
                          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 fragment sequences from DHF files

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^.^1^95^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate c
arbamoyltransferase, Regulatory-chain, N-terminal domain^.^55.30^0.000e+00^2.00
0e-11
VRKIRSGVVIDHIPPGRAFTMLKALGLLPPRGYRWRIAVVINAESSKLGRKDILKIEGYKPRQRDLEVLGIIAPGATFN
VIEDYKVVEKVKLKLP
> Q9UX07^.^1^93^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate c
arbamoyltransferase, Regulatory-chain, N-terminal domain^.^59.20^0.000e+00^1.00
0e-12
VSKIRNGTVIDHIPAGRALAVLRILGIRGSEGYRVALVMNVESKKIGRKDIVKIEDRVIDEKEASLITLIAPSATINII
RDYVVTEKRHLEVP
> Q9KP65^.^1^92^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate c
arbamoyltransferase, Regulatory-chain, N-terminal domain^.^119.00^0.000e+00^9.0
00e-31
VEAIKNGTVIDHIPAKVGIKVLKLFDMHNSAQRVTIGLNLPSSALGSKDLLKIENVFISEAQANKLALYAPHATVNQIE
NYEVVKKLALQLP
> Q9K1K9^.^1^92^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate c
arbamoyltransferase, Regulatory-chain, N-terminal domain^.^91.90^0.000e+00^2.00
0e-22
VEAIEKGTVIDHIPAGRGLTILRQFKLLHYGNAVTVGFNLPSKTQGSKDIIKIKGVCLDDKAADRLALFAPEAVVNTID
NFKVVQKRHLNLP
> Q9JWY6^.^1^92^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate c
arbamoyltransferase, Regulatory-chain, N-terminal domain^.^90.40^0.000e+00^5.00
0e-22
VEAIEKGTVIDHIPAGRGLTILRQFKLLHYGNAVTVGFNLPSKTQGSKDIIKIKGVCLDDKAADRLALFAPEAVVNTID
HFKVVQKRHLNLP
> Q9HKM3^.^1^93^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate c
arbamoyltransferase, Regulatory-chain, N-terminal domain^.^71.90^0.000e+00^2.00
0e-16
ISKIRDGTVIDHVPSGKGIRVIGVLGVHEDVNYTVSLAIHVPSNKMGFKDVIKIENRFLDRNELDMISLIAPNATISII
KNYEISEKFQVELP
> Q9HHN3^.^1^93^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate c
arbamoyltransferase, Regulatory-chain, N-terminal domain^.^70.40^0.000e+00^4.00
0e-16
VSKIQAGTVIDHIPAGQALQVLQILGTNGASDDQITVGMNVTSERHHRKDIVKIEGRELSQDEVDVLSLIAPDATINIV
RDYEVDEKRRVDRP
> Q97FS4^.^1^90^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate c
arbamoyltransferase, Regulatory-chain, N-terminal domain^.^42.60^0.000e+00^1.00
0e-07
INSIKNGIVIDHIKAGHGIKIYNYLKLGEAEFPTALIMNAISKKNKAKDIIKIENVMDLDLAVLGFLDPNITVNIIEDE
KIRQKIQLKLP
> Q97B28^.^1^93^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate c
arbamoyltransferase, Regulatory-chain, N-terminal domain^.^71.90^0.000e+00^2.00
0e-16
ISKIKDGTVIDHIPSGKALRVLSILGIRDDVDYTVSVGMHVPSSKMEYKDVIKIENRSLDKNELDMISLTAPNATISII
KNYEISEKFKVELP
> Q970X3^.^1^91^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate c
arbamoyltransferase, Regulatory-chain, N-terminal domain^.^71.10^0.000e+00^3.00
0e-16
VSKIKNGTVIDHIPAGRALAVLRILKIAEGYRIALVMNVESKKMGKKDIVKIENKEVDEKEANLITLIAPTATINIIRD
YEVVEKKKLKIP
> Q8ZTG2^.^1^93^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate c
arbamoyltransferase, Regulatory-chain, N-terminal domain^.^58.00^0.000e+00^3.00
0e-12
VSKIENGTVIDHIPAGRALTVLRILGISGKEGLRVALVMNVESKKLGKKDIVKIEGRELTPEEVNIISAVAPTATINII
RNFAVVKKFKVTPP
> Q8ZB38^.^1^92^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate c
arbamoyltransferase, Regulatory-chain, N-terminal domain^.^143.00^0.000e+00^3.0
00e-38
VEAIKCGTVIDHIPAQIGFKLLSLFKLTATDQRITIGLNLPSKRSGRKDLIKIENTFLTEQQANQLAMYAPDATVNRID
NYEVVKKLTLSLP
> Q8Z130^.^1^92^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate c
arbamoyltransferase, Regulatory-chain, N-terminal domain^.^167.00^0.000e+00^0.0
00e+00
VEAIKCGTVIDHIPAQVGFKLLSLFKLTETDQRITIGLNLPSGEMGRKDLIKIENTFLTDEQVNQLALYAPQATVNRID
NYDVVGKSRPSLP
