
                          SEQFRAGGLE 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 fragments from DHF files (domain hits files) or other files of
   sequences

2.0 INPUTS & OUTPUTS

   SEQFRAGGLE reads a directory of domain hits files and for each
   individual file writes a new domain hits file in which sequence hits
   deemed to be fragments are removed. Alternatively, SEQFRAGGLE will
   read and write any supported sequence set format, e.g. the common
   alignment formats. The base names of the output files are the same as
   the input files. The paths and file extensions for the output files
   (input and output) are specified by the user.

3.0 INPUT FILE FORMAT

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

4.0 OUTPUT FILE FORMAT

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

  Output files for usage example

  File: 54894.dhf

> Q9YBD5^.^11^105^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-lik
e^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate
 carbamoyltransferase, Regulatory-chain, N-terminal domain^.^61.50^0.000e+00^4.
000e-10
VRKIRSGVVIDHIPPGRAFTMLKALGLLPPRGYRWRIAVVINAESSKLGRKDILKIEGYKPRQRDLEVLGIIAPGATFN
VIEDYKVVEKVKLKLP
> Q9UX07^.^12^104^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-lik
e^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate
 carbamoyltransferase, Regulatory-chain, N-terminal domain^.^65.80^0.000e+00^2.
000e-11
VSKIRNGTVIDHIPAGRALAVLRILGIRGSEGYRVALVMNVESKKIGRKDIVKIEDRVIDEKEASLITLIAPSATINII
RDYVVTEKRHLEVP
> Q9KP65^.^9^100^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate
carbamoyltransferase, Regulatory-chain, N-terminal domain^.^128.00^0.000e+00^3.
000e-30
VEAIKNGTVIDHIPAKVGIKVLKLFDMHNSAQRVTIGLNLPSSALGSKDLLKIENVFISEAQANKLALYAPHATVNQIE
NYEVVKKLALQLP
> Q9K1K9^.^8^99^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^.^101.00^0.000e+00^5.0
00e-22
VEAIEKGTVIDHIPAGRGLTILRQFKLLHYGNAVTVGFNLPSKTQGSKDIIKIKGVCLDDKAADRLALFAPEAVVNTID
NFKVVQKRHLNLP
> Q9JWY6^.^8^99^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^.^98.90^0.000e+00^2.00
0e-21
VEAIEKGTVIDHIPAGRGLTILRQFKLLHYGNAVTVGFNLPSKTQGSKDIIKIKGVCLDDKAADRLALFAPEAVVNTID
HFKVVQKRHLNLP
> Q9HKM3^.^7^99^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^.^79.60^0.000e+00^2.00
0e-15
ISKIRDGTVIDHVPSGKGIRVIGVLGVHEDVNYTVSLAIHVPSNKMGFKDVIKIENRFLDRNELDMISLIAPNATISII
KNYEISEKFQVELP
> Q9HHN3^.^9^101^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate
carbamoyltransferase, Regulatory-chain, N-terminal domain^.^78.50^0.000e+00^4.0
00e-15
VSKIQAGTVIDHIPAGQALQVLQILGTNGASDDQITVGMNVTSERHHRKDIVKIEGRELSQDEVDVLSLIAPDATINIV
RDYEVDEKRRVDRP
> Q97FS4^.^4^93^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^.^49.20^0.000e+00^2.00
0e-06
INSIKNGIVIDHIKAGHGIKIYNYLKLGEAEFPTALIMNAISKKNKAKDIIKIENVMDLDLAVLGFLDPNITVNIIEDE
KIRQKIQLKLP
> Q97B28^.^8^100^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate
carbamoyltransferase, Regulatory-chain, N-terminal domain^.^79.20^0.000e+00^2.0
00e-15
ISKIKDGTVIDHIPSGKALRVLSILGIRDDVDYTVSVGMHVPSSKMEYKDVIKIENRSLDKNELDMISLTAPNATISII
KNYEISEKFKVELP
> Q970X3^.^11^101^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-lik
e^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate
 carbamoyltransferase, Regulatory-chain, N-terminal domain^.^78.50^0.000e+00^3.
000e-15
VSKIKNGTVIDHIPAGRALAVLRILKIAEGYRIALVMNVESKKMGKKDIVKIENKEVDEKEANLITLIAPTATINIIRD
YEVVEKKKLKIP
