YRC Public Data Repository - Protein Structure Prediction

Protein:	PMS1
Organism:	Saccharomyces cerevisiae
Length:	904 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 PMS1.

Description	E-value	Query Range	Subject Range
gi\|172203 - gi\|172203\|gb\|AAA34885.1\| DNA mismatch repair protein [Saccharomyces cerevisiae]	0.0	[1..904]	[1..904]
PMS2_MOUSE - Mismatch repair endonuclease PMS2 OS=Mus musculus GN=Pms2 PE=2 SV=1	0.0	[22..894]	[2..855]
gi\|189065468, gi... - gi\|557470\|gb\|AAA50390.1\| similar to S. cerevisiae PMS1 Swiss-Prot Accession Number P14242, S. cerevi...	0.0	[22..892]	[2..856]
gi\|153223913, gi... - gi\|153223913\|ref\|ZP_01954129.1\| DNA gyrase, subunit B [Vibrio cholerae MAK 757], gi\|124117960\|gb\|EAY... gi\|153819850, gi... - gi\|153819850\|ref\|ZP_01972517.1\| DNA gyrase, subunit B [Vibrio cholerae NCTC 8457], gi\|126509611\|gb\|E... gi\|229508861, gi... - gi\|229508861\|ref\|ZP_04398352.1\| DNA gyrase subunit B [Vibrio cholerae B33], gi\|229354136\|gb\|EEO19068... GYRB_VIBCH - DNA gyrase subunit B OS=Vibrio cholerae GN=gyrB PE=3 SV=1 gi\|75829895, gi\|... - gi\|75829895\|ref\|ZP_00759184.1\| COG0187: Type IIA topoisomerase (DNA gyrase/topo II, topoisomerase IV... gi\|227008140, gi... - gi\|227080252\|ref\|YP_002808803.1\| DNA gyrase, subunit B [Vibrio cholerae M66-2], gi\|227008140\|gb\|ACP0... gi\|75828133, gi\|... - gi\|75828133\|ref\|ZP_00757568.1\| COG0187: Type IIA topoisomerase (DNA gyrase/topo II, topoisomerase IV... gi\|229508300, gi... - gi\|229508300\|ref\|ZP_04397804.1\| DNA gyrase subunit B [Vibrio cholerae BX 330286], gi\|229354573\|gb\|EE... gi\|121727887, gi... - gi\|75814471\|ref\|ZP_00745055.1\| COG0187: Type IIA topoisomerase (DNA gyrase/topo II, topoisomerase IV... gi\|229346195, gi... - gi\|229517132\|ref\|ZP_04406578.1\| DNA gyrase subunit B [Vibrio cholerae RC9], gi\|229346195\|gb\|EEO11167... gi\|229369229, gi... - gi\|229606574\|ref\|YP_002877222.1\| DNA gyrase subunit B [Vibrio cholerae MJ-1236], gi\|229369229\|gb\|ACQ... GYRB_VIBCH - DNA gyrase subunit B OS=Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961) GN=gyr...	0.0	[27..550]	[2..505]
GYRB_SALTY - DNA gyrase subunit B OS=Salmonella typhimurium GN=gyrB PE=3 SV=2 gi\|224470162, gi... - gi\|224585634\|ref\|YP_002639433.1\| DNA gyrase subunit B [Salmonella enterica subsp. enterica serovar P... gi\|214001463 - gi\|214001463\|ref\|ZP_03412198.1\| DNA gyrase subunit B [Salmonella enterica subsp. enterica serovar Ty... gi\|213424954 - gi\|213424954\|ref\|ZP_03357704.1\| DNA gyrase subunit B [Salmonella enterica subsp. enterica serovar Ty... gi\|207859061, gi... - gi\|207859061\|ref\|YP_002245712.1\| DNA gyrase subunit B [Salmonella enterica subsp. enterica serovar E... GYRB_SALTI - DNA gyrase subunit B OS=Salmonella typhi GN=gyrB PE=3 SV=2 GYRB_SALTY - DNA gyrase subunit B OS=Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) GN=gyrB PE=1 SV... GYRB_SALTI - DNA gyrase subunit B OS=Salmonella typhi GN=gyrB PE=3 SV=2 lcl\|NC_016856.1_... - [gene=gyrB] [protein=DNA