> Q8U374^.^1^94^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate c
arbamoyltransferase, Regulatory-chain, N-terminal domain^.^82.70^0.000e+00^1.00
0e-19
VSAIKEGTVIDHIPAGKGLKVIQILGLGELKNGGAVLLAMNVPSKKLGRKDIVKVEGKFLSEEEVNKIALVAPTATVNI
IREYKVVEKFKVEIP
> Q8TVB1^.^1^92^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate c
arbamoyltransferase, Regulatory-chain, N-terminal domain^.^65.40^0.000e+00^2.00
0e-14
VKRIEMGTVLDHLPPGTAPQIMRILDIDPTETTLLVAINVESSKMGRKDILKIEGKILSEEEANKVALVAPNATVNIVR
DYSVAEKFQVKPP
> Q8THL3^.^1^92^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate c
arbamoyltransferase, Regulatory-chain, N-terminal domain^.^66.50^0.000e+00^7.00
0e-15
IQAIENGTVIDHITAGQALNVLRILRISSAFRATVSFVMNAPGARGKKDVVKIEGKELSVEELNRIALISPKATINIIR
DFEVVQKNKVVLP
> Q8PXK6^.^1^92^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate c
arbamoyltransferase, Regulatory-chain, N-terminal domain^.^60.70^0.000e+00^4.00
0e-13
VQAIESGTVIDHIKSGQALNVLRILGISSAFRATISFVMNAPGAGGKKDVVKIEGKELSVEELNRIALISPKATINIIR
DFVVVQKNNVVLP
> Q8K9H8^.^1^92^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate c
arbamoyltransferase, Regulatory-chain, N-terminal domain^.^135.00^0.000e+00^1.0
00e-35
VEAIKSGSVIDHIPAHIGFKLLSLFRFTETEKRITIGLNLPSQKLDKKDIIKIENTFLSDDQINQLAIYAPCATVNYIE
KYNLVGKIFPSLP
> Q8DCF7^.^1^92^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate c
arbamoyltransferase, Regulatory-chain, N-terminal domain^.^116.00^0.000e+00^5.0
00e-30
VEAIKNGTVIDHIPAQVGIKVLKLFDMHNSSQRVTIGLNLPSSALGNKDLLKIENVFINEEQASKLALYAPHATVNQIE
DYQVVKKLALELP
> Q8D1W6^.^1^92^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate c
arbamoyltransferase, Regulatory-chain, N-terminal domain^.^113.00^0.000e+00^5.0
00e-29
VEAIFGGTVIDHIPAQVGLKLLSLFKWLHTKERITMGLNLPSNQQKKKDLIKLENVLLNEDQANQLSIYAPLATVNQIK
NYIVIKKQKLKLP
> Q8A9S4^.^1^92^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate c
arbamoyltransferase, Regulatory-chain, N-terminal domain^.^57.30^0.000e+00^4.00
0e-12
VAALKNGTVIDHIPSEKLFTVVQLLGVEQMKCNITIGFNLDSKKLGKKGIIKIADKFFCDEEINRISVVAPYVKLNIIR
DYEVVEKKEVRMP
> Q891I9^.^1^91^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate c
arbamoyltransferase, Regulatory-chain, N-terminal domain^.^46.10^0.000e+00^1.00
0e-08
ITSIKDGIVIDHIKSGYGIKIFNYLNLKNVEYSVALIMNVFSSKLGKKDIIKIANKEIDIDFTVLGLIDPTITINIIED
EKIKEKLNLELP
> Q87LF7^.^1^92^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate c
arbamoyltransferase, Regulatory-chain, N-terminal domain^.^121.00^0.000e+00^2.0
00e-31
VEAIKNGTVIDHIPAQIGIKVLKLFDMHNSSQRVTIGLNLPSSALGHKDLLKIENVFINEEQASKLALYAPHATVNQIE
NYEVVKKLALELP
> Q83IL8^.^1^92^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate c
arbamoyltransferase, Regulatory-chain, N-terminal domain^.^174.00^0.000e+00^0.0
00e+00
VEAIKRGTVIDHIPAQIGFKLLSLFKLTETDQRITIGLNLPSGEMGRKDLIKIENTFLSEEQVDQLALYAPQATVNRID
NYEVVGKSRPSLP
> Q7P144^.^1^92^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate c
arbamoyltransferase, Regulatory-chain, N-terminal domain^.^117.00^0.000e+00^3.0
00e-30
VEALKQGTVIDHIPAGEGVKILRLFKLTETGERVTVGLNLVSRHMGSKDLIKVENVALTEEQANELALFAPKATVNVID
NFEVVKKHKLTLP
> Q7MZ14^.^1^92^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate c
arbamoyltransferase, Regulatory-chain, N-terminal domain^.^139.00^0.000e+00^6.0
00e-37
VEAIRCGTVIDHIPAQVGFKLLSLFKLTETDQRITIGLNLPSNRLGKKDLIKIENTFLTEQQANQLAMYAPNATVNCIE
NYEVVKKLPINLP
> Q7MX57^.^1^92^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate c
arbamoyltransferase, Regulatory-chain, N-terminal domain^.^72.70^0.000e+00^1.00
0e-16
VAAIRNGIVIDHIPPTKLFKVATLLQLDDLDKRITIGNNLRSRSHGSKGVIKIEDKTFEEEELNRIALIAPNVRLNIIR
DYEVVEKRQVEVP
> Q7MHF0^.^1^92^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate c
arbamoyltransferase, Regulatory-chain, N-terminal domain^.^116.00^0.000e+00^5.0
00e-30
VEAIKNGTVIDHIPAQVGIKVLKLFDMHNSSQRVTIGLNLPSSALGNKDLLKIENVFINEEQASKLALYAPHATVNQIE
DYQVVKKLALELP
> Q58801^.^1^91^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate c
arbamoyltransferase, Regulatory-chain, N-terminal domain^.^53.40^0.000e+00^6.00
0e-11
VKKITNGTVIDHIDAGKALMVFKVLNVPKETSVMIAINVPSKKKGKKDILKIEGIELKKEDVDKISLISPDVTINIIRN
GKVVEKLKPQIP
> P96175^.^1^92^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate c
arbamoyltransferase, Regulatory-chain, N-terminal domain^.^98.10^0.000e+00^2.00
0e-24
VEAICNGYVIDHIPSGQGVKILRLFSLTDTKQRVTVGFNLPSHDGTTKDLIKVENTEITKSQANQLALLAPNATVNIIE
NFKVTDKHSLALP
> P96111^.^1^98^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate c
arbamoyltransferase, Regulatory-chain, N-terminal domain^.^42.20^0.000e+00^1.00
0e-07
GIKPIENGTVIDHIAKGKTPEEIYSTILKIRKILRLYDVDSADGIFRSSDGSFKGYISLPDRYLSKKEIKKLSAISPNT
TVNIIKNSTVVEKYRIKLP
> P77919^.^1^94^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate c
arbamoyltransferase, Regulatory-chain, N-terminal domain^.^83.80^0.000e+00^4.00
0e-20
VSAIKEGTVIDHIPAGKGLKVIEILKLGKLTNGGAVLLAMNVPSKKLGRKDIVKVEGRFLSEEEVNKIALVAPNATVNI
IRDYKVVEKFKVEVP
> P74766^.^1^93^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate c
arbamoyltransferase, Regulatory-chain, N-terminal domain^.^67.30^0.000e+00^4.00
0e-15
VSKIKNGTVIDHIPAGRAFAVLNVLGIKGHEGFRIALVINVDSKKMGKKDIVKIEDKEISDTEANLITLIAPTATINIV
REYEVVKKTKLEVP
> P57451^.^1^92^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate c
arbamoyltransferase, Regulatory-chain, N-terminal domain^.^131.00^0.000e+00^2.0
00e-34
VEAIKSGSVIDHIPEYIGFKLLSLFRFTETEKRITIGLNLPSKKLGRKDIIKIENTFLSDEQINQLAIYAPHATVNYIN
EYNLVRKVFPTLP
> P19936^.^1^92^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate c
arbamoyltransferase, Regulatory-chain, N-terminal domain^.^147.00^0.000e+00^0.0
00e+00
VEAIKCGTVIDHIPAQIGFKLLTLFKLTATDQRITIGLNLPSNELGRKDLIKIENTFLTEQQANQLAMYAPKATVNRID
NYEVVRKLTLSLP
> P08421^.^1^92^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate c
arbamoyltransferase, Regulatory-chain, N-terminal domain^.^168.00^0.000e+00^0.0
00e+00
VEAIKCGTVIDHIPAQVGFKLLSLFKLTETDQRITIGLNLPSGEMGRKDLIKIENTFLTEEQVNQLALYAPQATVNRID
NYDVVGKSRPSLP
> P00478^.^1^92^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate c
arbamoyltransferase, Regulatory-chain, N-terminal domain^.^175.00^0.000e+00^0.0
00e+00
VEAIKRGTVIDHIPAQIGFKLLSLFKLTETDQRITIGLNLPSGEMGRKDLIKIENTFLSEDQVDQLALYAPQATVNRID
NYEVVGKSRPSLP
> O58452^.^1^94^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate c
arbamoyltransferase, Regulatory-chain, N-terminal domain^.^85.40^0.000e+00^2.00
0e-20
VSAIKEGTVIDHIPAGKGLKVIEILGLSKLSNGGSVLLAMNVPSKKLGRKDIVKVEGKFLSEEEVNKIALVAPTATVNI
IRNYKVVEKFKVEVP
> O30129^.^1^93^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate c
arbamoyltransferase, Regulatory-chain, N-terminal domain^.^70.40^0.000e+00^5.00
0e-16
VSKIKEGTVIDHINAGKALLVLKILKIQPGTDLTVSMAMNVPSSKMGKKDIVKVEGMFIRDEELNKIALISPNATINLI
RDYEIERKFKVSPP
> O26938^.^1^91^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate c
arbamoyltransferase, Regulatory-chain, N-terminal domain^.^73.80^0.000e+00^4.00
0e-17
VKPIKNGTVIDHITANRSLNVLNILGLPDGRSKVTVAMNMDSSQLGSKDIVKIENRELKPSEVDQIALIAPRATINIVR
DYKIVEKAKVRL

  File: 55074.dhf

> Q9WVI4^.^1^149^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase c