> Q8ZTG2^.^7^99^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^.^66.10^0.000e+00^2.00
0e-11
VSKIENGTVIDHIPAGRALTVLRILGISGKEGLRVALVMNVESKKLGKKDIVKIEGRELTPEEVNIISAVAPTATINII
RNFAVVKKFKVTPP
> Q8ZB38^.^9^100^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate
carbamoyltransferase, Regulatory-chain, N-terminal domain^.^156.00^0.000e+00^0.
000e+00
VEAIKCGTVIDHIPAQIGFKLLSLFKLTATDQRITIGLNLPSKRSGRKDLIKIENTFLTEQQANQLAMYAPDATVNRID
NYEVVKKLTLSLP
> Q8Z130^.^8^99^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^.^181.00^0.000e+00^0.0
00e+00
VEAIKCGTVIDHIPAQVGFKLLSLFKLTETDQRITIGLNLPSGEMGRKDLIKIENTFLTDEQVNQLALYAPQATVNRID
NYDVVGKSRPSLP
> Q8U374^.^6^99^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^.^92.00^0.000e+00^3.00
0e-19
VSAIKEGTVIDHIPAGKGLKVIQILGLGELKNGGAVLLAMNVPSKKLGRKDIVKVEGKFLSEEEVNKIALVAPTATVNI
IREYKVVEKFKVEIP
> Q8TVB1^.^7^98^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^.^72.70^0.000e+00^2.00
0e-13
VKRIEMGTVLDHLPPGTAPQIMRILDIDPTETTLLVAINVESSKMGRKDILKIEGKILSEEEANKVALVAPNATVNIVR
DYSVAEKFQVKPP
> Q8THL3^.^9^100^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate
carbamoyltransferase, Regulatory-chain, N-terminal domain^.^69.20^0.000e+00^2.0
00e-12
IQAIENGTVIDHITAGQALNVLRILRISSAFRATVSFVMNAPGARGKKDVVKIEGKELSVEELNRIALISPKATINIIR
DFEVVQKNKVVLP
> Q8PXK6^.^9^100^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate
carbamoyltransferase, Regulatory-chain, N-terminal domain^.^62.70^0.000e+00^2.0
00e-10
VQAIESGTVIDHIKSGQALNVLRILGISSAFRATISFVMNAPGAGGKKDVVKIEGKELSVEELNRIALISPKATINIIR
DFVVVQKNNVVLP
> Q8K9H8^.^8^99^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^.^146.00^0.000e+00^1.0
00e-35
VEAIKSGSVIDHIPAHIGFKLLSLFRFTETEKRITIGLNLPSQKLDKKDIIKIENTFLSDDQINQLAIYAPCATVNYIE
KYNLVGKIFPSLP
> Q8DCF7^.^9^100^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate
carbamoyltransferase, Regulatory-chain, N-terminal domain^.^127.00^0.000e+00^9.
000e-30
VEAIKNGTVIDHIPAQVGIKVLKLFDMHNSSQRVTIGLNLPSSALGNKDLLKIENVFINEEQASKLALYAPHATVNQIE
DYQVVKKLALELP
> Q8D1W6^.^9^100^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate
carbamoyltransferase, Regulatory-chain, N-terminal domain^.^123.00^0.000e+00^1.
000e-28
VEAIFGGTVIDHIPAQVGLKLLSLFKWLHTKERITMGLNLPSNQQKKKDLIKLENVLLNEDQANQLSIYAPLATVNQIK
NYIVIKKQKLKLP
> Q8A9S4^.^10^101^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-lik
e^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate
 carbamoyltransferase, Regulatory-chain, N-terminal domain^.^63.80^0.000e+00^9.
000e-11
VAALKNGTVIDHIPSEKLFTVVQLLGVEQMKCNITIGFNLDSKKLGKKGIIKIADKFFCDEEINRISVVAPYVKLNIIR
DYEVVEKKEVRMP
> Q891I9^.^4^94^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^.^52.30^0.000e+00^2.00
0e-07
ITSIKDGIVIDHIKSGYGIKIFNYLNLKNVEYSVALIMNVFSSKLGKKDIIKIANKEIDIDFTVLGLIDPTITINIIED
EKIKEKLNLELP
> Q87LF7^.^9^100^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate
carbamoyltransferase, Regulatory-chain, N-terminal domain^.^130.00^0.000e+00^7.
000e-31
VEAIKNGTVIDHIPAQIGIKVLKLFDMHNSSQRVTIGLNLPSSALGHKDLLKIENVFINEEQASKLALYAPHATVNQIE
NYEVVKKLALELP
> Q83IL8^.^8^99^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^.^189.00^0.000e+00^0.0
00e+00
VEAIKRGTVIDHIPAQIGFKLLSLFKLTETDQRITIGLNLPSGEMGRKDLIKIENTFLSEEQVDQLALYAPQATVNRID
NYEVVGKSRPSLP
> Q7P144^.^7^98^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^.^128.00^0.000e+00^3.0
00e-30
VEALKQGTVIDHIPAGEGVKILRLFKLTETGERVTVGLNLVSRHMGSKDLIKVENVALTEEQANELALFAPKATVNVID
NFEVVKKHKLTLP
