                             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^A
spartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate car
bamoyltransferase, Regulatory-chain, N-terminal domain^.^56.10^0.000e+00^9.000e-
12
VRKIRSGVVIDHIPPGRAFTMLKALGLLPPRGYRWRIAVVINAESSKLGRKDILKIEGYKPRQRDLEVLGIIAPGATFNV
IEDYKVVEKVKLKLP
> Q97FS4^.^1^90^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^A
spartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate car
bamoyltransferase, Regulatory-chain, N-terminal domain^.^43.40^0.000e+00^6.000e-
08
INSIKNGIVIDHIKAGHGIKIYNYLKLGEAEFPTALIMNAISKKNKAKDIIKIENVMDLDLAVLGFLDPNITVNIIEDEK
IRQKIQLKLP
> Q7MX57^.^1^92^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^A
spartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate car
bamoyltransferase, Regulatory-chain, N-terminal domain^.^73.80^0.000e+00^5.000e-
17
VAAIRNGIVIDHIPPTKLFKVATLLQLDDLDKRITIGNNLRSRSHGSKGVIKIEDKTFEEEELNRIALIAPNVRLNIIRD
YEVVEKRQVEVP
> P96111^.^1^98^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^A
spartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate car
bamoyltransferase, Regulatory-chain, N-terminal domain^.^43.00^0.000e+00^9.000e-
08
GIKPIENGTVIDHIAKGKTPEEIYSTILKIRKILRLYDVDSADGIFRSSDGSFKGYISLPDRYLSKKEIKKLSAISPNTT
VNIIKNSTVVEKYRIKLP

  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 cat
alytic domain^.^46.20^0.000e+00^4.000e-08
DCVCVMFASIPDFKEFYTESDVNKEGLECLRLLNEIIADFDDLLSKPKFSGVEKIKTIGSTYMAATGLSAVPSQEHSQEP
ERQYMHIGTMVEFAFALVGKLDAINKHSFNDFKLRVGINHGPVIAGVIGAQKPQYDIWGNTVNVASRMDSTGVLDKIQVT
EETSLVL
> Q03101^.^1^149^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase cat
alytic domain^.^65.80^0.000e+00^4.000e-14
NNACVFFLDIAGFTRFSSIHSPEQVIQVLIKIFNSMDLLCAKHGIEKIKTIGDAYMATCGIFPKCDDIRHNTYKMLGFAM
DVLEFIPKEMSFHLGLQVRVGIHCGPVISGVISGYAKPHFDVWGDTVNVASRMESTGIAGQIHVSDRVY
> Q02153^.^1^165^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase cat
alytic domain^.^68.90^0.000e+00^4.000e-15
HKRPVPAKRYDNVTILFSGIVGFNAFCSKHASGEGAMKIVNLLNDLYTRFDTLTDSRKNPFVYKVETVGDKYMTVSGLPE
PCIHHARSICHLALDMMEIAGQVQVDGESVQITIGIHTGEVVTGVIGQRMPRYCLFGNTVNLTSRTETTGEKGKINVSEY
TYRCL
> P46197^.^1^168^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase cat
alytic domain^.^78.50^0.000e+00^7.000e-18
VQAEAFDSVTIYFSDIVGFTALSAESTPMQVVTLLNDLYTCFDAIIDNFDVYKVETIGDAYMVVSGLPGRNGQRHAPEIA
RMALALLDAVSSFRIRHRPHDQLRLRIGVHTGPVCAGVVGLKMPRYCLFGDTVNTASRMESNGQALKIHVSSTTKDALDE
LGCFQLEL
> P40137^.^1^139^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase cat
alytic domain^.^48.50^0.000e+00^6.000e-09
VTLLFADIRDFTSLSERLRPEQVVTLLNEYYGRMVEVVFRHGGTLDKFIGDALMVYFGAPIADPAHARRGVQCALDMVQE
LETVNALRSARGEPCLRIGVGVHTGPAVLGNIGSATRRLEYTAIGDTVNLASRIESLTK
> P23466^.^1^154^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase cat
alytic domain^.^50.80^0.000e+00^1.000e-09
PTGNVAIVFTDIKNSTFLWELFPDAMRAAIKTHNDIMRRQLRIYGGYEVKTEGDAFMVAFPTPTSALVWCLSVQLKLLEA
EWPEEITSIQDGCLITDNSGTKVYLGLSVRMGVHWGCPVPEIDLVTQRMDYLGPVVNKAARVSGVADGGQITLS
> O30820^.^1^149^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase cat
alytic domain^.^75.40^0.000e+00^6.000e-17
DEASVLFADIVGFTERASSTAPADLVRFLDRLYSAFDELVDQHGLEKIKVSGDSYMVVSGVPRPRPDHTQALADFALDMT
NVAAQLKDPRGNPVPLRVGLATGPVVAGVVGSRRFFYDVWGDAVNVASRMESTDSVGQIQVPDEVYERL

  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^A
spartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate car
bamoyltransferase, Regulatory-chain, N-terminal domain^.^60.00^0.000e+00^6.000e-
13
VSKIRNGTVIDHIPAGRALAVLRILGIRGSEGYRVALVMNVESKKIGRKDIVKIEDRVIDEKEASLITLIAPSATINIIR
DYVVTEKRHLEVP
> Q9KP65^.^1^92^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^A
spartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate car
bamoyltransferase, Regulatory-chain, N-terminal domain^.^120.00^0.000e+00^4.000e
-31
VEAIKNGTVIDHIPAKVGIKVLKLFDMHNSAQRVTIGLNLPSSALGSKDLLKIENVFISEAQANKLALYAPHATVNQIEN
YEVVKKLALQLP
> Q9K1K9^.^1^92^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^A
spartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate car
bamoyltransferase, Regulatory-chain, N-terminal domain^.^93.10^0.000e+00^7.000e-
23
VEAIEKGTVIDHIPAGRGLTILRQFKLLHYGNAVTVGFNLPSKTQGSKDIIKIKGVCLDDKAADRLALFAPEAVVNTIDN
FKVVQKRHLNLP
> Q9JWY6^.^1^92^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^A
spartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate car
bamoyltransferase, Regulatory-chain, N-terminal domain^.^91.60^0.000e+00^2.000e-
22
VEAIEKGTVIDHIPAGRGLTILRQFKLLHYGNAVTVGFNLPSKTQGSKDIIKIKGVCLDDKAADRLALFAPEAVVNTIDH
FKVVQKRHLNLP
> Q9HKM3^.^1^93^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^A
spartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate car
bamoyltransferase, Regulatory-chain, N-terminal domain^.^73.10^0.000e+00^8.000e-
17
ISKIRDGTVIDHVPSGKGIRVIGVLGVHEDVNYTVSLAIHVPSNKMGFKDVIKIENRFLDRNELDMISLIAPNATISIIK
NYEISEKFQVELP
> Q9HHN3^.^1^93^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^A
spartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate car
bamoyltransferase, Regulatory-chain, N-terminal domain^.^71.50^0.000e+00^2.000e-
16
VSKIQAGTVIDHIPAGQALQVLQILGTNGASDDQITVGMNVTSERHHRKDIVKIEGRELSQDEVDVLSLIAPDATINIVR
DYEVDEKRRVDRP
> Q97B28^.^1^93^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^A
spartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate car
bamoyltransferase, Regulatory-chain, N-terminal domain^.^72.70^0.000e+00^8.000e-
17
ISKIKDGTVIDHIPSGKALRVLSILGIRDDVDYTVSVGMHVPSSKMEYKDVIKIENRSLDKNELDMISLTAPNATISIIK
NYEISEKFKVELP
> Q970X3^.^1^91^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^A
spartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate car
bamoyltransferase, Regulatory-chain, N-terminal domain^.^71.90^0.000e+00^1.000e-
16
VSKIKNGTVIDHIPAGRALAVLRILKIAEGYRIALVMNVESKKMGKKDIVKIENKEVDEKEANLITLIAPTATINIIRDY
EVVEKKKLKIP
> Q8ZTG2^.^1^93^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^A
spartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate car
bamoyltransferase, Regulatory-chain, N-terminal domain^.^58.80^0.000e+00^1.000e-
12
VSKIENGTVIDHIPAGRALTVLRILGISGKEGLRVALVMNVESKKLGKKDIVKIEGRELTPEEVNIISAVAPTATINIIR
NFAVVKKFKVTPP
> Q8ZB38^.^1^92^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^A
spartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate car
bamoyltransferase, Regulatory-chain, N-terminal domain^.^145.00^0.000e+00^8.000e
-39
VEAIKCGTVIDHIPAQIGFKLLSLFKLTATDQRITIGLNLPSKRSGRKDLIKIENTFLTEQQANQLAMYAPDATVNRIDN
YEVVKKLTLSLP
> Q8Z130^.^1^92^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^A
spartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate car
bamoyltransferase, Regulatory-chain, N-terminal domain^.^168.00^0.000e+00^1.401e
-45
VEAIKCGTVIDHIPAQVGFKLLSLFKLTETDQRITIGLNLPSGEMGRKDLIKIENTFLTDEQVNQLALYAPQATVNRIDN
YDVVGKSRPSLP
> Q8U374^.^1^94^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^A
spartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate car
bamoyltransferase, Regulatory-chain, N-terminal domain^.^83.90^0.000e+00^4.000e-
20
VSAIKEGTVIDHIPAGKGLKVIQILGLGELKNGGAVLLAMNVPSKKLGRKDIVKVEGKFLSEEEVNKIALVAPTATVNII
REYKVVEKFKVEIP
> Q8TVB1^.^1^92^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^A
spartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate car
bamoyltransferase, Regulatory-chain, N-terminal domain^.^66.10^0.000e+00^9.000e-
15
VKRIEMGTVLDHLPPGTAPQIMRILDIDPTETTLLVAINVESSKMGRKDILKIEGKILSEEEANKVALVAPNATVNIVRD
YSVAEKFQVKPP
> Q8THL3^.^1^92^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^A
spartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate car
bamoyltransferase, Regulatory-chain, N-terminal domain^.^67.30^0.000e+00^4.000e-
15
IQAIENGTVIDHITAGQALNVLRILRISSAFRATVSFVMNAPGARGKKDVVKIEGKELSVEELNRIALISPKATINIIRD
FEVVQKNKVVLP
> Q8PXK6^.^1^92^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^A
spartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate car
bamoyltransferase, Regulatory-chain, N-terminal domain^.^61.50^0.000e+00^2.000e-
13
VQAIESGTVIDHIKSGQALNVLRILGISSAFRATISFVMNAPGAGGKKDVVKIEGKELSVEELNRIALISPKATINIIRD
FVVVQKNNVVLP
> Q8K9H8^.^1^92^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^A
spartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate car
bamoyltransferase, Regulatory-chain, N-terminal domain^.^137.00^0.000e+00^4.000e
-36
VEAIKSGSVIDHIPAHIGFKLLSLFRFTETEKRITIGLNLPSQKLDKKDIIKIENTFLSDDQINQLAIYAPCATVNYIEK
YNLVGKIFPSLP
> Q8DCF7^.^1^92^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^A
spartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate car
bamoyltransferase, Regulatory-chain, N-terminal domain^.^118.00^0.000e+00^2.000e
-30
VEAIKNGTVIDHIPAQVGIKVLKLFDMHNSSQRVTIGLNLPSSALGNKDLLKIENVFINEEQASKLALYAPHATVNQIED
YQVVKKLALELP
> Q8D1W6^.^1^92^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^A
spartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate car
bamoyltransferase, Regulatory-chain, N-terminal domain^.^115.00^0.000e+00^2.000e
-29
VEAIFGGTVIDHIPAQVGLKLLSLFKWLHTKERITMGLNLPSNQQKKKDLIKLENVLLNEDQANQLSIYAPLATVNQIKN
YIVIKKQKLKLP
> Q8A9S4^.^1^92^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^A
spartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate car
bamoyltransferase, Regulatory-chain, N-terminal domain^.^57.70^0.000e+00^3.000e-
12
VAALKNGTVIDHIPSEKLFTVVQLLGVEQMKCNITIGFNLDSKKLGKKGIIKIADKFFCDEEINRISVVAPYVKLNIIRD
YEVVEKKEVRMP
> Q891I9^.^1^91^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^A
spartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate car
bamoyltransferase, Regulatory-chain, N-terminal domain^.^46.90^0.000e+00^5.000e-
09
ITSIKDGIVIDHIKSGYGIKIFNYLNLKNVEYSVALIMNVFSSKLGKKDIIKIANKEIDIDFTVLGLIDPTITINIIEDE
KIKEKLNLELP
> Q87LF7^.^1^92^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^A
spartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate car
bamoyltransferase, Regulatory-chain, N-terminal domain^.^122.00^0.000e+00^8.000e
-32
VEAIKNGTVIDHIPAQIGIKVLKLFDMHNSSQRVTIGLNLPSSALGHKDLLKIENVFINEEQASKLALYAPHATVNQIEN
YEVVKKLALELP
> Q83IL8^.^1^92^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^A
spartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate car
bamoyltransferase, Regulatory-chain, N-terminal domain^.^175.00^0.000e+00^0.000e
+00
VEAIKRGTVIDHIPAQIGFKLLSLFKLTETDQRITIGLNLPSGEMGRKDLIKIENTFLSEEQVDQLALYAPQATVNRIDN
YEVVGKSRPSLP
> Q7P144^.^1^92^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^A
spartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate car
bamoyltransferase, Regulatory-chain, N-terminal domain^.^118.00^0.000e+00^1.000e
-30
VEALKQGTVIDHIPAGEGVKILRLFKLTETGERVTVGLNLVSRHMGSKDLIKVENVALTEEQANELALFAPKATVNVIDN
FEVVKKHKLTLP
> Q7MZ14^.^1^92^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^A
spartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate car
bamoyltransferase, Regulatory-chain, N-terminal domain^.^141.00^0.000e+00^2.000e
-37
VEAIRCGTVIDHIPAQVGFKLLSLFKLTETDQRITIGLNLPSNRLGKKDLIKIENTFLTEQQANQLAMYAPNATVNCIEN
YEVVKKLPINLP
> Q7MHF0^.^1^92^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^A
spartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate car
bamoyltransferase, Regulatory-chain, N-terminal domain^.^118.00^0.000e+00^2.000e
-30
VEAIKNGTVIDHIPAQVGIKVLKLFDMHNSSQRVTIGLNLPSSALGNKDLLKIENVFINEEQASKLALYAPHATVNQIED
YQVVKKLALELP
> Q58801^.^1^91^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^A
spartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate car
bamoyltransferase, Regulatory-chain, N-terminal domain^.^53.40^0.000e+00^6.000e-
11
VKKITNGTVIDHIDAGKALMVFKVLNVPKETSVMIAINVPSKKKGKKDILKIEGIELKKEDVDKISLISPDVTINIIRNG
KVVEKLKPQIP
> P96175^.^1^92^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^A
spartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate car
bamoyltransferase, Regulatory-chain, N-terminal domain^.^99.30^0.000e+00^9.000e-
25
VEAICNGYVIDHIPSGQGVKILRLFSLTDTKQRVTVGFNLPSHDGTTKDLIKVENTEITKSQANQLALLAPNATVNIIEN
FKVTDKHSLALP
> P77919^.^1^94^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^A
spartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate car
bamoyltransferase, Regulatory-chain, N-terminal domain^.^85.00^0.000e+00^2.000e-
20
VSAIKEGTVIDHIPAGKGLKVIEILKLGKLTNGGAVLLAMNVPSKKLGRKDIVKVEGRFLSEEEVNKIALVAPNATVNII
RDYKVVEKFKVEVP
> P74766^.^1^93^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^A
spartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate car
bamoyltransferase, Regulatory-chain, N-terminal domain^.^68.10^0.000e+00^2.000e-
15
VSKIKNGTVIDHIPAGRAFAVLNVLGIKGHEGFRIALVINVDSKKMGKKDIVKIEDKEISDTEANLITLIAPTATINIVR
EYEVVKKTKLEVP
> P57451^.^1^92^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^A
spartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate car
bamoyltransferase, Regulatory-chain, N-terminal domain^.^133.00^0.000e+00^6.000e
-35
VEAIKSGSVIDHIPEYIGFKLLSLFRFTETEKRITIGLNLPSKKLGRKDIIKIENTFLSDEQINQLAIYAPHATVNYINE
YNLVRKVFPTLP
> P19936^.^1^92^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^A
spartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate car
bamoyltransferase, Regulatory-chain, N-terminal domain^.^148.00^0.000e+00^1.000e
-39
VEAIKCGTVIDHIPAQIGFKLLTLFKLTATDQRITIGLNLPSNELGRKDLIKIENTFLTEQQANQLAMYAPKATVNRIDN
YEVVRKLTLSLP
> P08421^.^1^92^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^A
spartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate car
bamoyltransferase, Regulatory-chain, N-terminal domain^.^170.00^0.000e+00^0.000e
+00
VEAIKCGTVIDHIPAQVGFKLLSLFKLTETDQRITIGLNLPSGEMGRKDLIKIENTFLTEEQVNQLALYAPQATVNRIDN
YDVVGKSRPSLP
> P00478^.^1^92^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^A
spartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate car
bamoyltransferase, Regulatory-chain, N-terminal domain^.^177.00^0.000e+00^0.000e
+00
VEAIKRGTVIDHIPAQIGFKLLSLFKLTETDQRITIGLNLPSGEMGRKDLIKIENTFLSEDQVDQLALYAPQATVNRIDN
YEVVGKSRPSLP
> O58452^.^1^94^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^A
spartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate car
bamoyltransferase, Regulatory-chain, N-terminal domain^.^86.20^0.000e+00^8.000e-
21
VSAIKEGTVIDHIPAGKGLKVIEILGLSKLSNGGSVLLAMNVPSKKLGRKDIVKVEGKFLSEEEVNKIALVAPTATVNII
RNYKVVEKFKVEVP
> O30129^.^1^93^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^A
spartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate car
bamoyltransferase, Regulatory-chain, N-terminal domain^.^71.10^0.000e+00^3.000e-
16
VSKIKEGTVIDHINAGKALLVLKILKIQPGTDLTVSMAMNVPSSKMGKKDIVKVEGMFIRDEELNKIALISPNATINLIR
DYEIERKFKVSPP
> O26938^.^1^91^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^A
spartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate car
bamoyltransferase, Regulatory-chain, N-terminal domain^.^75.00^0.000e+00^2.000e-
17
VKPIKNGTVIDHITANRSLNVLNILGLPDGRSKVTVAMNMDSSQLGSKDIVKIENRELKPSEVDQIALIAPRATINIVRD
YKIVEKAKVRL

  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 cat
alytic domain^.^77.00^0.000e+00^2.000e-17
DDVTMLFSDIVGFTAICAQCTPMQVISMLNELYTRFDHQCGFLDIYKVETIGDAYCVASGLHRKSLCHAKPIALMALKMM
ELSEEVLTPDGRPIQMRIGIHSGSVLAGVVGVRMPRYCLFGNNVTLASKFESGSHPRRINISPTTYQLL
> Q9ERL9^.^1^152^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase cat
alytic domain^.^67.70^0.000e+00^9.000e-15
VTMLFSDIVGFTAICSQCSPLQVITMLNALYTRFDQQCGELDVYKVETIGDAYCVAGGLHRESDTHAVQIALMALKMMEL
SNEVMSPHGEPIKMRIGLHSGSVFAGVVGVKMPRYCLFGNNVTLANKFESCSVPRKINVSPTTYRLLKDCPG