atalytic domain^.^84.40^0.000e+00^1.000e-19
DDVTMLFSDIVGFTAICAQCTPMQVISMLNELYTRFDHQCGFLDIYKVETIGDAYCVASGLHRKSLCHAKPIALMALKM
MELSEEVLTPDGRPIQMRIGIHSGSVLAGVVGVRMPRYCLFGNNVTLASKFESGSHPRRINISPTTYQLL
> Q9ERL9^.^1^152^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase c
atalytic domain^.^72.10^0.000e+00^5.000e-16
VTMLFSDIVGFTAICSQCSPLQVITMLNALYTRFDQQCGELDVYKVETIGDAYCVAGGLHRESDTHAVQIALMALKMME
LSNEVMSPHGEPIKMRIGLHSGSVFAGVVGVKMPRYCLFGNNVTLANKFESCSVPRKINVSPTTYRLLKDCPG
> Q9DGG6^.^1^181^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase c
atalytic domain^.^142.00^0.000e+00^4.000e-37
EQVSILFADIVGFTKMSANKSAHALVGLLNDLFGRFDRLCEDTKCEKISTLGDCYYCVAGCPEPRADHAYCCIEMGLGM
IKAIEQFCQEKKEMVNMRVGVHTGTVLCGILGMRRFKFDVWSNDVNLANLMEQLGVAGKVHISEATAKYLDDRYEMEDG
KVTERVGQSAVADQLKGLKTYLI
> Q99396^.^1^212^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase c
atalytic domain^.^192.00^0.000e+00^0.000e+00
KELADPVTLIFTDIESSTAQWATQPELMPDAVATHHSMVRSLIENYDCYEVKTVGDSFMIACKSPFAAVQLAQELQLRF
LRLDWGTTVFDEFYREFEERHAEEGDGKYKPPTARLDPEVYRQLWNGLRVRVGIHTGLCDIRYDEVTKGYDYYGQTANT
AARTESVGNGGQVLMTCETYHSLSTAERSQFDVTPLGGVPLRGVSEPVEVYQLN
> Q99280^.^1^216^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase c
atalytic domain^.^218.00^0.000e+00^0.000e+00
NDSAPKEPTGPVTLIFTDIESSTALWAAHPDLMPDAVATHHRLIRSLITRYECYEVKTVGDSFMIASKSPFAAVQLAQE
LQLRFLRLDWETNALDESYREFEEQRAEGECEYTPPTAHMDPEVYSRLWNGLRVRVGIHTGLCDIRYDEVTKGYDYYGR
TSNMAARTESVANGGQVLMTHAAYMSLSGEDRNQLDVTTLGATVLRGVPEPVRMYQLN
> Q99279^.^1^218^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase c
atalytic domain^.^258.00^0.000e+00^0.000e+00
NNNRAPKEPTDPVTLIFTDIESSTALWAAHPDLMPDAVAAHHRMVRSLIGRYKCYEVKTVGDSFMIASKSPFAAVQLAQ
ELQLCFLHHDWGTNALDDSYREFEEQRAEGECEYTPPTAHMDPEVYSRLWNGLRVRVGIHTGLCDIIRHDEVTKGYDYY
GRTPNMAARTESVANGGQVLMTHAAYMSLSAEDRKQIDVTALGDVALRGVSDPVKMYQLN
> Q91WF3^.^1^165^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase c
atalytic domain^.^54.30^0.000e+00^1.000e-10
VCVLFASVPDFKEFYSESNINHEGLECLRLLNEIIADFDELLSKPKFSGVEKIKTIGSTYMAATGLNATSGQDTQQDSE
RSCSHLGTMVEFAVALGSKLGVINKHSFNNFRLRVGLNHGPVVAGVIGAQKPQYDIWGNTVNVASRMESTGVLGKIQVT
EETARAL
> Q91WF3^.^1^158^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase c
atalytic domain^.^160.00^0.000e+00^0.000e+00
FHSLYVKRHQGVSVLYADIVGFTRLASECSPKELVLMLNELFGKFDQIAKEHECMRIKILGDCYYCVSGLPLSLPDHAI
NCVRMGLDMCRAIRKLRVATGVDINMRVGVHSGSVLCGVIGLQKWQYDVWSHDVTLANHMEAGGVPGRVHITGATLALL
> Q8VHH7^.^1^186^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase c
atalytic domain^.^178.00^0.000e+00^0.000e+00
FNTMYMYRHENVSILFADIVGFTQLSSACSAQELVKLLNELFARFDKLAAKYHQLRIKILGDCYYCICGLPDYREDHAV
CSILMGLAMVEAISYVREKTKTGVDMRVGVHTGTVLGGVLGQKRWQYDVWSTDVTVANKMEAGGIPGRVHISQSTMDCL
KGEFDVEPGDGGSRCDYLDEKGIETYLI
> Q8NFM4^.^1^161^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase c
atalytic domain^.^54.70^0.000e+00^9.000e-11
VCVLFASVPDFKEFYSESNINHEGLECLRLLNEIIADFDELLSKPKFSGVEKIKTIGSTYMAATGLNATSGQDAQQDAE
RSCSHLGTMVEFAVALGSKLDVINKHSFNNFRLRVGLNHGPVVAGVIGAQKPQYDIWGNTVNVASRMESTGVLGKIQVT
EET
> Q8NFM4^.^1^158^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase c
atalytic domain^.^160.00^0.000e+00^0.000e+00
FHSLYVKRHQGVSVLYADIVGFTRLASECSPKELVLMLNELFGKFDQIAKEHECMRIKILGDCYYCVSGLPLSLPDHAI
NCVRMGLDMCRAIRKLRAATGVDINMRVGVHSGSVLCGVIGLQKWQYDVWSHDVTLANHMEAGGVPGRVHITGATLALL
> Q29450^.^1^186^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase c
atalytic domain^.^179.00^0.000e+00^0.000e+00
FHNLYVKRHQNVSILYADIVGFTRLASDCSPKELVVVLNELFGKFDQIAKANECMRIKILGDCYYCVSGLPVSLPNHAR