> Q7MZ14^.^9^100^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate
carbamoyltransferase, Regulatory-chain, N-terminal domain^.^150.00^0.000e+00^6.
000e-37
VEAIRCGTVIDHIPAQVGFKLLSLFKLTETDQRITIGLNLPSNRLGKKDLIKIENTFLTEQQANQLAMYAPNATVNCIE
NYEVVKKLPINLP
> Q7MX57^.^8^99^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^.^80.80^0.000e+00^7.00
0e-16
VAAIRNGIVIDHIPPTKLFKVATLLQLDDLDKRITIGNNLRSRSHGSKGVIKIEDKTFEEEELNRIALIAPNVRLNIIR
DYEVVEKRQVEVP
> Q7MHF0^.^9^100^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate
carbamoyltransferase, Regulatory-chain, N-terminal domain^.^127.00^0.000e+00^8.
000e-30
VEAIKNGTVIDHIPAQVGIKVLKLFDMHNSSQRVTIGLNLPSSALGNKDLLKIENVFINEEQASKLALYAPHATVNQIE
DYQVVKKLALELP
> Q58801^.^9^99^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^.^61.50^0.000e+00^5.00
0e-10
VKKITNGTVIDHIDAGKALMVFKVLNVPKETSVMIAINVPSKKKGKKDILKIEGIELKKEDVDKISLISPDVTINIIRN
GKVVEKLKPQIP
> P96175^.^8^99^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^.^107.00^0.000e+00^7.0
00e-24
VEAICNGYVIDHIPSGQGVKILRLFSLTDTKQRVTVGFNLPSHDGTTKDLIKVENTEITKSQANQLALLAPNATVNIIE
NFKVTDKHSLALP
> P96111^.^375^472^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-li
ke^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartat
e carbamoyltransferase, Regulatory-chain, N-terminal domain^.^47.30^0.000e+00^9
.000e-06
GIKPIENGTVIDHIAKGKTPEEIYSTILKIRKILRLYDVDSADGIFRSSDGSFKGYISLPDRYLSKKEIKKLSAISPNT
TVNIIKNSTVVEKYRIKLP
> P77919^.^6^99^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^.^93.50^0.000e+00^1.00
0e-19
VSAIKEGTVIDHIPAGKGLKVIEILKLGKLTNGGAVLLAMNVPSKKLGRKDIVKVEGRFLSEEEVNKIALVAPNATVNI
IRDYKVVEKFKVEVP
> P74766^.^12^104^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-lik
e^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate
 carbamoyltransferase, Regulatory-chain, N-terminal domain^.^74.20^0.000e+00^7.
000e-14
VSKIKNGTVIDHIPAGRAFAVLNVLGIKGHEGFRIALVINVDSKKMGKKDIVKIEDKEISDTEANLITLIAPTATINIV
REYEVVKKTKLEVP
> P57451^.^8^99^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+00^1.0
00e-34
VEAIKSGSVIDHIPEYIGFKLLSLFRFTETEKRITIGLNLPSKKLGRKDIIKIENTFLSDEQINQLAIYAPHATVNYIN
EYNLVRKVFPTLP
> P19936^.^8^99^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^.^159.00^0.000e+00^0.0
00e+00
VEAIKCGTVIDHIPAQIGFKLLTLFKLTATDQRITIGLNLPSNELGRKDLIKIENTFLTEQQANQLAMYAPKATVNRID
NYEVVRKLTLSLP
> P08421^.^8^99^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^.^183.00^0.000e+00^0.0
00e+00
VEAIKCGTVIDHIPAQVGFKLLSLFKLTETDQRITIGLNLPSGEMGRKDLIKIENTFLTEEQVNQLALYAPQATVNRID
NYDVVGKSRPSLP
> P00478^.^8^99^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^.^191.00^0.000e+00^0.0
00e+00
VEAIKRGTVIDHIPAQIGFKLLSLFKLTETDQRITIGLNLPSGEMGRKDLIKIENTFLSEDQVDQLALYAPQATVNRID
NYEVVGKSRPSLP
> O58452^.^6^99^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^.^94.30^0.000e+00^6.00
0e-20
VSAIKEGTVIDHIPAGKGLKVIEILGLSKLSNGGSVLLAMNVPSKKLGRKDIVKVEGKFLSEEEVNKIALVAPTATVNI
IRNYKVVEKFKVEVP
> O30129^.^6^98^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^.^79.60^0.000e+00^2.00
0e-15
VSKIKEGTVIDHINAGKALLVLKILKIQPGTDLTVSMAMNVPSSKMGKKDIVKVEGMFIRDEELNKIALISPNATINLI
RDYEIERKFKVSPP
> O26938^.^11^101^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-lik
e^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate
 carbamoyltransferase, Regulatory-chain, N-terminal domain^.^81.90^0.000e+00^3.
000e-16
VKPIKNGTVIDHITANRSLNVLNILGLPDGRSKVTVAMNMDSSQLGSKDIVKIENRELKPSEVDQIALIAPRATINIVR
DYKIVEKAKVRL

