YRC Public Data Repository - Protein Structure Prediction

Protein:	SRS2
Organism:	Saccharomyces cerevisiae
Length:	1174 amino acids
Reference:	Malmström L, et al. (2007) Superfamily assignments for the yeast proteome through integration of structure prediction with the gene ontology. PLoS Biol 5(4): e76. doi:10.1371/journal.pbio.0050076

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Top Sequence Alignment Hits

Listed below are up to the top 10 sequence alignment matches, by species, for the PSI-BLAST search against the protein sequence for SRS2.

Description	E-value	Query Range	Subject Range
SRS2 - DNA helicase and DNA-dependent ATPase involved in DNA repair, needed for proper timing of commitment... SRS2_YEAST - ATP-dependent DNA helicase SRS2 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=SRS2 PE=...	0.0	[1..1174]	[1..1175]
gi\|253326607, gi... - gi\|254290505\|ref\|YP_003056253.1\| DNA-dependent ATPase I and helicase II [Escherichia coli BL21(DE3)]... gi\|13364219, gi\|... - gi\|15833997\|ref\|NP_312770.1\| DNA-dependent helicase II [Escherichia coli O157:H7 str. Sakai], gi\|133... gi\|253975656, gi... - gi\|254163755\|ref\|YP_003046863.1\| DNA-dependent ATPase I and helicase II [Escherichia coli B str. REL... gi\|110345730, gi... - gi\|110644138\|ref\|YP_671868.1\| DNA-dependent helicase II [Escherichia coli 536], gi\|110345730\|gb\|ABG7... gi\|227888602, gi... - gi\|227888602\|ref\|ZP_04006407.1\| excision endonuclease subunit UvrD [Escherichia coli 83972], gi\|2278... gi\|251787070, gi... - gi\|251787070\|ref\|YP_003001374.1\| hypothetical protein B21_03638 [Escherichia coli BL21], gi\|24237934... gi\|74314325, gi\|... - gi\|74314325\|ref\|YP_312744.1\| DNA-dependent helicase II [Shigella sonnei Ss046], gi\|73857802\|gb\|AAZ90... gi\|254795809, gi... - gi\|254795809\|ref\|YP_003080646.1\| DNA-dependent ATPase I and helicase II [Escherichia coli O157:H7 st... gi\|115515196, gi... - gi\|117626072\|ref\|YP_859395.1\| DNA-dependent helicase II [Escherichia coli APEC O1], gi\|115515196\|gb\|... gi\|25290766, gi\|... - pir\|\|B86068 DNA-dependent ATPase I and helicase II [imported] - Escherichia coli (strain O157:H7, su... gi\|15804402, gi\|... - gi\|15804402\|ref\|NP_290442.1\| DNA-dependent helicase II [Escherichia coli O157:H7 EDL933], gi\|1251868... gi\|13364219, gi\|... - gi\|15833997\|ref\|NP_312770.1\| DNA-dependent ATPase I and helicase II [Escherichia coli O157:H7], gi\|1... gi\|195938102 - gi\|195938102\|ref\|ZP_03083484.1\| DNA-dependent helicase II [Escherichia coli O157:H7 str. EC4024] gi\|208727159, gi... - gi\|208807358\|ref\|ZP_03249695.1\| DNA helicase II [Escherichia coli O157:H7 str. EC4206], gi\|208727159... gi\|208735256, gi... - gi\|208813979\|ref\|ZP_03255308.1\| DNA helicase II [Escherichia coli O157:H7 str. EC4045], gi\|208735256... gi\|208739927, gi... - gi\|208819804\|ref\|ZP_03260124.1\| DNA helicase II [Escherichia coli O157:H7 str. EC4042], gi\|208739927... gi\|168801123, gi... - gi\|189376660\|gb\|EDU95076.1\| DNA helicase II [Escherichia coli O157:H7 str. EC508], gi\|168801123\|ref\|... gi\|170679582, gi... - gi\|170679582\|ref\|YP_001746130.1\| DNA helicase II [Escherichia coli SMS-3-5], gi\|170517300\|gb\|ACB1547... gi\|191174264, gi... - gi\|191174264\|ref\|ZP_03035773.1\| DNA helicase II [Escherichia coli F11], gi\|190905447\|gb\|EDV65077.1\| ... gi\|194438675, gi... - gi\|194438675\|ref\|ZP_03070763.1\| DNA helicase II [Escherichia coli 101-1], gi\|194422479\|gb\|EDX38478.1... gi\|168768094, gi... - gi\|189362636\|gb\|EDU81055.1\| DNA helicase II [Escherichia coli O157:H7 str. EC4486], gi\|168768094\|ref... gi\|168775636, gi... - gi\|187768818\|gb\|EDU32662.1\| DNA helicase II [Escherichia coli O157:H7 str. EC4196], gi\|168775636\|ref... gi\|189001426, gi... - gi\|189001426\|gb\|EDU70412.1\| DNA helicase II [Escherichia coli O157:H7 str. EC4076], gi\|168780712\|ref... gi\|189373276, gi... - gi\|189373276\|gb\|EDU91692.1\| DNA helicase II [Escherichia coli O157:H7 str. EC869], gi\|168786651\|ref\|... gi\|161486051 - gi\|161486051\|ref\|NP_756593.2\| DNA-dependent helicase II [Escherichia coli CFT073] gi\|162138327 - gi\|162138327\|ref\|YP_543324.2\| DNA-dependent helicase II [Escherichia coli UTI89] gi\|168750375, gi... - gi\|188015427\|gb\|EDU53549.1\| DNA helicase II [Escherichia coli O157:H7 str. EC4113], gi\|168750375\|ref... gi\|189359023, gi... - gi\|189359023\|gb\|EDU77442.1\| DNA helicase II [Escherichia coli O157:H7 str. EC4401], gi\|168753710\|ref... gi\|209157402, gi... - gi\|209396002\|ref\|YP_002273330.1\| DNA helicase II [Escherichia coli O157:H7 str. EC4115], gi\|20915740... gi\|215489141, gi... - gi\|215489141\|ref\|YP_002331572.1\| DNA-dependent helicase II [Escherichia coli O127:H6 str. E2348/69],... gi\|218550963, gi... - gi\|218550963\|ref\|YP_002384754.1\| DNA-dependent helicase II [Escherichia fergusonii ATCC 35469], gi\|2...	0.0	[10..814]	[5..693]
gi\|2625021 - gi\|2625021\|gb\|AAC46278.1\| DNA helicase II [Serratia marcescens]	0.0	[10..814]	[5..693]
gi\|85676237, gi\|... - gi\|89110206\|ref\|AP_003986.1\| DNA-dependent ATPase I and helicase II [Escherichia coli str. K-12 subs... gi\|194429230, gi... - gi\|194429230\|ref\|ZP_03061758.1\| DNA helicase II [Escherichia coli B171], gi\|194412742\|gb\|EDX29036.1\|... gi\|194434041, gi... - gi\|194434041\|ref\|ZP_03066311.1\| DNA helicase II [Shigella dysenteriae 1012], gi\|194417699\|gb\|EDX3379... gi\|238902889, gi... - gi\|238902889\|ref\|YP_002928685.1\| DNA-dependent ATPase I and helicase II [Escherichia coli BW2952], g... gi\|218354263, gi... - gi\|218697531\|ref\|YP_002405198.1\| DNA-dependent helicase II [Escherichia coli 55989], gi\|218354263\|em... UVRD_ECOLI - DNA helicase II (EC 3.6.1.-) - Escherichia coli gi\|170083295, gi... - gi\|170083295\|ref\|YP_001732615.1\| DNA-dependent ATPase I and helicase II [Escherichia coli str. K-12 ... gi\|192926639, gi... - gi\|193065672\|ref\|ZP_03046737.1\| DNA helicase II [Escherichia coli E22], gi\|192926639\|gb\|EDV81268.1\| ... EG11064 - DNA-dependent ATPase I and helicase II / ATP-dependent 3'-5' DNA helicase II; unwinds forked DNA str... EG11064 - DNA-dependent ATPase I and helicase II / ATP-dependent 3'-5' DNA helicase II; unwinds forked DNA str...	0.0	[10..814]	[5..693]
gi\|16762183 - gi\|16762183\|ref\|NP_457800.1\| DNA-dependent helicase II [Salmonella enterica subsp. enterica serovar ... gi\|213425413 - gi\|213425413\|ref\|ZP_03358163.1\| DNA-dependent helicase II [Salmonella enterica subsp. enterica serov... gi\|213649574 - gi\|213649574\|ref\|ZP_03379627.1\| DNA-dependent helicase II [Salmonella enterica subsp. enterica serov... gi\|25290775, gi\|... - gi\|25290775\|pir\|\|AG0918 DNA helicase II [imported] - Salmonella enterica subsp. enterica serovar Typ... gi\|213865062 - gi\|213865062\|ref\|ZP_03387181.1\| DNA-dependent helicase II [Salmonella enterica subsp. enterica serov... gi\|29139307, gi\|... - gi\|29143672\|ref\|NP_807014.1\| DNA-dependent helicase II [Salmonella enterica subsp. enterica serovar ... gi\|213161539 - gi\|213161539\|ref\|ZP_03347249.1\| DNA-dependent helicase II [Salmonella enterica subsp. enterica serov...	0.0	[10..814]	[5..693]
gi\|148212\|gb\|AAA... - DNA helicase II [Escherichia coli] gi\|148212 - gi\|148212\|gb\|AAA67609.1\| DNA helicase II [Escherichia coli]	0.0	[10..814]	[5..693]
UVRD_SALTY - DNA helicase II OS=Salmonella typhimurium GN=uvrD PE=3 SV=2 lcl\|NC_016856.1_... - [gene=uvrD] [protein=DNA-dependent helicase II] [protein_id=YP_005240211.1] [location=4169232..41713... UVRD_SALTY - DNA helicase II OS=Salmonella typhimurium GN=uvrD PE=3 SV=2 gi\|197242160, gi... - gi\|197263905\|ref\|ZP_03163979.1\| DNA helicase II [Salmonella enterica subsp. enterica serovar Saintpa... UVRD_SALTY - DNA helicase II OS=Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) GN=uvrD PE=3 SV=2 gi\|167993889, gi... - gi\|205328129\|gb\|EDZ14893.1\| DNA helicase II [Salmonella enterica subsp. enterica serovar 4,[5],12:i:...	0.0	[10..814]	[5..693]