gyrase subunit B] [protein_id=YP_005240101.1] [location=complement(4052548.... gi\|29143978, gi\|... - gi\|29143978\|ref\|NP_807320.1\| DNA gyrase subunit B [Salmonella enterica subsp. enterica serovar Typhi... gi\|16762490 - gi\|16762490\|ref\|NP_458107.1\| DNA gyrase subunit B [Salmonella enterica subsp. enterica serovar Typhi... gi\|238913088 - gi\|238913088\|ref\|ZP_04656925.1\| DNA gyrase subunit B [Salmonella enterica subsp. enterica serovar Te... gi\|205325567, gi... - gi\|205325567\|gb\|EDZ13406.1\| DNA gyrase, B subunit [Salmonella enterica subsp. enterica serovar Saint... GYRB_SALTY - DNA gyrase subunit B OS=Salmonella typhimurium GN=gyrB PE=3 SV=2 gi\|161616952, gi... - gi\|161616952\|ref\|YP_001590917.1\| DNA gyrase subunit B [Salmonella enterica subsp. enterica serovar P... gi\|197240529, gi... - gi\|197262274\|ref\|ZP_03162348.1\| DNA gyrase, B subunit [Salmonella enterica subsp. enterica serovar S... gi\|194712574, gi... - gi\|194737072\|ref\|YP_002116779.1\| DNA gyrase, B subunit [Salmonella enterica subsp. enterica serovar ... gi\|194472695, gi... - gi\|194472695\|ref\|ZP_03078679.1\| DNA gyrase, B subunit [Salmonella enterica subsp. enterica serovar K... gi\|194449732, gi... - gi\|194449732\|ref\|YP_002047868.1\| DNA gyrase subunit B [Salmonella enterica subsp. enterica serovar H... gi\|205354578, gi... - gi\|205354578\|ref\|YP_002228379.1\| DNA gyrase subunit B [Salmonella enterica subsp. enterica serovar G... gi\|204322190, gi... - gi\|204928757\|ref\|ZP_03219956.1\| DNA gyrase, B subunit [Salmonella enterica subsp. enterica serovar J... gi\|199604199, gi... - gi\|200387101\|ref\|ZP_03213713.1\| DNA gyrase, B subunit [Salmonella enterica subsp. enterica serovar V... gi\|197938563, gi... - gi\|198244047\|ref\|YP_002217785.1\| DNA gyrase, B subunit [Salmonella enterica subsp. enterica serovar ... gi\|205338996, gi... - gi\|205338996\|gb\|EDZ25760.1\| DNA gyrase, B subunit [Salmonella enterica subsp. enterica serovar Heide... gi\|197291517, gi... - gi\|197291517\|gb\|EDY30869.1\| DNA gyrase, B subunit [Salmonella enterica subsp. enterica serovar Schwa... gi\|168233389, gi... - gi\|205332584\|gb\|EDZ19348.1\| DNA gyrase, B subunit [Salmonella enterica subsp. enterica serovar Kentu... gi\|205329403, gi... - gi\|205329403\|gb\|EDZ16167.1\| DNA gyrase, B subunit [Salmonella enterica subsp. enterica serovar 4,[5]... gi\|194442844, gi... - gi\|194442844\|ref\|YP_002043085.1\| DNA gyrase, B subunit [Salmonella enterica subsp. enterica serovar ... gi\|168818305, gi... - gi\|205344661\|gb\|EDZ31425.1\| DNA gyrase, B subunit [Salmonella enterica subsp. enterica serovar Welte... gi\|195632426, gi... - gi\|195632426\|gb\|EDX50910.1\| DNA gyrase, B subunit [Salmonella enterica subsp. enterica serovar Newpo... gi\|168260381, gi... - gi\|205350152\|gb\|EDZ36783.1\| DNA gyrase, B subunit [Salmonella enterica subsp. enterica serovar Hadar...	0.0	[27..550]	[2..504]
gi\|1617217\|emb\|C... - subunit B of DNA gyrase [Salmonella typhimurium] gi\|1617217 - gi\|1617217\|emb\|CAA69665.1\| subunit B of DNA gyrase [Salmonella typhimurium]	0.0	[27..550]	[2..504]
gi\|107098998 - gi\|107098998\|ref\|ZP_01362916.1\| hypothetical protein PaerPA_01000004 [Pseudomonas aeruginosa PACS2] gi\|218768973, gi... - gi\|218888750\|ref\|YP_002437614.1\| DNA gyrase subunit B [Pseudomonas aeruginosa LESB58], gi\|218768973\|... GYRB_PSEAE - DNA gyrase subunit B OS=Pseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228)... GYRB_PSEAE - DNA gyrase subunit B OS=Pseudomonas aeruginosa GN=gyrB PE=3 SV=1 gi\|32043147, gi\|... - gi\|32043147\|ref\|ZP_00140409.1\| COG0187: Type IIA topoisomerase (DNA gyrase/topo II, topoisomerase IV...	0.0	[27..550]	[4..506]
gi\|15603341, gi\|... - gi\|15603341\|ref\|NP_246415.1\| DNA gyrase subunit B [Pasteurella multocida subsp. multocida str. Pm70]...	0.0	[24..577]	[3..552]
GYRB_SHIFL - DNA gyrase subunit B OS=Shigella flexneri GN=gyrB PE=3 SV=2 GYRB_ECOLI - DNA gyrase subunit B (EC 5.99.1.3) - Escherichia coli gi\|30043268, gi\|... - gi\|30065007\|ref\|NP_839178.1\| DNA gyrase subunit B [Shigella flexneri 2a str. 2457T], gi\|30043268\|gb\|... gi\|157068859, gi... - gi\|75197597\|ref\|ZP_00707667.1\| COG0187: Type IIA topoisomerase (DNA gyrase/topo II, topoisomerase IV... GYRB_ECO57 - DNA gyrase subunit B OS=Escherichia coli O157:H7 GN=gyrB PE=3 SV=2 gi\|75210689, gi\|... - gi\|75210689\|ref\|ZP_00710830.1\| COG0187: Type IIA topoisomerase (DNA gyrase/topo II, topoisomerase IV... EG10424 - DNA gyrase, subunit B / DNA gyrase, subunit B; novobiocin, coumermycin resistance gi\|194425377, gi... - gi\|83588435\|ref\|ZP_00927059.1\| COG0187: Type IIA topoisomerase (DNA gyrase/topo II, topoisomerase IV... gi\|157077909, gi... - gi\|75188456\|ref\|ZP_00701723.1\| COG0187: Type IIA topoisomerase (DNA gyrase/topo II, topoisomerase IV... gi\|110617159, gi... - gi\|110807611\|ref\|YP_691131.1\| DNA gyrase subunit B [Shigella flexneri 5 str. 8401], gi\|110617159\|gb\|... gi\|168772266, gi... - gi\|187771557\|gb\|EDU35401.1\| DNA gyrase, B subunit [Escherichia coli O157:H7 str. EC4196], gi\|1687722... gi\|189364475, gi... - gi\|189364475\|gb\|EDU82894.1\| DNA gyrase, B subunit [Escherichia coli O157:H7 str. EC4486], gi\|1687661... gi\|189374237, gi... - gi\|189374237\|gb\|EDU92653.1\| DNA gyrase, B subunit [Escherichia coli O157:H7 str. EC869], gi\|16878565... gi\|168779921, gi... - gi\|189002544\|gb\|EDU71530.1\| DNA gyrase, B subunit [Escherichia coli O157:H7 str. EC4076], gi\|1687799... gi\|170018065, gi... - gi\|170018065\|ref\|YP_001723019.1\| DNA gyrase subunit B [Escherichia coli ATCC 8739], gi\|169752993\|gb\|... gi\|168798734, gi... - gi\|189378801\|gb\|EDU97217.1\| DNA gyrase, B subunit [Escherichia coli O157:H7 str. EC508], gi\|16879873... gi\|208728266, gi... - gi\|208808465\|ref\|ZP_03250802.1\| DNA gyrase, B subunit [Escherichia coli O157:H7 str. EC4206], gi\|208... gi\|15833888, gi\|... - gi\|15833888\|ref\|NP_312661.1\| DNA gyrase subunit B [Escherichia coli O157:H7 str. Sakai], gi\|13364109... gi\|195936320 - gi\|195936320\|ref\|ZP_03081702.1\| DNA gyrase subunit B [Escherichia coli O157:H7 str. EC4024] gi\|168748585, gi... - gi\|188016891\|gb\|EDU55013.1\| DNA gyrase, B subunit [Escherichia coli O157:H7 str. EC4113], gi\|1687485... gi\|189369611, gi... - gi\|189369611\|gb\|EDU88027.1\| DNA gyrase, B subunit [Escherichia coli O157:H7 str. EC4501], gi\|1687598... gi\|168753588, gi... - gi\|189359308\|gb\|EDU77727.1\| DNA gyrase, B subunit [Escherichia coli O157:H7 str. EC4401], gi\|1687535... gi\|238860819, gi... - gi\|238902789\|ref\|YP_002928585.1\| DNA gyrase, subunit B [Escherichia coli BW2952], gi\|238860819\|gb\|AC... gi\|251786965, gi... - gi\|251786965\|ref\|YP_003001269.1\| hypothetical protein B21_03526 [Escherichia coli BL21], gi\|24237923... gi\|253979707, gi... - gi\|254290400\|ref\|YP_003056148.1\| DNA gyrase subunit B [Escherichia coli BL21(DE3)], gi\|253979707\|gb\|... gi\|254163650, gi... - gi\|254163650\|ref\|YP_003046758.1\| DNA gyrase subunit B [Escherichia coli B str. REL606], gi\|253975551... gi\|254795702, gi... - gi\|254795702\|ref\|YP_003080539.1\| DNA gyrase, subunit B [Escherichia coli O157:H7 str. TW14359], gi\|2... gi\|208742117, gi... - gi\|208821994\|ref\|ZP_03262314.1\| DNA gyrase, B subunit [Escherichia coli O157:H7 str. EC4042], gi\|208... gi\|208733443, gi... - gi\|208812166\|ref\|ZP_03253495.1\| DNA gyrase, B subunit [Escherichia coli O157:H7 str. EC4045], gi\|208... gi\|218363033, gi... - gi\|218556264\|ref\|YP_002389178.1\| DNA gyrase subunit B [Escherichia coli IAI1], gi\|218363033\|emb\|CAR0... gi\|209921176, gi... - gi\|209921176\|ref\|YP_002295260.1\| DNA gyrase subunit B [Escherichia coli SE11], gi\|209914435\|dbj\|BAG7... gi\|218354153, gi... - gi\|218697421\|ref\|YP_002405088.1\| DNA gyrase subunit B [Escherichia coli 55989], gi\|218354153\|emb\|CAV... EG10424 - DNA gyrase, subunit B / DNA gyrase, subunit B; novobiocin, coumermycin resistance gi\|124529046, gi... - gi\|124529046\|ref\|ZP_01700192.1\| DNA gyrase, B subunit [Escherichia coli B], gi\|124500185\|gb\|EAY47662... gi\|75258239, gi\|... - gi\|75258239\|ref\|ZP_00729687.1\| COG0187: Type IIA topoisomerase (DNA gyrase/topo II, topoisomerase IV... gi\|75514238, gi\|... - gi\|75514238\|ref\|ZP_00736546.1\| COG0187: Type IIA topoisomerase (DNA gyrase/topo II, topoisomerase IV... gi\|190904111, gi... - gi\|75231030\|ref\|ZP_00717465.1\| COG0187: Type IIA topoisomerase (DNA gyrase/topo II, topoisomerase IV... gi\|192957551, gi... - gi\|75236423\|ref\|ZP_00720519.1\| COG0187: Type IIA topoisomerase (DNA gyrase/topo II, topoisomerase IV... gi\|56480411, gi\|... - gi\|56480411\|ref\|NP_709501.2\| DNA gyrase subunit B [Shigella flexneri 2a str. 301], gi\|56383962\|gb\|AA... gi\|74314013, gi\|... - gi\|74314013\|ref\|YP_312432.1\| DNA gyrase subunit B [Shigella sonnei Ss046], gi\|73857490\|gb\|AAZ90197.1... gi\|89110314, gi\|... - gi\|89110314\|ref\|AP_004094.1\| DNA gyrase, subunit B [Escherichia coli str. K-12 substr. W3110], gi\|85...	0.0	[27..550]	[2..504]