  File: 55074.dhf

> Q9WVI4^.^513^667^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-li
ke^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase
 catalytic domain^.^113.00^0.000e+00^2.000e-25
RKFDDVTMLFSDIVGFTAICAQCTPMQVISMLNELYTRFDHQCGFLDIYKVETIGDAYCVASGLHRKSLCHAKPIALMA
LKMMELSEEVLTPDGRPIQMRIGIHSGSVLAGVVGVRMPRYCLFGNNVTLASKFESGSHPRRINISPTTYQLLKRE
> Q9ERL9^.^475^626^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-li
ke^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase
 catalytic domain^.^101.00^0.000e+00^9.000e-22
KKFSEVTMLFSDIVGFTAICSQCSPLQVITMLNALYTRFDQQCGELDVYKVETIGDAYCVAGGLHRESDTHAVQIALMA
LKMMELSNEVMSPHGEPIKMRIGLHSGSVFAGVVGVKMPRYCLFGNNVTLANKFESCSVPRKINVSPTTYRLL
> Q9DGG6^.^1032^1200^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-
like^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cycla
se catalytic domain^.^72.70^0.000e+00^4.000e-13
YSKNHDSGGVIFASIVNFSEFYEENYEGGKECYRVLNELIGDFDELLSKPHYSSIEKIKTIGATYMAASGLNTSQCQDS
NHPHGHLQTLFEFAKEMMRVVDDFNNNMLWFNFKLRIGFNHGPLTAGVIGTTKLLYDIWGDTVNIASRMDTIGVECRIQ
VSEETYRILSK
> Q9DGG6^.^369^560^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-li
ke^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase
 catalytic domain^.^172.00^0.000e+00^0.000e+00
IIFRPFKMQQIEQVSILFADIVGFTKMSANKSAHALVGLLNDLFGRFDRLCEDTKCEKISTLGDCYYCVAGCPEPRADH
AYCCIEMGLGMIKAIEQFCQEKKEMVNMRVGVHTGTVLCGILGMRRFKFDVWSNDVNLANLMEQLGVAGKVHISEATAK
YLDDRYEMEDGKVTERVGQSAVADQLKGLKTYLI
> Q99396^.^250^473^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-li
ke^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase
 catalytic domain^.^182.00^0.000e+00^0.000e+00
IMRNKRDNDNAPKELADPVTLIFTDIESSTAQWATQPELMPDAVATHHSMVRSLIENYDCYEVKTVGDSFMIACKSPFA
AVQLAQELQLRFLRLDWGTTVFDEFYREFEERHAEEGDGKYKPPTARLDPEVYRQLWNGLRVRVGIHTGLCDIRYDEVT
KGYDYYGQTANTAARTESVGNGGQVLMTCETYHSLSTAERSQFDVTPLGGVPLRGVSEPVEVYQLN
> Q99280^.^877^1092^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-l
ike^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclas
e catalytic domain^.^204.00^0.000e+00^0.000e+00
NDSAPKEPTGPVTLIFTDIESSTALWAAHPDLMPDAVATHHRLIRSLITRYECYEVKTVGDSFMIASKSPFAAVQLAQE
LQLRFLRLDWETNALDESYREFEEQRAEGECEYTPPTAHMDPEVYSRLWNGLRVRVGIHTGLCDIRYDEVTKGYDYYGR
TSNMAARTESVANGGQVLMTHAAYMSLSGEDRNQLDVTTLGATVLRGVPEPVRMYQLN
> Q99279^.^888^1105^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-l
ike^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclas
e catalytic domain^.^242.00^0.000e+00^0.000e+00
NNNRAPKEPTDPVTLIFTDIESSTALWAAHPDLMPDAVAAHHRMVRSLIGRYKCYEVKTVGDSFMIASKSPFAAVQLAQ
ELQLCFLHHDWGTNALDDSYREFEEQRAEGECEYTPPTAHMDPEVYSRLWNGLRVRVGIHTGLCDIIRHDEVTKGYDYY
GRTPNMAARTESVANGGQVLMTHAAYMSLSAEDRKQIDVTALGDVALRGVSDPVKMYQLN
> Q91WF3^.^863^1038^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-l
ike^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclas
e catalytic domain^.^81.20^0.000e+00^1.000e-15
NEDLYHQSYECVCVLFASVPDFKEFYSESNINHEGLECLRLLNEIIADFDELLSKPKFSGVEKIKTIGSTYMAATGLNA
TSGQDTQQDSERSCSHLGTMVEFAVALGSKLGVINKHSFNNFRLRVGLNHGPVVAGVIGAQKPQYDIWGNTVNVASRME
STGVLGKIQVTEETARAL
> Q91WF3^.^261^446^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-li
ke^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase
 catalytic domain^.^210.00^0.000e+00^0.000e+00
FHSLYVKRHQGVSVLYADIVGFTRLASECSPKELVLMLNELFGKFDQIAKEHECMRIKILGDCYYCVSGLPLSLPDHAI
NCVRMGLDMCRAIRKLRVATGVDINMRVGVHSGSVLCGVIGLQKWQYDVWSHDVTLANHMEAGGVPGRVHITGATLALL
AGAYAVERADTEHRDPYLRELGEPTYLV
> Q8VHH7^.^914^1090^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-l
ike^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclas
e catalytic domain^.^67.30^0.000e+00^2.000e-11
ELYSQSYDEIGVMFASLPNFADFYTEESINNGGIECLRFLNEIISDFDSLLDNPKFRVITKIKTIGSTYMAASGVTPDV
NTNGFTSSSKEEKSDKERWQHLADLADFALAMKDTLTNINNQSFNNFMLRIGMNKGGVLAGVIGARKPHYDIWGNTVNV
ASRMESTGVMGNIQVVEET
> Q8VHH7^.^307^492^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-li
ke^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase
 catalytic domain^.^228.00^0.000e+00^0.000e+00
FNTMYMYRHENVSILFADIVGFTQLSSACSAQELVKLLNELFARFDKLAAKYHQLRIKILGDCYYCICGLPDYREDHAV
CSILMGLAMVEAISYVREKTKTGVDMRVGVHTGTVLGGVLGQKRWQYDVWSTDVTVANKMEAGGIPGRVHISQSTMDCL
KGEFDVEPGDGGSRCDYLDEKGIETYLI
> Q8NFM4^.^861^1032^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-l
ike^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclas
e catalytic domain^.^81.20^0.000e+00^1.000e-15
NEDLYHQSYECVCVLFASVPDFKEFYSESNINHEGLECLRLLNEIIADFDELLSKPKFSGVEKIKTIGSTYMAATGLNA
TSGQDAQQDAERSCSHLGTMVEFAVALGSKLDVINKHSFNNFRLRVGLNHGPVVAGVIGAQKPQYDIWGNTVNVASRME
STGVLGKIQVTEET
> Q8NFM4^.^261^446^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-li
ke^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase
 catalytic domain^.^210.00^0.000e+00^0.000e+00
FHSLYVKRHQGVSVLYADIVGFTRLASECSPKELVLMLNELFGKFDQIAKEHECMRIKILGDCYYCVSGLPLSLPDHAI
NCVRMGLDMCRAIRKLRAATGVDINMRVGVHSGSVLCGVIGLQKWQYDVWSHDVTLANHMEAGGVPGRVHITGATLALL
AGAYAVEDAGMEHRDPYLRELGEPTYLV
> Q29450^.^864^1041^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-l
ike^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclas
e catalytic domain^.^84.30^0.000e+00^1.000e-16
LNEDWYHQSYDCVCVMFASVPDFKVFYTECDVNKEGLECLRLLNEIIADFDELLLKPKFSGVEKIKTIGSTYMAAAGLS
VPSGPENQDLERQHAHIGIMVEFSTALMSKLDGINRHSFNSFRLRVGINHGPVIAGVIGARKPQYDIWGNTVNVASRME
STGELGKIQVTEETCTILQG
> Q29450^.^267^452^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-li
ke^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase
 catalytic domain^.^230.00^0.000e+00^0.000e+00
FHNLYVKRHQNVSILYADIVGFTRLASDCSPKELVVVLNELFGKFDQIAKANECMRIKILGDCYYCVSGLPVSLPNHAR
NCVKMGLDMCEAIKQVREATGVDISMRVGIHSGNVLCGVIGLRKWQYDVWSHDVSLANRMEAAGVPGRVHITEATLKHL
DKAYEVEDGHGQQRDPYLKEMNIRTYLV
> Q27675^.^920^1136^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-l
ike^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclas
e catalytic domain^.^154.00^0.000e+00^1.000e-37
NNDAAPKDGDEPVTLLFTDIESSTALWAALPQLMSDAIAAHHRVIRQLVKKYGCYEVKTIGDSFMIACRSAHSAVSLAC
EIQTKLLKHDWGTEALDRAYREFELARVDTLDDYEPPTARLSEEEYAALWCGLRVRVGIHTGLTDIRYDEVTKGYDYYG
DTSNMAARTEAVANGGQVVATEAAWWALSNDERAGIAHTAMGPQGLRGVPFAVEMFQLN
> Q26896^.^381^587^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-li
ke^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase
 catalytic domain^.^177.00^0.000e+00^0.000e+00
DPVTLIFTDIESSTALWAAHPGMMADAVATHHRLIRSLIALYGAYEVKTVGDSFMIACRSAFAAVELARDLQLTLVHHD
WGTVAIDESYRKFEEERAVEDSDYAPPTARLDSAVYCKLWNGLRVRAGIHTGLCDIAHDEVTKGYDYYGRTPNLAARTE
SAANGGQVLVTGATYYSLSVAERARLDATPIGPVPLRGVPEPVEMYQLN
> Q26721^.^898^1103^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-l
ike^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclas
e catalytic domain^.^206.00^0.000e+00^0.000e+00
PVTLIFTDIESSTALWAAHPEVMPDAVATHHRLIRTLISKYECYEVKTVGDSFMIASKSPFAAVQLAQELQLCFLHHDW
GTNAIDESYQQFEQQRAEDDSDYTPPTARLDPKVYSRLWNGLRVRVGIHTGLCDIRRDEVTKGYDYYGRTSNMAARTES
VANGGQVLMTHAAYMSLSAEERQQIDVTALGDVPLRGVPKPVEMYRLN
> Q25263^.^927^1143^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-l
ike^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclas
e catalytic domain^.^153.00^0.000e+00^2.000e-37
NNDAAPKDGDEPVTLLFTDIESSTALWAALPQLMSDAIAAHHRVIRQLVKKYGCYEVKTIGDSFMIACRSAHSAVSLAC
EIQTKLLKHDWGTEALDRAYREFELARVDTLDDYEPPTARLSEEEYAALWCGLRVRVGIHTGLTDIRYDEVTRGYDYYG
DTSNMAARTEAVANGGQVVATEAAWWALSNDERAGIAHTAMGPQGLRGVPFAVEMFQLN
> Q11055^.^203^335^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-li
ke^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase
 catalytic domain^.^49.20^0.000e+00^6.000e-06
ERAAGKPLPGARQVTVAFADLVGFTQLGEVVSAEELGHLAGRLAGLARDLTAPPVWFIKTIGDAVMLVCPDPAPLLDTV
LKLVEVVDTDNNFPRLRAGVASGMAVSRAGDWFGSPVNVASRVTGVARPGAVLV
> Q10551^.^91^213^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-lik
e^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase
catalytic domain^.^53.40^0.000e+00^3.000e-07
VTLLLADVEESTHLWQMCPEDMATAIAHLDHTVSEAITNHGGVQPVKRYEGDSFVAAFTRASDAAACALDLQRTSLAPI
RLRIGLHTGEVQLRDELYVGPTINRTARLRDLAHGGQVVLSAAT
> Q09435^.^891^1050^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-l
ike^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclas
e catalytic domain^.^101.00^0.000e+00^9.000e-22
PEGFDSVTVFFSDVVKFTILASKCSPFQTVNLLNDLYSNFDTIIEQHGVYKVESIGDGYLCVSGLPTRNGYAHIKQIVD
MSLKFMEYCKSFNIPHLPRENVELRIGVNSGPCVAGVVGLSMPRYCLFGDTVNTASRMESNGKPSLIHLTNDAHSLLTT
HY
> Q08828^.^576^750^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-li
ke^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase
 catalytic domain^.^76.20^0.000e+00^4.000e-14
NMDLYYQSYSQVGVMFASIPNFNDFYIELDGNNMGVECLRLLNEIIADFDELMEKDFYKDIEKIKTIGSTYMAAVGLAP
TSGTKAKKSISSHLSTLADFAIEMFDVLDEINYQSYNDFVLRVGINVGPVVAGVIGARRPQYDIWGNTVNVASRMDSTG
VQGRIQVTEEVHRLLRR
> Q08828^.^10^196^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-lik
e^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase
catalytic domain^.^266.00^0.000e+00^0.000e+00
IFHKIYIQRHDNVSILFADIVGFTGLASQCTAQELVKLLNELFGKFDELATENHCRRIKILGDCYYCVSGLTQPKTDHA
HCCVEMGLDMIDTITSVAEATEVDLNMRVGLHTGRVLCGVLGLRKWQYDVWSNDVTLANVMEAAGLPGKVHITKTTLAC
LNGDYEVEPGYGHERNSFLKTHNIETFFI
> Q08462^.^873^1077^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-l
ike^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclas
e catalytic domain^.^79.60^0.000e+00^4.000e-15
LKNEELYHQSYDCVCVMFASIPDFKEFYTESDVNKEGLECLRLLNEIIADFDDLLSKPKFSGVEKIKTIGSTYMAATGL
SAVPSQEHSQEPERQYMHIGTMVEFAFALVGKLDAINKHSFNDFKLRVGINHGPVIAGVIGAQKPQYDIWGNTVNVASR
MDSTGVLDKIQVTEETSLVLQTLGYTCTCRGIINVKGKGDLKTYFVN


  [Part of this file has been deleted for brevity]

DSVTIYFSDIVGFTALSAESTPMQVVTLLNDLYTCFDAIIDNFDVYKVETIGDAYMVVSGLPGRNGQRHAPEIARMALA
LLDAVSSFRIRHRPHDQLRLRIGVHTGPVCAGVVGLKMPRYCLFGDTVNTASRMESNGQALKIHVSSTTKDALDELGCF
QLELRGDVE
> P19754^.^859^1033^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-l
ike^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclas
e catalytic domain^.^78.50^0.000e+00^8.000e-15
NMDLYYQSYSQVGVMFASIPNFNDFYIELDGNNMGVECLRLLNEIIADFDELMDKDFYKDLEKIKTIGSTYMAAVGLAP
TAGTKAKKCISSHLSTLADFAIEMFDVLDEINYQSYNDFVLRVGINVGPVVAGVIGARRPQYDIWGNTVNVASRMDSTG
VQGRIQVTEEVHRLLRR
> P19754^.^292^478^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-li
ke^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase
 catalytic domain^.^266.00^0.000e+00^0.000e+00
IFHKIYIQRHDNVSILFADIVGFTGLASQCTAQELVKLLNELFGKFDELATENHCRRIKILGDCYYCVSGLTQPKTDHA
HCCVEMGLDMIDTITSVAEATEVDLNMRVGLHTGRVLCGVLGLRKWQYDVWSNDVTLANVMEAAGLPGKVHITKTTLAC
LNGDYEVEPGHGHERNSFLKTHNIETFFI
> P19687^.^471^627^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-li
ke^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase
 catalytic domain^.^102.00^0.000e+00^4.000e-22
HAVQAKRFGNVTMLFSDIVGFTAICSQCSPLQVITMLNALYTRFDRQCGELDVYKVETIGDAYCVAGGLHKESDTHAVQ
IALMALKMMELSHEVVSPHGEPIKMRIGLHSGSVFAGVVGVKMPRYCLFGNNVTLANKFESCSVPRKINVSPTTYRLL
> P19686^.^474^625^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-li
ke^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase
 catalytic domain^.^102.00^0.000e+00^6.000e-22
KKFNEVTMLFSDIVGFTAICSQCSPLQVITMLNALYTRFDQQCGELDVYKVETIGDAYCVAGGLHRESDTHAVQIALMA
LKMMELSNEVMSPHGEPIKMRIGLHSGSVFAGVVGVKMPRYCLFGNNVTLANKFESCSVPRKINVSPTTYRLL
> P19485^.^470^607^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-li
ke^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase
 catalytic domain^.^61.10^0.000e+00^1.000e-09
VTAMFTDIYDFTTISEGRSPEEVVAMLSEYFDLFSEVVAAHDGTIIQFHGDSVFAMWNAPVADTRHAEHACRCALAVEE
RLEAFNSAQRASGLPEFRTRFGIHTGTAVVGSVGAKERLQYTAMGDTVNVASRLEGMNK
> P18910^.^869^1048^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-l
ike^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclas
e catalytic domain^.^107.00^0.000e+00^1.000e-23
DSVTIYFSDIVGFTALSAESTPMQVVTLLNDLYTCFDAVIDNFDVYKVETIGDAYMVVSGLPVRNGQLHAREVARMALA
LLDAVRSFRIRHRPQEQLRLRIGIHTGPVCAGVVGLKMPRYCLFGDTVNTASRMESNGEALKIHLSSETKAVLEEFDGF
ELELRGDVEMKGKGKVRTYWLL
> P18293^.^869^1048^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-l
ike^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclas
e catalytic domain^.^108.00^0.000e+00^6.000e-24
DSVTIYFSDIVGFTALSAESTPMQVVTLLNDLYTCFDAVIDNFDVYKVETIGDAYMVVSGLPVRNGQLHAREVARMALA
LLDAVRSFRIRHRPQEQLRLRIGIHTGPVCAGVVGLKMPRYCLFGDTVNTASRMESNGEALRIHLSSETKAVLEEFDGF
ELELRGDVEMKGKGKVRTYWLL
> P16068^.^406^572^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-li
ke^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase
 catalytic domain^.^100.00^0.000e+00^1.000e-21
LRHKRPVPAKRYDNVTILFSGIVGFNAFCSKHASGEGAMKIVNLLNDLYTRFDTLTDSRKNPFVYKVETVGDKYMTVSG
LPEPCIHHARSICHLALDMMEIAGQVQVDGESVQITIGIHTGEVVTGVIGQRMPRYCLFGNTVNLTSRTETTGEKGKIN
VSEYTYRCL
> P16067^.^858^1024^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-l
ike^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclas
e catalytic domain^.^107.00^0.000e+00^2.000e-23
DSVTIYFSDIVGFTALSAESTPMQVVTLLNDLYTCFDAIIDNFDVYKVETIGDAYMVVSGLPGRNGQRHAPEIARMALA
LLDAVSSFRIRHRPHDQLRLRIGVHTGPVCAGVVGLKMPRYCLFGDTVNTASRMESNGQALKIHVSSTTKDALDELGCF
QLELRGDVE
> P16066^.^873^1052^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-l
ike^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclas
e catalytic domain^.^107.00^0.000e+00^2.000e-23
DSVTIYFSDIVGFTALSAESTPMQVVTLLNDLYTCFDAVIDNFDVYKVETIGDAYMVVSGLPVRNGRLHACEVARMALA
LLDAVRSFRIRHRPQEQLRLRIGIHTGPVCAGVVGLKMPRYCLFGDTVNTASRMESNGEALKIHLSSETKAVLEEFGGF
ELELRGDVEMKGKGKVRTYWLL
> P16065^.^907^1055^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-l
ike^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclas
e catalytic domain^.^105.00^0.000e+00^6.000e-23
PETFEMVSIFFSDIVGFTALSAASTPIQVVNLLNDLYTLFDAIISNYDVYKVETIGDAYMLVSGLPLRNGDRHAGQIAS
TAHHLLESVKGFIVPHKPEVFLKLRIGIHSGSCVAGVVGLTMPRYCLFGDTVNTASRMESNGLALRIHVS
> P14605^.^1320^1501^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-
like^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cycla
se catalytic domain^.^69.60^0.000e+00^4.000e-12
MNREVSPPKGCIAMVFTDIKNSTLLWERHPIAMRSAIKTHNTIMRRQLRATGGYEVKTEGDAFMVCFQTVPAALLWCFS
VQLQLLSADWPNEIVESVQGRLVLGSKNEVLYRGLSVRIGVNYGVTVSELDPITRRMDYYGPVVNRTSRVVSVADGGQI
AVSAEVVSVLNQLDSETMSSEKTN
> P08678^.^1666^1825^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-
