YRC Public Data Repository - Protein Structure Prediction

Protein:	MSH1
Organism:	Saccharomyces cerevisiae
Length:	959 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 MSH1.

Description	E-value	Query Range	Subject Range
MSH1_YEAST - DNA mismatch repair protein MSH1, mitochondrial OS=Saccharomyces cerevisiae (strain ATCC 204508 / S2... MSH1 - DNA-binding protein of the mitochondria involved in repair of mitochondrial DNA, has ATPase activity...	0.0	[1..959]	[1..959]
gi\|205324663, gi... - gi\|205324663\|gb\|EDZ12502.1\| DNA mismatch repair protein MutS [Salmonella enterica subsp. enterica se... gi\|167993148, gi... - gi\|205328749\|gb\|EDZ15513.1\| DNA mismatch repair protein MutS [Salmonella enterica subsp. enterica se... gi\|168242649, gi... - gi\|205338197\|gb\|EDZ24961.1\| DNA mismatch repair protein MutS [Salmonella enterica subsp. enterica se... MUTS_SALCH - DNA mismatch repair protein MutS OS=Salmonella choleraesuis (strain SC-B67) GN=mutS PE=3 SV=1 lcl\|NC_016856.1_... - [gene=mutS] [protein=DNA mismatch repair protein] [protein_id=YP_005239020.1] [location=3070516..307... MUTS_SALTY - DNA mismatch repair protein mutS OS=Salmonella typhimurium GN=mutS PE=1 SV=1 MUTS_SALCH - DNA mismatch repair protein mutS OS=Salmonella choleraesuis GN=mutS PE=3 SV=1 MUTS_SALCH - DNA mismatch repair protein mutS OS=Salmonella choleraesuis GN=mutS PE=3 SV=1 MUTS_SALTI - DNA mismatch repair protein MutS OS=Salmonella typhi GN=mutS PE=3 SV=1 MUTS_SALG2 - DNA mismatch repair protein MutS OS=Salmonella gallinarum (strain 287/91 / NCTC 13346) GN=mutS PE=3 ... MUTS_SALTY - DNA mismatch repair protein MutS OS=Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) GN=... gi\|213854165 - gi\|213854165\|ref\|ZP_03382697.1\| DNA mismatch repair protein [Salmonella enterica subsp. enterica ser... MUTS_SALTY - DNA mismatch repair protein mutS OS=Salmonella typhimurium GN=mutS PE=1 SV=1 MUTS_SALPB - DNA mismatch repair protein mutS OS=Salmonella paratyphi B (strain ATCC BAA-1250 / SPB7) GN=mutS PE=... MUTS_SALPB - DNA mismatch repair protein MutS OS=Salmonella paratyphi B (strain ATCC BAA-1250 / SPB7) GN=mutS PE=... MUTS_SALTI - DNA mismatch repair protein mutS OS=Salmonella typhi GN=mutS PE=3 SV=1 gi\|168463951, gi... - gi\|195633763\|gb\|EDX52177.1\| DNA mismatch repair protein MutS [Salmonella enterica subsp. enterica se... MUTS_SALHS - DNA mismatch repair protein MutS OS=Salmonella heidelberg (strain SL476) GN=mutS PE=3 SV=1 gi\|29143167, gi\|... - gi\|29143167\|ref\|NP_806509.1\| DNA mismatch repair protein [Salmonella enterica subsp. enterica serova... MUTS_SALA4 - DNA mismatch repair protein MutS OS=Salmonella agona (strain SL483) GN=mutS PE=3 SV=1 gi\|16761683 - gi\|16761683\|ref\|NP_457300.1\| DNA mismatch repair protein [Salmonella enterica subsp. enterica serova... gi\|197240275, gi... - gi\|197262020\|ref\|ZP_03162094.1\| DNA mismatch repair protein MutS [Salmonella enterica subsp. enteric...	0.0	[70..958]	[3..795]
gi\|125617373, gi... - gi\|75829241\|ref\|ZP_00758551.1\| COG0249: Mismatch repair ATPase (MutS family) [Vibrio cholerae MO10],... gi\|229353916, gi... - gi\|229508991\|ref\|ZP_04398479.1\| DNA mismatch repair protein MutS [Vibrio cholerae B33], gi\|229353916... MUTS_VIBCH - DNA mismatch repair protein mutS OS=Vibrio cholerae GN=mutS PE=3 SV=1 MUTS_VIBCH - DNA mismatch repair protein MutS OS=Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N1... gi\|75815683 - gi\|75815683\|ref\|ZP_00746180.1\| COG0249: Mismatch repair ATPase (MutS family) [Vibrio cholerae V52] MUTS_VIBCM - DNA mismatch repair protein MutS OS=Vibrio cholerae serotype O1 (strain M66-2) GN=mutS PE=3 SV=1 gi\|229507146, gi... - gi\|229507146\|ref\|ZP_04396652.1\| DNA mismatch repair protein MutS [Vibrio cholerae BX 330286], gi\|229... gi\|229344348, gi... - gi\|229519659\|ref\|ZP_04409102.1\| DNA mismatch repair protein MutS [Vibrio cholerae RC9], gi\|229344348... MUTS_VIBC3 - DNA mismatch repair protein MutS OS=Vibrio cholerae serotype O1 (strain ATCC 39541 / Classical Ogawa... gi\|153223827, gi... - gi\|153223827\|ref\|ZP_01954082.1\| DNA mismatch repair protein MutS [Vibrio cholerae MAK 757], gi\|12411... gi\|126510344, gi... - gi\|153819112\|ref\|ZP_01971779.1\| DNA mismatch repair protein MutS [Vibrio cholerae NCTC 8457], gi\|126...	0.0	[71..958]	[7..800]
gi\|22124746, gi\|... - gi\|22124746\|ref\|NP_668169.1\| DNA mismatch repair protein [Yersinia pestis KIM], gi\|21957565\|gb\|AAM84... gi\|218930372, gi... - gi\|218930372\|ref\|YP_002348247.1\| DNA mismatch repair protein MutS [Yersinia pestis CO92], gi\|1612350... gi\|45435046, gi\|... - gi\|45440190\|ref\|NP_991729.1\| DNA mismatch repair protein [Yersinia pestis biovar Microtus str. 91001... MUTS_YERPG - DNA mismatch repair protein MutS OS=Yersinia pestis bv. Antiqua (strain Angola) GN=mutS PE=3 SV=1 gi\|167469363 - gi\|167469363\|ref\|ZP_02334067.1\| DNA mismatch repair protein MutS [Yersinia pestis FV-1] gi\|167423797, gi... - gi\|167423797\|ref\|ZP_02315550.1\| DNA mismatch repair protein MutS [Yersinia pestis biovar Mediaevalis... gi\|149289239, gi... - gi\|153997602\|ref\|ZP_02022702.1\| DNA mismatch repair protein MutS [Yersinia pestis CA88-4125], gi\|149... MUTS_YERPP - DNA mismatch repair protein MutS OS=Yersinia pestis (strain Pestoides F) GN=mutS PE=3 SV=1 gi\|166010151, gi... - gi\|166010151\|ref\|ZP_02231049.1\| DNA mismatch repair protein MutS [Yersinia pestis biovar Antiqua str... MUTS_YERPE - DNA mismatch repair protein MutS OS=Yersinia pestis GN=mutS PE=3 SV=1 gi\|165922488, gi... - gi\|165925876\|ref\|ZP_02221708.1\| DNA mismatch repair protein MutS [Yersinia pestis biovar Orientalis ... gi\|229695346, gi... - gi\|229838980\|ref\|ZP_04459139.1\| methyl-directed mismatch repair protein [Yersinia pestis biovar Orie... gi\|167421538, gi... - gi\|167421538\|ref\|ZP_02313291.1\| DNA mismatch repair protein MutS [Yersinia pestis biovar Orientalis ... gi\|229687039, gi... - gi\|229899547\|ref\|ZP_04514688.1\| methyl-directed mismatch repair protein [Yersinia pestis biovar Orie... gi\|166205736, gi... - gi\|166212949\|ref\|ZP_02238984.1\| DNA mismatch repair protein MutS [Yersinia pestis biovar Antiqua str... gi\|165936708, gi... - gi\|89105881\|ref\|ZP_01178393.1\| COG0249: Mismatch repair ATPase (MutS family) [Yersinia pestis biovar... MUTS_YERPN - DNA mismatch repair protein MutS OS=Yersinia pestis bv. Antiqua (strain Nepal516) GN=mutS PE=3 SV=1	0.0	[78..958]	[9..793]
MUTS_HAEIN - DNA mismatch repair protein mutS OS=Haemophilus influenzae GN=mutS PE=3 SV=1 MUTS_HAEIN - DNA mismatch repair protein MutS OS=Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / R...	0.0	[73..958]	[4..795]
gi\|254594075, gi... - gi\|254794675\|ref\|YP_003079512.1\| methyl-directed mismatch repair protein [Escherichia coli O157:H7 s... gi\|208739537, gi... - gi\|208819414\|ref\|ZP_03259734.1\| DNA mismatch repair protein MutS [Escherichia coli O157:H7 str. EC40... gi\|208735412, gi... - gi\|208814135\|ref\|ZP_03255464.1\| DNA mismatch repair protein MutS [Escherichia coli O157:H7 str. EC40... MUTS_ECO8A - DNA mismatch repair protein MutS OS=Escherichia coli O8 (strain IAI1) GN=mutS PE=3 SV=1 MUTS_ECO5E - DNA mismatch repair protein MutS OS=Escherichia coli O157:H7 (strain EC4115 / EHEC) GN=mutS PE=3 SV=... gi\|192957000, gi... - gi\|193069637\|ref\|ZP_03050589.1\| DNA mismatch repair protein MutS [Escherichia coli E110019], gi\|1929... gi\|191166787, gi... - gi\|191166787\|ref\|ZP_03028613.1\| DNA mismatch repair protein MutS [Escherichia coli B7A], gi\|19090315... gi\|208807935, gi... - gi\|208807935\|ref\|ZP_03250272.1\| DNA mismatch repair protein MutS [Escherichia coli O157:H7 str. EC42... gi\|195938486 - gi\|195938486\|ref\|ZP_03083868.1\| DNA mismatch repair protein [Escherichia coli O157:H7 str. EC4024] gi\|15832843, gi\|... - gi\|15832843\|ref\|NP_311616.1\| DNA mismatch repair protein MutS [Escherichia coli O157:H7 str. Sakai],... gi\|168787991, gi... - gi\|189372119\|gb\|EDU90535.1\| DNA mismatch repair protein MutS [Escherichia coli O157:H7 str. EC869], ... gi\|168778718, gi... - gi\|189003145\|gb\|EDU72131.1\| DNA mismatch repair protein MutS [Escherichia coli O157:H7 str. EC4076],... gi\|188493251, gi... - gi\|188493251\|ref\|ZP_03000521.1\| DNA mismatch repair protein MutS [Escherichia coli 53638], gi\|188488... gi\|189377459, gi... - gi\|189377459\|gb\|EDU95875.1\| DNA mismatch repair protein MutS [Escherichia coli O157:H7 str. EC508], ... gi\|189357264, gi... - gi\|189357264\|gb\|EDU75683.1\| DNA mismatch repair protein MutS [Escherichia coli O157:H7 str. EC4401],... gi\|188015814, gi... - gi\|188015814\|gb\|EDU53936.1\| DNA mismatch repair protein MutS [Escherichia coli O157:H7 str. EC4113],... gi\|168774732, gi... - gi\|187769600\|gb\|EDU33444.1\| DNA mismatch repair protein MutS [Escherichia coli O157:H7 str. EC4196],... gi\|168768827, gi... - gi\|189362111\|gb\|EDU80530.1\| DNA mismatch repair protein MutS [Escherichia coli O157:H7 str. EC4486],... MUTS_ECO57 - DNA mismatch repair protein MutS OS=Escherichia coli O157:H7 GN=mutS PE=3 SV=1 gi\|25317150, gi\|... - gi\|4887554\|emb\|CAB43497.1\| mismatch repair protein [Escherichia coli], pir\|\|E91077 MutS protein [imp...	0.0	[78..958]	[9..793]
gi\|17017340 - gi\|17017340\|gb\|AAL33627.1\|AF440200_1 MutS [Escherichia coli]	0.0	[78..958]	[8..792]
gi\|12517186, gi\|... - gi\|15803252\|ref\|NP_289284.1\| DNA mismatch repair protein [Escherichia coli O157:H7 EDL933], gi\|12517... gi\|25317161 - gi\|25317161\|pir\|\|F85922 methyl-directed mismatch repair [imported] - Escherichia coli (strain O157:H...	0.0	[78..958]	[9..793]
EG10625 - methyl-directed mismatch repair protein / Methyl-directed mismatch repair protein, weak ATPase; dime... MUTS_ECOHS - DNA mismatch repair protein MutS OS=Escherichia coli O9:H4 (strain HS) GN=mutS PE=3 SV=1 gi\|124500877, gi... - gi\|124527985\|ref\|ZP_01699338.1\| DNA mismatch repair protein MutS [Escherichia coli B], gi\|124500877\|... MUTS_ECOLC - DNA mismatch repair protein MutS OS=Escherichia coli (strain ATCC 8739 / DSM 1576 / Crooks) GN=mutS ... gi\|85675554, gi\|... - gi\|89109520\|ref\|AP_003300.1\| methyl-directed mismatch repair protein [Escherichia coli str. K-12 sub... MUTS_ECODH - DNA mismatch repair protein MutS OS=Escherichia coli (strain K12 / DH10B) GN=mutS PE=3 SV=1 gi\|194438950, gi... - gi\|194438950\|ref\|ZP_03071034.1\| DNA mismatch repair protein MutS [Escherichia coli 101-1], gi\|194422... gi\|254289425, gi... - gi\|254289425\|ref\|YP_003055173.1\| DNA mismatch repair protein [Escherichia coli BL21(DE3)], gi\|253978... gi\|253974565, gi... - gi\|254162664\|ref\|YP_003045772.1\| DNA mismatch repair protein [Escherichia coli B str. REL606], gi\|25... MUTS_ECOLI - DNA mismatch repair protein mutS - Escherichia coli MUTS_ECOBW - DNA mismatch repair protein MutS OS=Escherichia coli (strain K12 / MC4100 / BW2952) GN=mutS PE=3 SV=... EG10625 - methyl-directed mismatch repair protein / Methyl-directed mismatch repair protein, weak ATPase; dime... gi\|242378289, gi... - gi\|251786016\|ref\|YP_003000320.1\| hypothetical protein B21_02548 [Escherichia coli BL21], gi\|24237828...	0.0	[78..958]	[9..793]

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Predicted Domain #1

Region A:
Residues: [1-68]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MKHFFRLPTA FRPISRVSLR YSSTDTAQPK ISKLKISFNK ISESNSEKKD NLGSIDTRNC  60
   61 LSTQQDDK

[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 functions:

Term	Confidence	Notes
DNA-dependent ATPase activity	2.72462789867829	bayes_pls_golite062009
mismatched DNA binding	2.51625633651862	bayes_pls_golite062009
binding	2.4974940028864	bayes_pls_golite062009
DNA helicase activity	2.10134737488849	bayes_pls_golite062009
double-strand/single-strand DNA junction binding	2.02697209084624	bayes_pls_golite062009
	1.85506769032946	bayes_pls_golite062009
nucleoside-triphosphatase activity	1.84050240798436	bayes_pls_golite062009
pyrophosphatase activity	1.81138802583782	bayes_pls_golite062009
hydrolase activity, acting on acid anhydrides	1.78927528875848	bayes_pls_golite062009
hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides	1.78903889318615	bayes_pls_golite062009
ATP-dependent DNA helicase activity	1.71882026185027	bayes_pls_golite062009
helicase activity	1.70242731830224	bayes_pls_golite062009
guanine/thymine mispair binding	1.69026972999845	bayes_pls_golite062009
DNA insertion or deletion binding	1.68890613599528	bayes_pls_golite062009
microtubule motor activity	1.6537049553461	bayes_pls_golite062009
RNA helicase activity	1.63960194106079	bayes_pls_golite062009
ATP-dependent RNA helicase activity	1.61735400124552	bayes_pls_golite062009
nucleic acid binding	1.60768715809391	bayes_pls_golite062009
RNA-dependent ATPase activity	1.60404584546501	bayes_pls_golite062009
oxidized purine DNA binding	1.30673778631233	bayes_pls_golite062009
oxidized DNA binding	1.30673778631233	bayes_pls_golite062009
single guanine insertion binding	1.30673778631233	bayes_pls_golite062009
hydrolase activity	1.29419296935491	bayes_pls_golite062009
structure-specific DNA binding	1.2539059700735	bayes_pls_golite062009
ATP-dependent helicase activity	1.19311444180077	bayes_pls_golite062009
purine NTP-dependent helicase activity	1.19311444180077	bayes_pls_golite062009
ATPase activity	1.18431260772292	bayes_pls_golite062009
motor activity	1.14667913749579	bayes_pls_golite062009
double-stranded DNA binding	1.117585097627	bayes_pls_golite062009
DNA binding	1.11699929651302	bayes_pls_golite062009
protein-DNA loading ATPase activity	1.08464552192299	bayes_pls_golite062009
DNA-directed DNA polymerase activity	1.02269224635866	bayes_pls_golite062009
catalytic activity	1.00104173493322	bayes_pls_golite062009
transcription regulator activity	0.989226939888218	bayes_pls_golite062009
DNA polymerase activity	0.987648886158896	bayes_pls_golite062009
DNA clamp loader activity	0.91282941965371	bayes_pls_golite062009
dinucleotide repeat insertion binding	0.645326857719269	bayes_pls_golite062009
single base insertion or deletion binding	0.629563765934841	bayes_pls_golite062009
single-stranded DNA binding	0.568457189190858	bayes_pls_golite062009
cytoskeletal protein binding	0.500462538667228	bayes_pls_golite062009
protein binding	0.193768631623192	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
transcription factor activity	0.0434163635422169	bayes_pls_golite062009
actin binding	0.00482938540552702	bayes_pls_golite062009

Predicted Domain #2

Region A:
Residues: [69-185]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 LSSTEPSKAS LPPSLQYVRD LMDLYKDHVV LTQMGSFYEL YFEQAIRYAP ELNISLTNRA  60
   61 YSHGKVPFAG FPVHQLSRHL KMLVNNCGYS VTIAEQFKKK DVADNEANKF YRRVTRI

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	1421.54902
Match:	1e3mA_
Description:	DNA repair protein MutS, domain III; DNA repair protein MutS, the C-terminal domain; DNA repair protein MutS, domain II; DNA repair protein MutS, domain I
Matching Structure (courtesy of the PDB):

Predicted Domain #3

Region A:
Residues: [186-360]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 VTPGTFIDEA FENLRENTYL LNIEFPENCM SQVADTSLKV GICWCDVSTG EIFVQQVYLR  60
   61 DLVSAITRIQ PKEILLDERL LEFHIESGTW YPELVELKKF FIKYQKMPSQ HRTIESFYGL 120
  121 FNLGGKEATE RQLKIQFQTF TQKELAALRN TLIYVSNHLP DFSINFQIPQ RQLAT

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	1421.54902
Match:	1e3mA_
Description:	DNA repair protein MutS, domain III; DNA repair protein MutS, the C-terminal domain; DNA repair protein MutS, domain II; DNA repair protein MutS, domain I
Matching Structure (courtesy of the PDB):

Predicted Domain #4

Region A:
Residues: [361-386]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 AIMQIDSRTS TALELHSTVR DNNKKG

[Run NCBI BLAST on this sequence.]

Region B:
Residues: [717-959]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 NERNLVCPKV DESNKLEVVN GRHLMVEEGL SARSLETFTA NNCELAKDNL WVITGPNMGG  60
   61 KSTFLRQNAI IVILAQIGCF VPCSKARVGI VDKLFSRVGS ADDLYNEMST FMVEMIETSF 120
  121 ILQGATERSL AILDEIGRGT SGKEGISIAY ATLKYLLENN QCRTLFATHF GQELKQIIDN 180
  181 KCSKGMSEKV KFYQSGITDL GGNNFCYNHK LKPGICTKSD AIRVAELAGF PMEALKEARE 240
  241 ILG

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	1421.54902
Match:	1e3mA_
Description:	DNA repair protein MutS, domain III; DNA repair protein MutS, the C-terminal domain; DNA repair protein MutS, domain II; DNA repair protein MutS, domain I
Matching Structure (courtesy of the PDB):

Predicted Domain #5

Region A:
Residues: [387-577]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 SLLSSIRRTV TPSGTRLLSQ WLSGPSLDLK EIKKRQKIVA FFKDNRDITE TLRTMLKKVN  60
   61 DLSRILQKFS FGRGEALELI QMARSLEVSR EIRKYLLNNT SLMKATLKSQ ITQLTESLNF 120
  121 EKNLIDDILK FLNEEELAKS QDAKQNADVT RMLDIDVKDK KESNKDEIFE LRDFIVNPSF 180
  181 NTKLRKLHDT Y

[Run NCBI BLAST on this sequence.]

Region B:
Residues: [669-716]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 LLNLKIRNEE ANIIDLFKRK FIDRSNEVRQ VATTLGYLDT LSSFAVLA

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	1421.54902
Match:	1e3mA_
Description:	DNA repair protein MutS, domain III; DNA repair protein MutS, the C-terminal domain; DNA repair protein MutS, domain II; DNA repair protein MutS, domain I
Matching Structure (courtesy of the PDB):

Predicted Domain #6

Region A:
Residues: [578-668]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 QGVWQKKTEY NALLKGFFVG DLGAKTFTLK ERQNGEYALH VTGTASSLKK IDELISKSTE  60
   61 YHGSCFHILQ KSSQTRWLSH KIWTDLGHEL E

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	1421.54902
Match:	1e3mA_
Description:	DNA repair protein MutS, domain III; DNA repair protein MutS, the C-terminal domain; DNA repair protein MutS, domain II; DNA repair protein MutS, domain I
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: