) with
                                  domain classification information, in the
                                  DHF format (FASTA or EMBL-like). The hits
                                  are relatives to a SCOP or CATH family and
                                  are found from a search of a sequence
                                  database. Files containing hits retrieved by
                                  PSIBLAST are generated by using SEQSEARCH.
   -logfile            outfile    [seqnr.log] This option specifies the name
                                  of SEQNR log file (output). The log file
                                  contains messages about any errors arising
                                  while SEQNR ran.

   Additional (Optional) qualifiers:
   -matrix             matrixf    [EBLOSUM62] This option specifies the
                                  residue substitution matrix that is used for
                                  sequence comparison.
   -gapopen            float      [10.0 for any sequence] This option
                                  specifies the gap insertion penalty. The gap
                                  insertion penalty is the score taken away
                                  when a gap is created. The best value
                                  depends on the choice of comparison matrix.
                                  The default value assumes you are using the
                                  EBLOSUM62 matrix for protein sequences, and
                                  the EDNAFULL matrix for nucleotide
                                  sequences. (Floating point number from 1.0
                                  to 100.0)
   -gapextend          float      [0.5 for any sequence] This option specifies
                                  the gap extension penalty. The gap
                                  extension, penalty is added to the standard
                                  gap penalty for each base or residue in the
                                  gap. This is how long gaps are penalized.
                                  Usually you will expect a few long gaps
                                  rather than many short gaps, so the gap
                                  extension penalty should be lower than the
                                  gap penalty. (Floating point number from 0.0
                                  to 10.0)

   Advanced (Unprompted) qualifiers: (none)
   Associated qualifiers:

   "-logfile" associated qualifiers
   -odirectory         string     Output directory

   General qualifiers:
   -auto               boolean    Turn off prompts
   -stdout             boolean    Write standard output
   -filter             boolean    Read standard input, write standard output
   -options            boolean    Prompt for standard and additional values
   -debug              boolean    Write debug output to program.dbg
   -verbose            boolean    Report some/full command line options
   -help               boolean    Report command line options. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   -warning            boolean    Report warnings
   -error              boolean    Report errors
   -fatal              boolean    Report fatal errors
   -die                boolean    Report dying program messages