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Predicted Domain #1

Region A:
Residues: [1-313]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MSSNNDLWLH LVSQLNTQQR AAALFDYTRG LQVIAGPGTG KTKVLTSRVA YLILHHHIHP  60
   61 RDIIVTTFTN KAANEMKERL QEMLRGAGVN ISELLIGTFH SICLKILYRF GHLVDLQKDW 120
  121 RIIDEKEIDV ILDDMIEKVP DQIRDYASSI TRKVNLCMPS KNGDEWTIHP KLIKKQISKL 180
  181 KSNAILPEEY ILDSNHDAAL GYFYQIYQSE LSKKNTLDFD DLLMYTFRLL TRVRVLSNIK 240
  241 HVLVDEFQDT NGIQLDLMFL FAKGNHHLSR GMTIVGDPDQ SIYAFRNALA HNFLEMGRKC 300
  301 PIEYSTIILV ENY

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	715.9691
Match:	1pjr__
Description:	DEXX box DNA helicase
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
binding	2.44689197844883	bayes_pls_golite062009
nucleoside-triphosphatase activity	1.5002869400376	bayes_pls_golite062009
pyrophosphatase activity	1.49611313354225	bayes_pls_golite062009
hydrolase activity, acting on acid anhydrides	1.47468810672455	bayes_pls_golite062009
hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides	1.47371190790284	bayes_pls_golite062009
hydrolase activity	1.29419296935491	bayes_pls_golite062009
DNA-dependent ATPase activity	1.2155186842031	bayes_pls_golite062009
helicase activity	1.16085745407703	bayes_pls_golite062009
nucleic acid binding	1.08697924060619	bayes_pls_golite062009
catalytic activity	1.00104173493322	bayes_pls_golite062009
ATPase activity	0.844502974582959	bayes_pls_golite062009
DNA helicase activity	0.72881469450553	bayes_pls_golite062009
structure-specific DNA binding	0.720649395550746	bayes_pls_golite062009
DNA binding	0.702147676354075	bayes_pls_golite062009
ATP-dependent helicase activity	0.59513742813869	bayes_pls_golite062009
purine NTP-dependent helicase activity	0.59513742813869	bayes_pls_golite062009
double-stranded DNA binding	0.58862275163252	bayes_pls_golite062009
transcription regulator activity	0.287777990975748	bayes_pls_golite062009
ATP-dependent DNA helicase activity	0.22150712609541	bayes_pls_golite062009
nucleotide binding	0.114848452385726	bayes_pls_golite062009
purine nucleotide binding	0.10713474095071	bayes_pls_golite062009
purine ribonucleotide binding	0.0916519414118148	bayes_pls_golite062009
ribonucleotide binding	0.0915913646217636	bayes_pls_golite062009
protein binding	0.071010918255742	bayes_pls_golite062009