NCVKMGLDMCEAIKQVREATGVDISMRVGIHSGNVLCGVIGLRKWQYDVWSHDVSLANRMEAAGVPGRVHITEATLKHL
DKAYEVEDGHGQQRDPYLKEMNIRTYLV
> Q27675^.^1^217^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase c
atalytic domain^.^167.00^0.000e+00^0.000e+00
NNDAAPKDGDEPVTLLFTDIESSTALWAALPQLMSDAIAAHHRVIRQLVKKYGCYEVKTIGDSFMIACRSAHSAVSLAC
EIQTKLLKHDWGTEALDRAYREFELARVDTLDDYEPPTARLSEEEYAALWCGLRVRVGIHTGLTDIRYDEVTKGYDYYG
DTSNMAARTEAVANGGQVVATEAAWWALSNDERAGIAHTAMGPQGLRGVPFAVEMFQLN
> Q26896^.^1^216^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase c
atalytic domain^.^195.00^0.000e+00^0.000e+00
NDSAPKEFTDPVTLIFTDIESSTALWAAHPGMMADAVATHHRLIRSLIALYGAYEVKTVGDSFMIACRSAFAAVELARD
LQLTLVHHDWGTVAIDESYRKFEEERAVEDSDYAPPTARLDSAVYCKLWNGLRVRAGIHTGLCDIAHDEVTKGYDYYGR
TPNLAARTESAANGGQVLVTGATYYSLSVAERARLDATPIGPVPLRGVPEPVEMYQLN
> Q26721^.^1^206^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase c
atalytic domain^.^223.00^0.000e+00^0.000e+00
PVTLIFTDIESSTALWAAHPEVMPDAVATHHRLIRTLISKYECYEVKTVGDSFMIASKSPFAAVQLAQELQLCFLHHDW
GTNAIDESYQQFEQQRAEDDSDYTPPTARLDPKVYSRLWNGLRVRVGIHTGLCDIRRDEVTKGYDYYGRTSNMAARTES
VANGGQVLMTHAAYMSLSAEERQQIDVTALGDVPLRGVPKPVEMYRLN
> Q25263^.^1^217^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase c
atalytic domain^.^166.00^0.000e+00^0.000e+00
NNDAAPKDGDEPVTLLFTDIESSTALWAALPQLMSDAIAAHHRVIRQLVKKYGCYEVKTIGDSFMIACRSAHSAVSLAC
EIQTKLLKHDWGTEALDRAYREFELARVDTLDDYEPPTARLSEEEYAALWCGLRVRVGIHTGLTDIRYDEVTRGYDYYG
DTSNMAARTEAVANGGQVVATEAAWWALSNDERAGIAHTAMGPQGLRGVPFAVEMFQLN
> Q09435^.^1^161^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase c
atalytic domain^.^79.80^0.000e+00^2.000e-18
DSVTVFFSDVVKFTILASKCSPFQTVNLLNDLYSNFDTIIEQHGVYKVESIGDGYLCVSGLPTRNGYAHIKQIVDMSLK
FMEYCKSFNIPHLPRENVELRIGVNSGPCVAGVVGLSMPRYCLFGDTVNTASRMESNGKPSLIHLTNDAHSLLTTHYPN
QYE
> Q08828^.^1^186^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase c
atalytic domain^.^217.00^0.000e+00^0.000e+00
FHKIYIQRHDNVSILFADIVGFTGLASQCTAQELVKLLNELFGKFDELATENHCRRIKILGDCYYCVSGLTQPKTDHAH
CCVEMGLDMIDTITSVAEATEVDLNMRVGLHTGRVLCGVLGLRKWQYDVWSNDVTLANVMEAAGLPGKVHITKTTLACL
NGDYEVEPGYGHERNSFLKTHNIETFFI
> Q08462^.^1^186^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase c
atalytic domain^.^180.00^0.000e+00^0.000e+00
FHNLYVKRHTNVSILYADIVGFTRLASDCSPGELVHMLNELFGKFDQIAKENECMRIKILGDCYYCVSGLPISLPNHAK
NCVKMGLDMCEAIKKVRDATGVDINMRVGVHSGNVLCGVIGLQKWQYDVWSHDVTLANHMEAGGVPGRVHISSVTLEHL
NGAYKVEEGDGDIRDPYLKQHLVKTYFV
> Q08462^.^1^167^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase c
atalytic domain^.^49.70^0.000e+00^3.000e-09
DCVCVMFASIPDFKEFYTESDVNKEGLECLRLLNEIIADFDDLLSKPKFSGVEKIKTIGSTYMAATGLSAVPSQEHSQE
PERQYMHIGTMVEFAFALVGKLDAINKHSFNDFKLRVGINHGPVIAGVIGAQKPQYDIWGNTVNVASRMDSTGVLDKIQ
VTEETSLVL
> Q07553^.^1^152^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase c
atalytic domain^.^82.50^0.000e+00^4.000e-19
DCVTILFSDIVGFTELCTTSTPFEVVEMLNDWYTCCDSIISNYDVYKVETIGDAYMVVSGLPLQNGSRHAGEIASLALH
LLETVGNLKIRHKPTETVQLRIGVHSGPCAAGVVGQKMPRYCLFGDTVNTASRMESTGDSMRIHISEATYQLL
> Q07093^.^1^158^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase c
atalytic domain^.^65.50^0.000e+00^5.000e-14
VTILFSDIVGFTSICSRATPFMVISMLEGLYKDFDEFCDFFDVYKVETIGDAYCVASGLHRASIYDAHRCLDGLKMIDA
CSKHITHDGEQIKMRIGLHTGTVLAGVVGRKMPRYCLFGHSVTIANKFESGSEALKINVSPTTKDWLTKHEGFEFELQP
> Q04400^.^1^189^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase c
atalytic domain^.^299.00^0.000e+00^0.000e+00
MMFHKIYIQKHDNVSILFADIEGFTSLASQCTAQELVMTLNELFARFDKLAAENHCLRIKILGDCYYCVSGLPEARADH
AHCCVEMGMDMIEAISSVREVTGVNVNMRVGIHSGRVHCGVLGLRKWQFDVWSNDVTLANHMEAGGKAGRIHITKATLN
YLNGDYEVEPGCGGERNAYLKEHSIETFLIL
> Q04400^.^1^159^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase c
atalytic domain^.^55.10^0.000e+00^7.000e-11
VAVMFASIANFSEFYVELEANNEGVECLRLLNEIIADFDEIISEDRFRQLEKIKTIGSTYMAASGLNDSTYDKAGKTHI
KALADFAMKLMDQMKYINEHSFNNFQMKIGLNIGPVVAGVIGARKPQYDIWGNTVNVASRMDSTGVPDRIQVTTDMYQV
L
> Q03343^.^1^189^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase c
atalytic domain^.^285.00^0.000e+00^0.000e+00
MMFHKIYIQKHDNVSILFADIEGFTSLASQCTAQELVMTLNELFARFDKLAAENHCLRIKILGDCYYCVSGLPEARADH
AHCCVEMGVDMIEAISLVREVTGVNVNMRVGIHSGRVHCGVLGLRKWQFDVWSNDVTLANHMEAGGRAGRIHITRATLQ
YLNGDYEVEPGRGGERNGYLKEQCIETFLIL


  [Part of this file has been deleted for brevity]

VTIYFSDIVGFTTICKYSTPMEVVDMLNDIYKSFDHIVDHHDVYKVETIGDAYMVASGLPKRNGNRHAIDIAKMALEIL
SFMGTFELEHLPGLPIWIRIGVHSGPCAAGVVGIKMPRYCLFGDTVNTASRMESTGLPLRIHVSGSTIAIL
> P23897^.^1^150^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase c
atalytic domain^.^71.70^0.000e+00^8.000e-16
VTIYFSDIVGFTTICKYSTPMEVVDMLNDIYKSFDQIVDHHDVYKVETIGDAYVVASGLPMRNGNRHAVDISKMALDIL
SFMGTFELEHLPGLPVWIRIGVHSGPCAAGVVGIKMPRYCLFGDTVNTASRMESTGLPLRIHMSSSTIAIL
> P23466^.^1^154^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase c
atalytic domain^.^55.90^0.000e+00^4.000e-11
PTGNVAIVFTDIKNSTFLWELFPDAMRAAIKTHNDIMRRQLRIYGGYEVKTEGDAFMVAFPTPTSALVWCLSVQLKLLE
AEWPEEITSIQDGCLITDNSGTKVYLGLSVRMGVHWGCPVPEIDLVTQRMDYLGPVVNKAARVSGVADGGQITLS
> P22717^.^1^147^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase c
atalytic domain^.^63.20^0.000e+00^3.000e-13
TILFSDVVTFTNICAACEPIQIVNMLNSMYSKFDRLTSVHDVYKVETIGDAYMVVGGVPVPVESHAQRVANFALGMRIS
AKEVMNPVTGEPIQIRVGIHTGPVLAGVVGDKMPRYCLFGDTVNTASRMESHGLPSKVHLSPTAHRAL
> P21932^.^1^186^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase c
atalytic domain^.^178.00^0.000e+00^0.000e+00
FNTMYMYRHENVSILFADIVGFTQLSSACSAQELVKLLNELFARFDKLAAKYHQLRIKILGDCYYCICGLPDYREDHAV
CSILMGLAMVEAISYVREKTKTGVDMRVGVHTGTVLGGVLGQKRWQYDVWSTDVTVANKMEAGGIPGRVHISQSTMDCL
KGEFDVEPGDGGSRCDYLDEKGIETYLI
> P20595^.^1^165^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase c
atalytic domain^.^75.90^0.000e+00^4.000e-17
HKRPVPAKRYDNVTILFSGIVGFNAFCSKHASGEGAMKIVNLLNDLYTRFDTLTDSRKNPFVYKVETVGDKYMTVSGLP
EPCIHHARSICHLALDMMEIAGQVQVDGESVQITIGIHTGEVVTGVIGQRMPRYCLFGNTVNLTSRTETTGEKGKINVS
EYTYRCL
> P20594^.^1^168^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase c
atalytic domain^.^84.40^0.000e+00^1.000e-19
VQAEAFDSVTIYFSDIVGFTALSAESTPMQVVTLLNDLYTCFDAIIDNFDVYKVETIGDAYMVVSGLPGRNGQRHAPEI
ARMALALLDAVSSFRIRHRPHDQLRLRIGVHTGPVCAGVVGLKMPRYCLFGDTVNTASRMESNGQALKIHVSSTTKDAL
DELGCFQLEL
> P19754^.^1^186^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase c
atalytic domain^.^217.00^0.000e+00^0.000e+00
FHKIYIQRHDNVSILFADIVGFTGLASQCTAQELVKLLNELFGKFDELATENHCRRIKILGDCYYCVSGLTQPKTDHAH
CCVEMGLDMIDTITSVAEATEVDLNMRVGLHTGRVLCGVLGLRKWQYDVWSNDVTLANVMEAAGLPGKVHITKTTLACL
NGDYEVEPGHGHERNSFLKTHNIETFFI
> P19687^.^1^161^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase c
atalytic domain^.^77.10^0.000e+00^1.000e-17
AVQAKRFGNVTMLFSDIVGFTAICSQCSPLQVITMLNALYTRFDRQCGELDVYKVETIGDAYCVAGGLHKESDTHAVQI
ALMALKMMELSHEVVSPHGEPIKMRIGLHSGSVFAGVVGVKMPRYCLFGNNVTLANKFESCSVPRKINVSPTTYRLLKD
CPG
> P19686^.^1^160^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase c
atalytic domain^.^72.50^0.000e+00^4.000e-16
VQAKKFNEVTMLFSDIVGFTAICSQCSPLQVITMLNALYTRFDQQCGELDVYKVETIGDAYCVAGGLHRESDTHAVQIA
LMALKMMELSNEVMSPHGEPIKMRIGLHSGSVFAGVVGVKMPRYCLFGNNVTLANKFESCSVPRKINVSPTTYRLLKDC
PG
> P18910^.^1^168^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase c
atalytic domain^.^84.40^0.000e+00^1.000e-19
VQAEAFDSVTIYFSDIVGFTALSAESTPMQVVTLLNDLYTCFDAVIDNFDVYKVETIGDAYMVVSGLPVRNGQLHAREV
ARMALALLDAVRSFRIRHRPQEQLRLRIGIHTGPVCAGVVGLKMPRYCLFGDTVNTASRMESNGEALKIHLSSETKAVL
EEFDGFELEL
> P18293^.^1^168^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase c
atalytic domain^.^85.90^0.000e+00^4.000e-20
VQAEAFDSVTIYFSDIVGFTALSAESTPMQVVTLLNDLYTCFDAVIDNFDVYKVETIGDAYMVVSGLPVRNGQLHAREV
ARMALALLDAVRSFRIRHRPQEQLRLRIGIHTGPVCAGVVGLKMPRYCLFGDTVNTASRMESNGEALRIHLSSETKAVL
EEFDGFELEL
> P16068^.^1^165^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase c
atalytic domain^.^75.90^0.000e+00^4.000e-17
HKRPVPAKRYDNVTILFSGIVGFNAFCSKHASGEGAMKIVNLLNDLYTRFDTLTDSRKNPFVYKVETVGDKYMTVSGLP
EPCIHHARSICHLALDMMEIAGQVQVDGESVQITIGIHTGEVVTGVIGQRMPRYCLFGNTVNLTSRTETTGEKGKINVS
EYTYRCL
> P16067^.^1^168^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase c
atalytic domain^.^84.40^0.000e+00^1.000e-19
VQAEAFDSVTIYFSDIVGFTALSAESTPMQVVTLLNDLYTCFDAIIDNFDVYKVETIGDAYMVVSGLPGRNGQRHAPEI
ARMALALLDAVSSFRIRHRPHDQLRLRIGVHTGPVCAGVVGLKMPRYCLFGDTVNTASRMESNGQALKIHVSSTTKDAL
DELGCFQLEL
> P16066^.^1^168^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase c
atalytic domain^.^84.80^0.000e+00^7.000e-20
VQAEAFDSVTIYFSDIVGFTALSAESTPMQVVTLLNDLYTCFDAVIDNFDVYKVETIGDAYMVVSGLPVRNGRLHACEV
ARMALALLDAVRSFRIRHRPQEQLRLRIGIHTGPVCAGVVGLKMPRYCLFGDTVNTASRMESNGEALKIHLSSETKAVL
EEFGGFELEL
> P16065^.^1^143^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase c
atalytic domain^.^82.10^0.000e+00^5.000e-19
VSIFFSDIVGFTALSAASTPIQVVNLLNDLYTLFDAIISNYDVYKVETIGDAYMLVSGLPLRNGDRHAGQIASTAHHLL
ESVKGFIVPHKPEVFLKLRIGIHSGSCVAGVVGLTMPRYCLFGDTVNTASRMESNGLALRIHVS
> O95622^.^1^189^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase c
atalytic domain^.^301.00^0.000e+00^0.000e+00
MMFHKIYIQKHDNVSILFADIEGFTSLASQCTAQELVMTLNELFARFDKLAAENHCLRIKILGDCYYCVSGLPEARADH
AHCCVEMGMDMIEAISLVREVTGVNVNMRVGIHSGRVHCGVLGLRKWQFDVWSNDVTLANHMEAGGKAGRIHITKATLN
YLNGDYEVEPGCGGERNAYLKEHSIETFLIL
> O95622^.^1^159^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase c
atalytic domain^.^55.10^0.000e+00^7.000e-11
VAVMFASIANFSEFYVELEANNEGVECLRLLNEIIADFDEIISEDRFRQLEKIKTIGSTYMAASGLNDSTYDKVGKTHI
KALADFAMKLMDQMKYINEHSFNNFQMKIGLNIGPVVAGVIGARKPQYDIWGNTVNVASRMDSTGVPDRIQVTTDMYQV
L
> O75343^.^1^147^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase c
atalytic domain^.^68.20^0.000e+00^8.000e-15
TILFSDVVTFTNICTACEPIQIVNVLNSMYSKFDRLTSVHAVYKVETIGDAYMVVGGVPVPIGNHAQRVANFALGMRIS
AKEVTNPVTGEPIQLRVGIHTGPVLADVVGDKMPRYCLFGDTVNTASRMESHGLPNKVHLSPTAYRAL
> O60503^.^1^179^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase c
atalytic domain^.^143.00^0.000e+00^2.000e-37
VSILFADIVGFTKMSANKSAHALVGLLNDLFGRFDRLCEETKCEKISTLGDCYYCVAGCPEPRADHAYCCIEMGLGMIK
AIEQFCQEKKEMVNMRVGVHTGTVLCGILGMRRFKFDVWSNDVNLANLMEQLGVAGKVHISEATAKYLDDRYEMEDGKV
IERLGQSVVADQLKGLKTYLI
> O60266^.^1^186^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase c
atalytic domain^.^179.00^0.000e+00^0.000e+00
FNTMYMYRHENVSILFADIVGFTQLSSACSAQELVKLLNELFARFDKLAAKYHQLRIKILGDCYYCICGLPDYREDHAV
CSILMGLAMVEAISYVREKTKTGVDMRVGVHTGTVLGGVLGQKRWQYDVWSTDVTVANKMEAGGIPGRVHISQSTMDCL
KGEFDVEPGDGGSRCDYLEEKGIETYLI
> O43306^.^1^189^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase c
atalytic domain^.^287.00^0.000e+00^0.000e+00
MMFHKIYIQKHDNVSILFADIEGFTSLASQCTAQELVMTLNELFARFDKLAAENHCLRIKILGDCYYCVSGLPEARADH
AHCCVEMGVDMIEAISLVREVTGVNVNMRVGIHSGRVHCGVLGLRKWQFDVWSNDVTLANHMEAGGRAGRIHITRATLQ
YLNGDYEVEPGRGGERNAYLKEQHIETFLIL
> O43306^.^1^159^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase c
atalytic domain^.^55.90^0.000e+00^3.000e-11
VAVMFASIANFSEFYVELEANNEGVECLRLLNEIIADFDEIISEERFRQLEKIKTIGSTYMAASGLNASTYDQVGRSHI
TALADYAMRLMEQMKHINEHSFNNFQMKIGLNMGPVVAGVIGARKPQYDIWGNTVNVSSRMDSTGVPDRIQVTTDLYQV
L
> O30820^.^1^149^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase c
atalytic domain^.^80.20^0.000e+00^2.000e-18
DEASVLFADIVGFTERASSTAPADLVRFLDRLYSAFDELVDQHGLEKIKVSGDSYMVVSGVPRPRPDHTQALADFALDM
TNVAAQLKDPRGNPVPLRVGLATGPVVAGVVGSRRFFYDVWGDAVNVASRMESTDSVGQIQVPDEVYERL
> O19179^.^1^161^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase c
atalytic domain^.^82.50^0.000e+00^4.000e-19
VTLYFSDIVGFTTISAMSEPIEVVDLLNDLYTLFDAIIGSHDVYKVETIGDAYMVASGLPQRNGQRHAAEIANMALDIL
SAVGSFRMRHMPEVPVRIRIGLHSGPCVAGVVGLTMPRYCLFGDTVNTASRMESTGLPYRIHVNMSTVRILHALDEGFQ
TEV
> O02740^.^1^162^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase c
atalytic domain^.^85.20^0.000e+00^7.000e-20
DLVTLYFSDIVGFTTISAMSEPIEVVDLLNDLYTLFDAIIGSHDVYKVETIGDAYMVASGLPKRNGMRHAAEIANMSLD
ILSSVGTFKMRHMPEVPVRIRIGLHSGPVVAGVVGLTMPRYCLFGDTVNTASRMESTGLPYRIHVSHSTVTILRTLGEG
YEVE

5.0 DATA FILES

   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 fragment sequences from DHF files.
Location of DHF files (domain hits files) or other sequence files (input). [./]
: ../seqsearch-keep
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/qa/seqsearch-keep/55074.dhf
Processing /ebi/services/idata/pmr/hgmp/test/qa/seqsearch-keep/54894.dhf

   Go to the output files for this example

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). Database hits (sequences)
   with domain classification information. The hits are relatives to a
   SCOP or CATH family (or other node in the structural hierarchies) and
   are found from a search of a discriminating element (e.g. a protein
   signature, hidden Markov model, simple frequency matrix, Gribskov
   profile or Hennikoff profile) against a sequence database. SEQSEARCH
   (hits retrieved by PSIBLAST). SIGSCAN (hits retrieved by sparse
   protein signature). LIBSCAN (hits retrieved by various types of HMM
   and profile). 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 Count specific versus non-specific contacts
   contacts     Generate intra-chain CON files from CCF files
   domainalign  Generate alignments (DAF file) for nodes in a DCF file
   domainrep    Reorder DCF file to identify representative structures
   domainreso   Remove low resolution domains from a DCF file
   interface    Generate inter-chain CON files from CCF files
   libgen       Generate discriminating elements from alignments
   matgen3d     Generate a 3D-1D scoring matrix from CCF files
   psiphi       Phi and psi torsion angles from protein coordinates
   rocon        Generates a hits file from comparing two DHF files
   rocplot      Performs ROC analysis on hits files
   scorecmapdir Contact scores for cleaned protein chain contact files
   seqalign     Extend alignments (DAF file) with sequences (DHF file)
   seqsearch    Generate PSI-BLAST hits (DHF file) from a DAF file
   seqsort      Remove ambiguous classified sequences from DHF files
   seqwords     Generates DHF files from keyword search of UniProt
   siggen       Generates a sparse protein signature from an alignment
   siggenlig    Generate ligand-binding signatures from a CON file
   sigscan      Generate hits (DHF file) from a signature search
   sigscanlig   Search ligand-signature library & write hits (LHF file)

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