> Q9DGG6^.^1^181^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase cat
alytic domain^.^124.00^0.000e+00^9.000e-32
EQVSILFADIVGFTKMSANKSAHALVGLLNDLFGRFDRLCEDTKCEKISTLGDCYYCVAGCPEPRADHAYCCIEMGLGMI
KAIEQFCQEKKEMVNMRVGVHTGTVLCGILGMRRFKFDVWSNDVNLANLMEQLGVAGKVHISEATAKYLDDRYEMEDGKV
TERVGQSAVADQLKGLKTYLI
> Q99396^.^1^212^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase cat
alytic domain^.^159.00^0.000e+00^2.000e-42
KELADPVTLIFTDIESSTAQWATQPELMPDAVATHHSMVRSLIENYDCYEVKTVGDSFMIACKSPFAAVQLAQELQLRFL
RLDWGTTVFDEFYREFEERHAEEGDGKYKPPTARLDPEVYRQLWNGLRVRVGIHTGLCDIRYDEVTKGYDYYGQTANTAA
RTESVGNGGQVLMTCETYHSLSTAERSQFDVTPLGGVPLRGVSEPVEVYQLN
> Q99280^.^6^216^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase cat
alytic domain^.^180.00^0.000e+00^0.000e+00
KEPTGPVTLIFTDIESSTALWAAHPDLMPDAVATHHRLIRSLITRYECYEVKTVGDSFMIASKSPFAAVQLAQELQLRFL
RLDWETNALDESYREFEEQRAEGECEYTPPTAHMDPEVYSRLWNGLRVRVGIHTGLCDIRYDEVTKGYDYYGRTSNMAAR
TESVANGGQVLMTHAAYMSLSGEDRNQLDVTTLGATVLRGVPEPVRMYQLN
> Q99279^.^1^218^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase cat
alytic domain^.^210.00^0.000e+00^0.000e+00
NNNRAPKEPTDPVTLIFTDIESSTALWAAHPDLMPDAVAAHHRMVRSLIGRYKCYEVKTVGDSFMIASKSPFAAVQLAQE
LQLCFLHHDWGTNALDDSYREFEEQRAEGECEYTPPTAHMDPEVYSRLWNGLRVRVGIHTGLCDIIRHDEVTKGYDYYGR
TPNMAARTESVANGGQVLMTHAAYMSLSAEDRKQIDVTALGDVALRGVSDPVKMYQLN
> Q91WF3^.^1^165^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase cat
alytic domain^.^51.90^0.000e+00^6.000e-10
VCVLFASVPDFKEFYSESNINHEGLECLRLLNEIIADFDELLSKPKFSGVEKIKTIGSTYMAATGLNATSGQDTQQDSER
SCSHLGTMVEFAVALGSKLGVINKHSFNNFRLRVGLNHGPVVAGVIGAQKPQYDIWGNTVNVASRMESTGVLGKIQVTEE
TARAL
> Q91WF3^.^1^158^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase cat
alytic domain^.^139.00^0.000e+00^2.000e-36
FHSLYVKRHQGVSVLYADIVGFTRLASECSPKELVLMLNELFGKFDQIAKEHECMRIKILGDCYYCVSGLPLSLPDHAIN
CVRMGLDMCRAIRKLRVATGVDINMRVGVHSGSVLCGVIGLQKWQYDVWSHDVTLANHMEAGGVPGRVHITGATLALL
> Q8VHH7^.^1^186^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase cat
alytic domain^.^154.00^0.000e+00^1.000e-40
FNTMYMYRHENVSILFADIVGFTQLSSACSAQELVKLLNELFARFDKLAAKYHQLRIKILGDCYYCICGLPDYREDHAVC
SILMGLAMVEAISYVREKTKTGVDMRVGVHTGTVLGGVLGQKRWQYDVWSTDVTVANKMEAGGIPGRVHISQSTMDCLKG
EFDVEPGDGGSRCDYLDEKGIETYLI
> Q8NFM4^.^1^161^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase cat
alytic domain^.^51.60^0.000e+00^7.000e-10
VCVLFASVPDFKEFYSESNINHEGLECLRLLNEIIADFDELLSKPKFSGVEKIKTIGSTYMAATGLNATSGQDAQQDAER
SCSHLGTMVEFAVALGSKLDVINKHSFNNFRLRVGLNHGPVVAGVIGAQKPQYDIWGNTVNVASRMESTGVLGKIQVTEE
T
> Q8NFM4^.^1^158^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase cat
alytic domain^.^139.00^0.000e+00^2.000e-36
FHSLYVKRHQGVSVLYADIVGFTRLASECSPKELVLMLNELFGKFDQIAKEHECMRIKILGDCYYCVSGLPLSLPDHAIN
CVRMGLDMCRAIRKLRAATGVDINMRVGVHSGSVLCGVIGLQKWQYDVWSHDVTLANHMEAGGVPGRVHITGATLALL
> Q29450^.^1^186^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase cat
alytic domain^.^154.00^0.000e+00^7.000e-41
FHNLYVKRHQNVSILYADIVGFTRLASDCSPKELVVVLNELFGKFDQIAKANECMRIKILGDCYYCVSGLPVSLPNHARN
CVKMGLDMCEAIKQVREATGVDISMRVGIHSGNVLCGVIGLRKWQYDVWSHDVSLANRMEAAGVPGRVHITEATLKHLDK
AYEVEDGHGQQRDPYLKEMNIRTYLV
> Q27675^.^1^217^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase cat
alytic domain^.^140.00^0.000e+00^1.000e-36
NNDAAPKDGDEPVTLLFTDIESSTALWAALPQLMSDAIAAHHRVIRQLVKKYGCYEVKTIGDSFMIACRSAHSAVSLACE
IQTKLLKHDWGTEALDRAYREFELARVDTLDDYEPPTARLSEEEYAALWCGLRVRVGIHTGLTDIRYDEVTKGYDYYGDT
SNMAARTEAVANGGQVVATEAAWWALSNDERAGIAHTAMGPQGLRGVPFAVEMFQLN
> Q26896^.^6^216^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase cat
alytic domain^.^163.00^0.000e+00^9.949e-44
KEFTDPVTLIFTDIESSTALWAAHPGMMADAVATHHRLIRSLIALYGAYEVKTVGDSFMIACRSAFAAVELARDLQLTLV
HHDWGTVAIDESYRKFEEERAVEDSDYAPPTARLDSAVYCKLWNGLRVRAGIHTGLCDIAHDEVTKGYDYYGRTPNLAAR
TESAANGGQVLVTGATYYSLSVAERARLDATPIGPVPLRGVPEPVEMYQLN
> Q26721^.^1^206^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase cat
alytic domain^.^184.00^0.000e+00^0.000e+00
PVTLIFTDIESSTALWAAHPEVMPDAVATHHRLIRTLISKYECYEVKTVGDSFMIASKSPFAAVQLAQELQLCFLHHDWG
TNAIDESYQQFEQQRAEDDSDYTPPTARLDPKVYSRLWNGLRVRVGIHTGLCDIRRDEVTKGYDYYGRTSNMAARTESVA
NGGQVLMTHAAYMSLSAEERQQIDVTALGDVPLRGVPKPVEMYRLN
> Q25263^.^1^217^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase cat
alytic domain^.^140.00^0.000e+00^2.000e-36
NNDAAPKDGDEPVTLLFTDIESSTALWAALPQLMSDAIAAHHRVIRQLVKKYGCYEVKTIGDSFMIACRSAHSAVSLACE
IQTKLLKHDWGTEALDRAYREFELARVDTLDDYEPPTARLSEEEYAALWCGLRVRVGIHTGLTDIRYDEVTRGYDYYGDT
SNMAARTEAVANGGQVVATEAAWWALSNDERAGIAHTAMGPQGLRGVPFAVEMFQLN
> Q09435^.^1^161^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase cat
alytic domain^.^75.10^0.000e+00^6.000e-17
DSVTVFFSDVVKFTILASKCSPFQTVNLLNDLYSNFDTIIEQHGVYKVESIGDGYLCVSGLPTRNGYAHIKQIVDMSLKF
MEYCKSFNIPHLPRENVELRIGVNSGPCVAGVVGLSMPRYCLFGDTVNTASRMESNGKPSLIHLTNDAHSLLTTHYPNQY
E
> Q08828^.^1^186^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase cat
alytic domain^.^183.00^0.000e+00^0.000e+00
FHKIYIQRHDNVSILFADIVGFTGLASQCTAQELVKLLNELFGKFDELATENHCRRIKILGDCYYCVSGLTQPKTDHAHC
CVEMGLDMIDTITSVAEATEVDLNMRVGLHTGRVLCGVLGLRKWQYDVWSNDVTLANVMEAAGLPGKVHITKTTLACLNG
DYEVEPGYGHERNSFLKTHNIETFFI
> Q08462^.^1^186^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase cat
alytic domain^.^155.00^0.000e+00^4.000e-41
FHNLYVKRHTNVSILYADIVGFTRLASDCSPGELVHMLNELFGKFDQIAKENECMRIKILGDCYYCVSGLPISLPNHAKN
CVKMGLDMCEAIKKVRDATGVDINMRVGVHSGNVLCGVIGLQKWQYDVWSHDVTLANHMEAGGVPGRVHISSVTLEHLNG
AYKVEEGDGDIRDPYLKQHLVKTYFV
> Q07553^.^1^152^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase cat
alytic domain^.^75.80^0.000e+00^4.000e-17
DCVTILFSDIVGFTELCTTSTPFEVVEMLNDWYTCCDSIISNYDVYKVETIGDAYMVVSGLPLQNGSRHAGEIASLALHL
LETVGNLKIRHKPTETVQLRIGVHSGPCAAGVVGQKMPRYCLFGDTVNTASRMESTGDSMRIHISEATYQLL
> Q07093^.^1^158^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase cat
alytic domain^.^62.30^0.000e+00^4.000e-13
VTILFSDIVGFTSICSRATPFMVISMLEGLYKDFDEFCDFFDVYKVETIGDAYCVASGLHRASIYDAHRCLDGLKMIDAC
SKHITHDGEQIKMRIGLHTGTVLAGVVGRKMPRYCLFGHSVTIANKFESGSEALKINVSPTTKDWLTKHEGFEFELQP
> Q04400^.^1^189^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase cat
alytic domain^.^245.00^0.000e+00^0.000e+00
MMFHKIYIQKHDNVSILFADIEGFTSLASQCTAQELVMTLNELFARFDKLAAENHCLRIKILGDCYYCVSGLPEARADHA
HCCVEMGMDMIEAISSVREVTGVNVNMRVGIHSGRVHCGVLGLRKWQFDVWSNDVTLANHMEAGGKAGRIHITKATLNYL
NGDYEVEPGCGGERNAYLKEHSIETFLIL
> Q04400^.^1^159^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase cat
alytic domain^.^51.60^0.000e+00^8.000e-10
VAVMFASIANFSEFYVELEANNEGVECLRLLNEIIADFDEIISEDRFRQLEKIKTIGSTYMAASGLNDSTYDKAGKTHIK
ALADFAMKLMDQMKYINEHSFNNFQMKIGLNIGPVVAGVIGARKPQYDIWGNTVNVASRMDSTGVPDRIQVTTDMYQVL
> Q03343^.^1^189^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase cat
alytic domain^.^235.00^0.000e+00^0.000e+00
MMFHKIYIQKHDNVSILFADIEGFTSLASQCTAQELVMTLNELFARFDKLAAENHCLRIKILGDCYYCVSGLPEARADHA
HCCVEMGVDMIEAISLVREVTGVNVNMRVGIHSGRVHCGVLGLRKWQFDVWSNDVTLANHMEAGGRAGRIHITRATLQYL
NGDYEVEPGRGGERNGYLKEQCIETFLIL
> Q03343^.^1^159^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase cat
alytic domain^.^51.90^0.000e+00^5.000e-10
VAVMFASIANFSEFYVELEANNEGVECLRLLNEIIADFDEIISEERFRQLEKIKTIGSTYMAASGLNASTYDQVGRSHIT
ALADYAMRLMEQMKHINEHSFNNFQMKIGLNMGPVVAGVIGARKPQYDIWGNTVNVSSRMDSTGVPDRIQVTTDLYQVL


  [Part of this file has been deleted for brevity]

DCVCVMFASIPDFKEFYTESDVNKEGLECLRLLNEIIADFDDLLSKPKFSGVEKIKTIGSTYMAATGLSAIPSQEHAQEP
ERQYMHIGTMVEFAYALVGKLDAINKHSFNDFKLRVGINHGPVIAGVIGAQKPQYDIWGNTVNVASRMDSTGVLDKIQVT
EET
> P26338^.^1^216^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase cat
alytic domain^.^191.00^0.000e+00^0.000e+00
NNLAPKELTDPVTLIFTDIESSTALWAAHPELMPDAVATHHRLIRSLIGRYGCYEVKTVGDSFMIASKSPFAAVQLAQEL
QLCFLHHDWGTNAIDESYQQLEQQRAEEDAKYTPPTARLDLKVYSRLWNGLRVRVGIHTGLCDIRRDEVTKGYDYYGRTS
NMAARTESVGNGGQVLMTTAAYMSLSAEEREQIDVTALGDVPLRGVAKPVEMYQLN
> P25092^.^1^150^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase cat
alytic domain^.^67.70^0.000e+00^9.000e-15
VTIYFSDIVGFTTICKYSTPMEVVDMLNDIYKSFDHIVDHHDVYKVETIGDAYMVASGLPKRNGNRHAIDIAKMALEILS
FMGTFELEHLPGLPIWIRIGVHSGPCAAGVVGIKMPRYCLFGDTVNTASRMESTGLPLRIHVSGSTIAIL
> P23897^.^1^150^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase cat
alytic domain^.^67.40^0.000e+00^1.000e-14
VTIYFSDIVGFTTICKYSTPMEVVDMLNDIYKSFDQIVDHHDVYKVETIGDAYVVASGLPMRNGNRHAVDISKMALDILS
FMGTFELEHLPGLPVWIRIGVHSGPCAAGVVGIKMPRYCLFGDTVNTASRMESTGLPLRIHMSSSTIAIL
> P22717^.^1^147^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase cat
alytic domain^.^61.20^0.000e+00^9.000e-13
TILFSDVVTFTNICAACEPIQIVNMLNSMYSKFDRLTSVHDVYKVETIGDAYMVVGGVPVPVESHAQRVANFALGMRISA
KEVMNPVTGEPIQIRVGIHTGPVLAGVVGDKMPRYCLFGDTVNTASRMESHGLPSKVHLSPTAHRAL
> P21932^.^1^186^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase cat
alytic domain^.^154.00^0.000e+00^1.000e-40
FNTMYMYRHENVSILFADIVGFTQLSSACSAQELVKLLNELFARFDKLAAKYHQLRIKILGDCYYCICGLPDYREDHAVC
SILMGLAMVEAISYVREKTKTGVDMRVGVHTGTVLGGVLGQKRWQYDVWSTDVTVANKMEAGGIPGRVHISQSTMDCLKG
EFDVEPGDGGSRCDYLDEKGIETYLI
> P20595^.^1^165^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase cat
alytic domain^.^68.90^0.000e+00^4.000e-15
HKRPVPAKRYDNVTILFSGIVGFNAFCSKHASGEGAMKIVNLLNDLYTRFDTLTDSRKNPFVYKVETVGDKYMTVSGLPE
PCIHHARSICHLALDMMEIAGQVQVDGESVQITIGIHTGEVVTGVIGQRMPRYCLFGNTVNLTSRTETTGEKGKINVSEY
TYRCL
> P20594^.^1^168^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase cat
alytic domain^.^78.50^0.000e+00^7.000e-18
VQAEAFDSVTIYFSDIVGFTALSAESTPMQVVTLLNDLYTCFDAIIDNFDVYKVETIGDAYMVVSGLPGRNGQRHAPEIA
RMALALLDAVSSFRIRHRPHDQLRLRIGVHTGPVCAGVVGLKMPRYCLFGDTVNTASRMESNGQALKIHVSSTTKDALDE
LGCFQLEL
> P19754^.^1^186^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase cat
alytic domain^.^183.00^0.000e+00^0.000e+00
FHKIYIQRHDNVSILFADIVGFTGLASQCTAQELVKLLNELFGKFDELATENHCRRIKILGDCYYCVSGLTQPKTDHAHC
CVEMGLDMIDTITSVAEATEVDLNMRVGLHTGRVLCGVLGLRKWQYDVWSNDVTLANVMEAAGLPGKVHITKTTLACLNG
DYEVEPGHGHERNSFLKTHNIETFFI
> P19687^.^1^161^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase cat
alytic domain^.^72.70^0.000e+00^3.000e-16
AVQAKRFGNVTMLFSDIVGFTAICSQCSPLQVITMLNALYTRFDRQCGELDVYKVETIGDAYCVAGGLHKESDTHAVQIA
LMALKMMELSHEVVSPHGEPIKMRIGLHSGSVFAGVVGVKMPRYCLFGNNVTLANKFESCSVPRKINVSPTTYRLLKDCP
G
> P19686^.^1^160^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase cat
alytic domain^.^68.50^0.000e+00^5.000e-15
VQAKKFNEVTMLFSDIVGFTAICSQCSPLQVITMLNALYTRFDQQCGELDVYKVETIGDAYCVAGGLHRESDTHAVQIAL
MALKMMELSNEVMSPHGEPIKMRIGLHSGSVFAGVVGVKMPRYCLFGNNVTLANKFESCSVPRKINVSPTTYRLLKDCPG
> P18910^.^1^168^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase cat
alytic domain^.^78.50^0.000e+00^6.000e-18
VQAEAFDSVTIYFSDIVGFTALSAESTPMQVVTLLNDLYTCFDAVIDNFDVYKVETIGDAYMVVSGLPVRNGQLHAREVA
RMALALLDAVRSFRIRHRPQEQLRLRIGIHTGPVCAGVVGLKMPRYCLFGDTVNTASRMESNGEALKIHLSSETKAVLEE
FDGFELEL
> P18293^.^1^168^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase cat
alytic domain^.^79.30^0.000e+00^3.000e-18
VQAEAFDSVTIYFSDIVGFTALSAESTPMQVVTLLNDLYTCFDAVIDNFDVYKVETIGDAYMVVSGLPVRNGQLHAREVA
RMALALLDAVRSFRIRHRPQEQLRLRIGIHTGPVCAGVVGLKMPRYCLFGDTVNTASRMESNGEALRIHLSSETKAVLEE
FDGFELEL
> P16068^.^1^165^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase cat
alytic domain^.^68.90^0.000e+00^4.000e-15
HKRPVPAKRYDNVTILFSGIVGFNAFCSKHASGEGAMKIVNLLNDLYTRFDTLTDSRKNPFVYKVETVGDKYMTVSGLPE
PCIHHARSICHLALDMMEIAGQVQVDGESVQITIGIHTGEVVTGVIGQRMPRYCLFGNTVNLTSRTETTGEKGKINVSEY
TYRCL
> P16067^.^1^168^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase cat
alytic domain^.^78.50^0.000e+00^7.000e-18
VQAEAFDSVTIYFSDIVGFTALSAESTPMQVVTLLNDLYTCFDAIIDNFDVYKVETIGDAYMVVSGLPGRNGQRHAPEIA
RMALALLDAVSSFRIRHRPHDQLRLRIGVHTGPVCAGVVGLKMPRYCLFGDTVNTASRMESNGQALKIHVSSTTKDALDE
LGCFQLEL
> P16066^.^1^168^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase cat
alytic domain^.^77.80^0.000e+00^9.000e-18
VQAEAFDSVTIYFSDIVGFTALSAESTPMQVVTLLNDLYTCFDAVIDNFDVYKVETIGDAYMVVSGLPVRNGRLHACEVA
RMALALLDAVRSFRIRHRPQEQLRLRIGIHTGPVCAGVVGLKMPRYCLFGDTVNTASRMESNGEALKIHLSSETKAVLEE
FGGFELEL
> P16065^.^1^143^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase cat
alytic domain^.^73.90^0.000e+00^1.000e-16
VSIFFSDIVGFTALSAASTPIQVVNLLNDLYTLFDAIISNYDVYKVETIGDAYMLVSGLPLRNGDRHAGQIASTAHHLLE
SVKGFIVPHKPEVFLKLRIGIHSGSCVAGVVGLTMPRYCLFGDTVNTASRMESNGLALRIHVS
> O95622^.^1^189^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase cat
alytic domain^.^247.00^0.000e+00^0.000e+00
MMFHKIYIQKHDNVSILFADIEGFTSLASQCTAQELVMTLNELFARFDKLAAENHCLRIKILGDCYYCVSGLPEARADHA
HCCVEMGMDMIEAISLVREVTGVNVNMRVGIHSGRVHCGVLGLRKWQFDVWSNDVTLANHMEAGGKAGRIHITKATLNYL
NGDYEVEPGCGGERNAYLKEHSIETFLIL
> O95622^.^1^159^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase cat
alytic domain^.^51.60^0.000e+00^8.000e-10
VAVMFASIANFSEFYVELEANNEGVECLRLLNEIIADFDEIISEDRFRQLEKIKTIGSTYMAASGLNDSTYDKVGKTHIK
ALADFAMKLMDQMKYINEHSFNNFQMKIGLNIGPVVAGVIGARKPQYDIWGNTVNVASRMDSTGVPDRIQVTTDMYQVL
> O75343^.^1^147^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase cat
alytic domain^.^66.60^0.000e+00^2.000e-14
TILFSDVVTFTNICTACEPIQIVNVLNSMYSKFDRLTSVHAVYKVETIGDAYMVVGGVPVPIGNHAQRVANFALGMRISA
KEVTNPVTGEPIQLRVGIHTGPVLADVVGDKMPRYCLFGDTVNTASRMESHGLPNKVHLSPTAYRAL
> O60503^.^1^179^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase cat
alytic domain^.^124.00^0.000e+00^9.000e-32
VSILFADIVGFTKMSANKSAHALVGLLNDLFGRFDRLCEETKCEKISTLGDCYYCVAGCPEPRADHAYCCIEMGLGMIKA
IEQFCQEKKEMVNMRVGVHTGTVLCGILGMRRFKFDVWSNDVNLANLMEQLGVAGKVHISEATAKYLDDRYEMEDGKVIE
RLGQSVVADQLKGLKTYLI
> O60266^.^1^186^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase cat
alytic domain^.^154.00^0.000e+00^8.000e-41
FNTMYMYRHENVSILFADIVGFTQLSSACSAQELVKLLNELFARFDKLAAKYHQLRIKILGDCYYCICGLPDYREDHAVC
SILMGLAMVEAISYVREKTKTGVDMRVGVHTGTVLGGVLGQKRWQYDVWSTDVTVANKMEAGGIPGRVHISQSTMDCLKG
EFDVEPGDGGSRCDYLEEKGIETYLI
> O43306^.^1^189^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase cat
alytic domain^.^236.00^0.000e+00^0.000e+00
MMFHKIYIQKHDNVSILFADIEGFTSLASQCTAQELVMTLNELFARFDKLAAENHCLRIKILGDCYYCVSGLPEARADHA
HCCVEMGVDMIEAISLVREVTGVNVNMRVGIHSGRVHCGVLGLRKWQFDVWSNDVTLANHMEAGGRAGRIHITRATLQYL
NGDYEVEPGRGGERNAYLKEQHIETFLIL
> O43306^.^1^159^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase cat
alytic domain^.^51.90^0.000e+00^5.000e-10
VAVMFASIANFSEFYVELEANNEGVECLRLLNEIIADFDEIISEERFRQLEKIKTIGSTYMAASGLNASTYDQVGRSHIT
ALADYAMRLMEQMKHINEHSFNNFQMKIGLNMGPVVAGVIGARKPQYDIWGNTVNVSSRMDSTGVPDRIQVTTDLYQVL
> O19179^.^1^150^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase cat
alytic domain^.^76.20^0.000e+00^3.000e-17
VTLYFSDIVGFTTISAMSEPIEVVDLLNDLYTLFDAIIGSHDVYKVETIGDAYMVASGLPQRNGQRHAAEIANMALDILS
AVGSFRMRHMPEVPVRIRIGLHSGPCVAGVVGLTMPRYCLFGDTVNTASRMESTGLPYRIHVNMSTVRIL
> O02740^.^1^162^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase cat
alytic domain^.^77.40^0.000e+00^1.000e-17
DLVTLYFSDIVGFTTISAMSEPIEVVDLLNDLYTLFDAIIGSHDVYKVETIGDAYMVASGLPKRNGMRHAAEIANMSLDI
LSSVGTFKMRHMPEVPVRIRIGLHSGPVVAGVVGLTMPRYCLFGDTVNTASRMESTGLPYRIHVSHSTVTILRTLGEGYE
VE

5.0 DATA FILES

   SEQNR requires a residue substitution matrix.

6.0 USAGE

  6.1 COMMAND LINE ARGUMENTS

Removes redundancy from DHF files.
Version: EMBOSS:6.2.0

   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 first file to standard output
   -filter             boolean    Read first file from standard input, write
                                  first file to 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 and exit. 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
   -version            boolean    Report version number and exit