like^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cycla
se catalytic domain^.^75.40^0.000e+00^8.000e-14
NLAMVFTDIKSSTFLWELFPNAMRTAIKTHNDIMRRQLRIYGGYEVKTEGDAFMVAFPTPTSGLTWCLSVQLKLLDAQW
PEEITSVQDGCQVTDRNGNIIYQGLSVRMGIHWGCPVPELDLVTQRMDYLGPMVNKAARVQGVADGGQIAMSSDFYSEF
NK
> O95622^.^692^861^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-li
ke^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase
 catalytic domain^.^86.20^0.000e+00^4.000e-17
NDELYYQSCECVAVMFASIANFSEFYVELEANNEGVECLRLLNEIIADFDEIISEDRFRQLEKIKTIGSTYMAASGLND
STYDKVGKTHIKALADFAMKLMDQMKYINEHSFNNFQMKIGLNIGPVVAGVIGARKPQYDIWGNTVNVASRMDSTGVPD
RIQVTTDMYQVL
> O95622^.^88^276^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-lik
e^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase
catalytic domain^.^350.00^0.000e+00^0.000e+00
MMFHKIYIQKHDNVSILFADIEGFTSLASQCTAQELVMTLNELFARFDKLAAENHCLRIKILGDCYYCVSGLPEARADH
AHCCVEMGMDMIEAISLVREVTGVNVNMRVGIHSGRVHCGVLGLRKWQFDVWSNDVTLANHMEAGGKAGRIHITKATLN
YLNGDYEVEPGCGGERNAYLKEHSIETFLIL
> O75343^.^381^540^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-li
ke^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase
 catalytic domain^.^97.70^0.000e+00^1.000e-20
KVAAGEFKSCTILFSDVVTFTNICTACEPIQIVNVLNSMYSKFDRLTSVHAVYKVETIGDAYMVVGGVPVPIGNHAQRV
ANFALGMRISAKEVTNPVTGEPIQLRVGIHTGPVLADVVGDKMPRYCLFGDTVNTASRMESHGLPNKVHLSPTAYRALK
NQ
> O60503^.^1050^1218^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-
like^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cycla
se catalytic domain^.^70.00^0.000e+00^3.000e-12
YSKNHDSGGVIFASIVNFSEFYEENYEGGKECYRVLNELIGDFDELLSKPDYSSIEKIKTIGATYMAASGLNTAQAQDG
SHPQEHLQILFEFAKEMMRVVDDFNNNMLWFNFKLRVGFNHGPLTAGVIGTTKLLYDIWGDTVNIASRMDTTGVECRIQ
VSEESYRVLSK
> O60503^.^388^571^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-li
ke^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase
 catalytic domain^.^172.00^0.000e+00^0.000e+00
QQIEEVSILFADIVGFTKMSANKSAHALVGLLNDLFGRFDRLCEETKCEKISTLGDCYYCVAGCPEPRADHAYCCIEMG
LGMIKAIEQFCQEKKEMVNMRVGVHTGTVLCGILGMRRFKFDVWSNDVNLANLMEQLGVAGKVHISEATAKYLDDRYEM
EDGKVIERLGQSVVADQLKGLKTYLI
> O60266^.^913^1089^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-l
ike^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclas
e catalytic domain^.^68.10^0.000e+00^1.000e-11
ELYSQTYDEIGVMFASLPNFADFYTEESINNGGIECLRFLNEIISDFDSLLDNPKFRVITKIKTIGSTYMAASGVTPDV
NTNGFASSNKEDKSERERWQHLADLADFALAMKDTLTNINNQSFNNFMLRIGMNKGGVLAGVIGARKPHYDIWGNTVNV
ASRMESTGVMGNIQVVEET
> O60266^.^307^492^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-li
ke^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase
 catalytic domain^.^228.00^0.000e+00^0.000e+00
FNTMYMYRHENVSILFADIVGFTQLSSACSAQELVKLLNELFARFDKLAAKYHQLRIKILGDCYYCICGLPDYREDHAV
CSILMGLAMVEAISYVREKTKTGVDMRVGVHTGTVLGGVLGQKRWQYDVWSTDVTVANKMEAGGIPGRVHISQSTMDCL
KGEFDVEPGDGGSRCDYLEEKGIETYLI
> O43306^.^967^1136^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-l
ike^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclas
e catalytic domain^.^87.30^0.000e+00^2.000e-17
NDELYYQSCECVAVMFASIANFSEFYVELEANNEGVECLRLLNEIIADFDEIISEERFRQLEKIKTIGSTYMAASGLNA
STYDQVGRSHITALADYAMRLMEQMKHINEHSFNNFQMKIGLNMGPVVAGVIGARKPQYDIWGNTVNVSSRMDSTGVPD
RIQVTTDLYQVL
> O43306^.^365^553^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-li
ke^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase
 catalytic domain^.^338.00^0.000e+00^0.000e+00
MMFHKIYIQKHDNVSILFADIEGFTSLASQCTAQELVMTLNELFARFDKLAAENHCLRIKILGDCYYCVSGLPEARADH
AHCCVEMGVDMIEAISLVREVTGVNVNMRVGIHSGRVHCGVLGLRKWQFDVWSNDVTLANHMEAGGRAGRIHITRATLQ
YLNGDYEVEPGRGGERNAYLKEQHIETFLIL
> O30820^.^241^400^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-li
ke^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase
 catalytic domain^.^115.00^0.000e+00^6.000e-26
NIIADKYDEASVLFADIVGFTERASSTAPADLVRFLDRLYSAFDELVDQHGLEKIKVSGDSYMVVSGVPRPRPDHTQAL
ADFALDMTNVAAQLKDPRGNPVPLRVGLATGPVVAGVVGSRRFFYDVWGDAVNVASRMESTDSVGQIQVPDEVYERLKD
DF
> O19179^.^871^1032^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-l
ike^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclas
e catalytic domain^.^109.00^0.000e+00^3.000e-24
MGTPVEPEYFEEVTLYFSDIVGFTTISAMSEPIEVVDLLNDLYTLFDAIIGSHDVYKVETIGDAYMVASGLPQRNGQRH
AAEIANMALDILSAVGSFRMRHMPEVPVRIRIGLHSGPCVAGVVGLTMPRYCLFGDTVNTASRMESTGLPYRIHVNMST
VRIL
> O02740^.^877^1042^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-l
ike^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclas
e catalytic domain^.^112.00^0.000e+00^4.000e-25
PEGFDLVTLYFSDIVGFTTISAMSEPIEVVDLLNDLYTLFDAIIGSHDVYKVETIGDAYMVASGLPKRNGMRHAAEIAN
MSLDILSSVGTFKMRHMPEVPVRIRIGLHSGPVVAGVVGLTMPRYCLFGDTVNTASRMESTGLPYRIHVSHSTVTILRT
LGEGYEVE

5.0 DATA FILES

   None.

6.0 USAGE

  6.1 COMMAND LINE ARGUMENTS

   Standard (Mandatory) qualifiers:
  [-dhfinpath]         dirlist    This option specifies the location of DHF
                                  files (domain hits files) or other sequence
                                  files (input). A 'domain hits file' contains
                                  database hits (sequences) with domain
                                  classification information, in FASTA or EMBL
                                  formats. 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. Alternatively, SEQFRAGGLE
                                  will accept sequence or sequence sets in any
                                  of the common formats.
   -thresh             integer    This option specifies the percentage of
                                  median length for definition of fragments.
                                  SEQFRAGGLE first determines the median
                                  length of all the sequences in the input
                                  file, then discards any hit sequences which
                                  are not within a threshold percentage of the
                                  median length. The remaining sequences are
                                  written to the output file.
  [-dhfoutdir]         outdir     This option specifies the location of DHF
                                  files (domain hits files) (output). A
                                  'domain hits file' contains database hits
                                  (sequences) with domain classification
                                  information, in FASTA or EMBL formats. 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.
                                  Alternatively, SEQFRAGGLE will write output
                                  files in any of the common formats.

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers: (none)
   Associated qualifiers: (none)
   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 deaths


   Standard (Mandatory) qualifiers Allowed values Default
   [-dhfinpath]
   (Parameter 1) This option specifies the location of DHF files (domain
   hits files) or other sequence files (input). A 'domain hits file'
   contains database hits (sequences) with domain classification
   information, in FASTA or EMBL formats. 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. Alternatively, SEQFRAGGLE will accept sequence or
   sequence sets in any of the common formats. Directory with files ./
   -thresh This option specifies the percentage of median length for
   definition of fragments. SEQFRAGGLE first determines the median length
   of all the sequences in the input file, then discards any hit
   sequences which are not within a threshold percentage of the median
   length. The remaining sequences are written to the output file. Any
   integer value 50
   [-dhfoutdir]
   (Parameter 2) This option specifies the location of DHF files (domain
   hits files) (output). A 'domain hits file' contains database hits
   (sequences) with domain classification information, in FASTA or EMBL
   formats. 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. Alternatively,
   SEQFRAGGLE will write output files in any of the common formats.
   Output directory ./
   Additional (Optional) qualifiers Allowed values Default
   (none)
   Advanced (Unprompted) qualifiers Allowed values Default
   (none)

  6.2 EXAMPLE SESSION

   An example of interactive use of SEQFRAGGLE is shown below. Here is a
   sample session with seqfraggle


% seqfraggle 
Removes fragments from DHF files (domain hits files) or other files of
sequences.
Location of DHF files (domain hits files) or other sequence files (input). [./]
: structure
Percentage of median length for definition of fragments. [50]: 50
Location of DHF files (domain hits files) (output). [./]: 

Processing /ebi/services/idata/pmr/hgmp/test/data/structure/54894.dhf
Processing /ebi/services/idata/pmr/hgmp/test/data/structure/55074.dhf

   Go to the output files for this example

   All the domain hits files with the file extension .dhf (specified in
   the ACD file) in the directory /test_data were read. In this case two
   files called 55074.dhf and 54894.dhf were read. Two domain hits files
   (with the extension .dhf specified in ACD) with fragment sequences
   removed were written to /test_data/seqfraggle.

7.0 KNOWN BUGS & WARNINGS

   None.

8.0 NOTES

   None.

  8.1 GLOSSARY OF FILE TYPES

   FILE TYPE FORMAT DESCRIPTION CREATED BY SEE ALSO
   Domain hits file DHF format (FASTA-like format with domain
   classification information). Database hits (sequences) with domain
   classification information. The hits are relatives to a SCOP or CATH
   family and are found from a search of a sequence database. SEQSEARCH
   (hits retrieved by PSIBLAST) N.A.

   Written (2003) - Jon Ison None

9.0 DESCRIPTION

   Fragmentary protein sequences occur in the sequence databases but are
   not necessarily biologically significant. Certain analyses will be
   distorted if fragmentary sequences are not filtered from the dataset.
   SEQFRAGGLE reads domain hits files (or a set of sequences in another
   format) and writes new domain hits file in which sequences deemed to
   be fragments are ommitted.

10.0 ALGORITHM

   SEQFRAGGLE first determines the median length of all the sequences in
   the input file, then discards any hit sequences which are not within a
   threshold percentage (user defined) of the median length. The
   remaining sequences are written to the output file.

11.0 RELATED APPLICATIONS

See also

   Program name Description
   contactcount Counts specific versus non-specific contacts in a
   directory of cleaned protein chain contact files
   contacts Reads CCF files (clean coordinate files) and writes CON files
   (contact files) of intra-chain residue-residue contact data
   domainalign Generates DAF files (domain alignment files) of
   structure-based sequence alignments for nodes in a DCF file (domain
   classification file)
   domainrep Reorder DCF file (domain classification file) so that the
   representative structure of each user-specified node is given first
   domainreso Removes low resolution domains from a DCF file (domain
   classification file)
   interface Reads CCF files (clean coordinate files) and writes CON
   files (contact files) of inter-chain residue-residue contact data
   libgen Generates various types of discriminating elements for each
   alignment in a directory
   psiphi Calculates phi and psi torsion angles from cleaned EMBOSS-style
   protein co-ordinate file
   rocon Reads a DHF file (domain hits file) of hits (sequences of
   unknown structural classification) and a DHF file of validation
   sequences (known classification) and writes a 'hits file' for the
   hits, which are classified and rank-ordered on the basis of score
   rocplot Provides interpretation and graphical display of the
   performance of discriminating elements (e.g. profiles for protein
   families). rocplot reads file(s) of hits from discriminator-database
   search(es), performs ROC analysis on the hits, and writes graphs
   illustrating the diagnostic performance of the discriminating elements
   seqalign Reads a DAF file (domain alignment file) and a DHF file
   (domain hits file) and writes a DAF file extended with the hits
   seqsearch Generate database hits (sequences) for nodes in a DCF file
   (domain classification file) by using PSI-BLAST
   seqsort Reads DHF files (domain hits files) of database hits
   (sequences) and removes hits of ambiguous classification
   seqwords Generates DHF files (domain hits files) of database hits
   (sequences) for nodes in a DCF file (domain classification file) by
   keyword search of UniProt
   siggen Generates a sparse protein signature from an alignment and
   residue contact data
   sigscan Generates a DHF file (domain hits file) of hits (sequences)
   from scanning a signature against a sequence database

12.0 DIAGNOSTIC ERROR MESSAGES

   None.

13.0 AUTHORS

   Matt Blades (mathew_blades@yahoo.co.uk)
   Jon Ison (jison@rfcgr.mrc.ac.uk)
   MRC Rosalind Franklin Centre for Genomics Research, Wellcome Trust
   Genome Campus, Hinxton, Cambridge, CB10 1SB, UK

14.0 REFERENCES

   Please cite the authors and EMBOSS.
   Rice P, Longden I and Bleasby A (2000) "EMBOSS - The European
   Molecular Biology Open Software Suite" Trends in Genetics, 15:276-278.
   
   See also http://emboss.sourceforge.net/

  14.1 Other useful references