Predicted Domain #2

Region A:
Residues: [314-839]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 RSSQKILNTS EILITQQNKG RQNRAPLRAQ FDLDFPPVYM NFPAYFLEAP SLVRELLYLK  60
   61 ALPNLFTFND FAILVRQRRQ IKRIESALIE HRIPYKIIRG HSFWDSKETR AMLNLLKLIF 120
  121 SPNDKHAILA SLLYPARGLG PATGEKIKNA LDTLATDVSC FQILKDISSK KIMLDIPTKG 180
  181 RSVIADFISM IENCQLLLQS TLLGGLSDLF DKLYELSGLK YEYLYKDGKK KNDQLEKSEP 240
  241 NLLNARHKNI ELLKNYFLAL LSKSESSDKE KNEAIKAATD EAEPIENKVI TPKEYLRNFF 300
  301 NSLSLHSDAA EEEESESNKD AKIKREKNGF VTISTIHGAK GLEWPVVFIP GCEEGIIPCV 360
  361 FNDDKKDESE EDEEEDQENS KKDASPKKTR VLSVEDSIDE ERRMFFVAQT RAKYLLYLSN 420
  421 TVTVEDVDRP RIASRFLTTD LIKAMSDSQK LFESTNSIKK LYRILNKKPP AEDDKLFSLD 480
  481 QLRKDYNQFI ENRRERMIWQ GIQMNDVYGI QLSRNKLLGS VSDFTS

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	715.9691
Match:	1pjr__
Description:	DEXX box DNA helicase
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
binding	2.44689197844883	bayes_pls_golite062009
nucleoside-triphosphatase activity	1.5002869400376	bayes_pls_golite062009
pyrophosphatase activity	1.49611313354225	bayes_pls_golite062009
hydrolase activity, acting on acid anhydrides	1.47468810672455	bayes_pls_golite062009
hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides	1.47371190790284	bayes_pls_golite062009
hydrolase activity	1.29419296935491	bayes_pls_golite062009
DNA-dependent ATPase activity	1.2155186842031	bayes_pls_golite062009
helicase activity	1.16085745407703	bayes_pls_golite062009
nucleic acid binding	1.08697924060619	bayes_pls_golite062009
catalytic activity	1.00104173493322	bayes_pls_golite062009
ATPase activity	0.844502974582959	bayes_pls_golite062009
DNA helicase activity	0.72881469450553	bayes_pls_golite062009
structure-specific DNA binding	0.720649395550746	bayes_pls_golite062009
DNA binding	0.702147676354075	bayes_pls_golite062009
ATP-dependent helicase activity	0.59513742813869	bayes_pls_golite062009
purine NTP-dependent helicase activity	0.59513742813869	bayes_pls_golite062009
double-stranded DNA binding	0.58862275163252	bayes_pls_golite062009
transcription regulator activity	0.287777990975748	bayes_pls_golite062009
ATP-dependent DNA helicase activity	0.22150712609541	bayes_pls_golite062009
nucleotide binding	0.114848452385726	bayes_pls_golite062009
purine nucleotide binding	0.10713474095071	bayes_pls_golite062009
purine ribonucleotide binding	0.0916519414118148	bayes_pls_golite062009
ribonucleotide binding	0.0915913646217636	bayes_pls_golite062009
protein binding	0.071010918255742	bayes_pls_golite062009

Predicted Domain #3

Region A:
Residues: [840-1174]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 AADQLRLETQ NSIFPQKKLI EKSRPSKING NYAPKSRVKS PEKRYAPETT SFHSPTKKKV  60
   61 YAPQYVSTTN VPSRQEFHSS TGKNIPFLRR EDRSITDISP RSSTRSLKGA SPNKTSHMSD 120
  121 DLMRPSPTRK DKVTRNIHFA TAGTFRIETQ SNVDELHPPE YSNKSGQSLT SSEFSGFSSA 180
  181 CSNSDQPTNL IEDINNELDL SDEELLNDIS IERRRELLGS KKTKKIKPKT RNRKSKRGDK 240
  241 VKVEEVIDLK SEFEEDDSRN TTAAELLHNP DDTTVDNRPI ISNAKFLADA AMKKTQKFSK 300
  301 KVKNEPASSQ MDIFSQLSRA KKKSKLNNGE IIVID

[Run NCBI BLAST on this sequence.]

Detection Method:	ORFEUS
Confidence:	10.98
Match:	1ei3A
Description:	Fibrinogen
Matching Structure (courtesy of the PDB):

TMHMM	2.0c	PSIPRED	v2.61
SignalP	3.0	COILS	1999
DISOPRED	v0.1	NCBI nr	06/2007
PSI-BLAST	2.2.18	FFAS	ffas03
PDB	06/2007	Pfam	22
HMMER	2.3.2

View Structure Prediction Details

Top Sequence Alignment Hits

Predicted functions:

Predicted functions: