                          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

   Remove 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^A
spartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate car
bamoyltransferase, Regulatory-chain, N-terminal domain^.^56.10^0.000e+00^9.000e+
00
VRKIRSGVVIDHIPPGRAFTMLKALGLLPPRGYRWRIAVVINAESSKLGRKDILKIEGYKPRQRDLEVLGIIAPGATFNV
IEDYKVVEKVKLKLP
> 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+
00
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
+00
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+
00
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+
00
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+
00
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+
00
VSKIQAGTVIDHIPAGQALQVLQILGTNGASDDQITVGMNVTSERHHRKDIVKIEGRELSQDEVDVLSLIAPDATINIVR
DYEVDEKRRVDRP
> 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+
00
INSIKNGIVIDHIKAGHGIKIYNYLKLGEAEFPTALIMNAISKKNKAKDIIKIENVMDLDLAVLGFLDPNITVNIIEDEK
IRQKIQLKLP
> 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+
00
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+
00
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+
00
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
+00
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+00^1.000e
+00
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+
00
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+
00
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+
00
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+
00
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
+00
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
+00
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
+00
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+
00
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+
00
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
+00
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+00^8.000e
+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
+00
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
+00
VEAIRCGTVIDHIPAQVGFKLLSLFKLTETDQRITIGLNLPSNRLGKKDLIKIENTFLTEQQANQLAMYAPNATVNCIEN
YEVVKKLPINLP
> 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+
00
VAAIRNGIVIDHIPPTKLFKVATLLQLDDLDKRITIGNNLRSRSHGSKGVIKIEDKTFEEEELNRIALIAPNVRLNIIRD
YEVVEKRQVEVP
> 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
+00
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+
00
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+
00
VEAICNGYVIDHIPSGQGVKILRLFSLTDTKQRVTVGFNLPSHDGTTKDLIKVENTEITKSQANQLALLAPNATVNIIEN
FKVTDKHSLALP
> 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+
00
GIKPIENGTVIDHIAKGKTPEEIYSTILKIRKILRLYDVDSADGIFRSSDGSFKGYISLPDRYLSKKEIKKLSAISPNTT
VNIIKNSTVVEKYRIKLP
> 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+
00
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+
00
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
+00
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
+00
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+00^4.000e
+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+00^2.000e
+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+
00
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+
00
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+
00
VKPIKNGTVIDHITANRSLNVLNILGLPDGRSKVTVAMNMDSSQLGSKDIVKIENRELKPSEVDQIALIAPRATINIVRD
YKIVEKAKVRL

  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 cat
alytic domain^.^77.00^0.000e+00^2.000e+00
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+00
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+00
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+00
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+00^1.000e+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+00^9.000e+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+00
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+00
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+00
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+00
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+00
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+00
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+00
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+00^1.000e+00
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+00^7.000e+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+00
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+00
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+00^2.000e+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+00
FHNLYVKRHTNVSILYADIVGFTRLASDCSPGELVHMLNELFGKFDQIAKENECMRIKILGDCYYCVSGLPISLPNHAKN
CVKMGLDMCEAIKKVRDATGVDINMRVGVHSGNVLCGVIGLQKWQYDVWSHDVTLANHMEAGGVPGRVHISSVTLEHLNG
AYKVEEGDGDIRDPYLKQHLVKTYFV
> 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+00
DCVCVMFASIPDFKEFYTESDVNKEGLECLRLLNEIIADFDDLLSKPKFSGVEKIKTIGSTYMAATGLSAVPSQEHSQEP
ERQYMHIGTMVEFAFALVGKLDAINKHSFNDFKLRVGINHGPVIAGVIGAQKPQYDIWGNTVNVASRMDSTGVLDKIQVT
EETSLVL
> 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+00
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+00
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+00^3.000e+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+00
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+00^3.000e+00
MMFHKIYIQKHDNVSILFADIEGFTSLASQCTAQELVMTLNELFARFDKLAAENHCLRIKILGDCYYCVSGLPEARADHA
HCCVEMGVDMIEAISLVREVTGVNVNMRVGIHSGRVHCGVLGLRKWQFDVWSNDVTLANHMEAGGRAGRIHITRATLQYL
NGDYEVEPGRGGERNGYLKEQCIETFLIL


  [Part of this file has been deleted for brevity]

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+00
VTIYFSDIVGFTTICKYSTPMEVVDMLNDIYKSFDQIVDHHDVYKVETIGDAYVVASGLPMRNGNRHAVDISKMALDILS
FMGTFELEHLPGLPVWIRIGVHSGPCAAGVVGIKMPRYCLFGDTVNTASRMESTGLPLRIHMSSSTIAIL
> 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+00
PTGNVAIVFTDIKNSTFLWELFPDAMRAAIKTHNDIMRRQLRIYGGYEVKTEGDAFMVAFPTPTSALVWCLSVQLKLLEA
EWPEEITSIQDGCLITDNSGTKVYLGLSVRMGVHWGCPVPEIDLVTQRMDYLGPVVNKAARVSGVADGGQITLS
> 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+00
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+00
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+00
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+00
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+00^2.000e+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+00
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+00
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+00
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+00
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+00
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+00
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+00
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+00
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+00^1.000e+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+00
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+00
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+00
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+00
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+00^1.000e+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+00
VAVMFASIANFSEFYVELEANNEGVECLRLLNEIIADFDEIISEERFRQLEKIKTIGSTYMAASGLNASTYDQVGRSHIT
ALADYAMRLMEQMKHINEHSFNNFQMKIGLNMGPVVAGVIGARKPQYDIWGNTVNVSSRMDSTGVPDRIQVTTDLYQVL
> 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+00
DEASVLFADIVGFTERASSTAPADLVRFLDRLYSAFDELVDQHGLEKIKVSGDSYMVVSGVPRPRPDHTQALADFALDMT
NVAAQLKDPRGNPVPLRVGLATGPVVAGVVGSRRFFYDVWGDAVNVASRMESTDSVGQIQVPDEVYERL
> 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+00
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+00
DLVTLYFSDIVGFTTISAMSEPIEVVDLLNDLYTLFDAIIGSHDVYKVETIGDAYMVASGLPKRNGMRHAAEIANMSLDI
LSSVGTFKMRHMPEVPVRIRIGLHSGPVVAGVVGLTMPRYCLFGDTVNTASRMESTGLPYRIHVSHSTVTILRTLGEGYE
VE

5.0 DATA FILES

   None.

6.0 USAGE

  6.1 COMMAND LINE ARGUMENTS

Remove fragment sequences from DHF files.
Version: EMBOSS:6.6.0.0

   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    [50] 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)
  [-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:

   "-dhfinpath" associated qualifiers
   -extension1         string     Default file extension

   "-dhfoutdir" associated qualifiers
   -extension2         string     Default file extension

   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