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Predicted Domain #1

Region A:
Residues: [1-249]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MFHHIENLLI ETEKRCKQKE QRYIPVKYLF SMTQIHQIND IDVHRITSGQ VITDLTTAVK  60
   61 ELVDNSIDAN ANQIEIIFKD YGLESIECSD NGDGIDPSNY EFLALKHYTS KIAKFQDVAK 120
  121 VQTLGFRGEA LSSLCGIAKL SVITTTSPPK ADKLEYDMVG HITSKTTTSR NKGTTVLVSQ 180
  181 LFHNLPVRQK EFSKTFKRQF TKCLTVIQGY AIINAAIKFS VWNITPKGKK NLILSTMRNS 240
  241 SMRKNISSV

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	832.218487
Match:	1ea6A_
Description:	DNA mismatch repair protein PMS2
Matching Structure (courtesy of the PDB):

Predicted Domain #2

Region A:
Residues: [250-411]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 FGAGGMRGLE EVDLVLDLNP FKNRMLGKYT DDPDFLDLDY KIRVKGYISQ NSFGCGRNSK  60
   61 DRQFIYVNKR PVEYSTLLKC CNEVYKTFNN VQFPAVFLNL ELPMSLIDVN VTPDKRVILL 120
  121 HNERAVIDIF KTTLSDYYNR QELALPKRMC SQSEQQAQKR LK

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	832.218487
Match:	1ea6A_
Description:	DNA mismatch repair protein PMS2
Matching Structure (courtesy of the PDB):

Predicted Domain #3

Region A:
Residues: [412-615]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 TEVFDDRSTT HESDNENYHT ARSESNQSNH AHFNSTTGVI DKSNGTELTS VMDGNYTNVT  60
   61 DVIGSECEVS VDSSVVLDEG NSSTPTKKLP SIKTDSQNLS DLNLNNFSNP EFQNITSPDK 120
  121 ARSLEKVVEE PVYFDIDGEK FQEKAVLSQA DGLVFVDNEC HEHTNDCCHQ ERRGSTDTEQ 180
  181 DDEADSIYAE IEPVEINVRT PLKN

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	2.30103
Match:	1lwzA_
Description:	No description for 1lwzA_ was found.

Predicted Domain #4

Region A:
Residues: [616-698]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 SRKSISKDNY RSLSDGLTHR KFEDEILEYN LSTKNFKEIS KNGKQMSSII SKRKSEAQEN  60
   61 IIKNKDELED FEQGEKYLTL TVS

[Run NCBI BLAST on this sequence.]

Detection Method:

deduced

Shown below is our most confident de novo (Rosetta) prediction for this domain.
Click here to view all matches.

Found no confident structure predictions for this domain.

Predicted Domain #5

Region A:
Residues: [699-904]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 KNDFKKMEVV GQFNLGFIIV TRKVDNKYDL FIVDQHASDE KYNFETLQAV TVFKSQKLII  60
   61 PQPVELSVID ELVVLDNLPV FEKNGFKLKI DEEEEFGSRV KLLSLPTSKQ TLFDLGDFNE 120
  121 LIHLIKEDGG LRRDNIRCSK IRSMFAMRAC RSSIMIGKPL NKKTMTRVVH NLSELDKPWN 180
  181 CPHGRPTMRH LMELRDWSSF SKDYEI

[Run NCBI BLAST on this sequence.]

Detection Method:

MSA

Shown below is our most confident prediction for this domain.
Click here to view all matches.

Found no confident structure predictions for this domain.

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