YRC Public Data Repository - Protein Structure Prediction

Protein:	MGS1
Organism:	Saccharomyces cerevisiae
Length:	587 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 MGS1.

Description	E-value	Query Range	Subject Range
MGS1 - Protein with DNA-dependent ATPase and ssDNA annealing activities involved in maintenance of genome; ... gi\|190409192 - gi\|190409192\|gb\|EDV12457.1\| DNA-dependent ATPase MGS1 [Saccharomyces cerevisiae RM11-1a] WRIP1_YEAST - DNA-dependent ATPase MGS1 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=MGS1 PE=1 SV=2 gi\|207341862 - gi\|207341862\|gb\|EDZ69804.1\| YNL218Wp-like protein [Saccharomyces cerevisiae AWRI1631]	0.0	[1..587]	[1..587]
gi\|31981384, gi\|... - gi\|31981384\|ref\|NP_084491.2\| Werner helicase interacting protein 1 [Mus musculus], gi\|14714682\|gb\|AA...	0.0	[72..562]	[158..656]
gi\|55661736, gi\|... - gi\|8886769\|gb\|AAF80563.1\|AF218313_1 putative helicase RUVBL [Homo sapiens], gi\|55661736\|emb\|CAH73665...	0.0	[132..562]	[4..441]
gi\|25329894 - pir\|\|H96939 ATPase related to the helicase chain of Holliday junction resolvase [imported] - Clostri... gi\|15023171, gi\|... - gi\|15893618\|ref\|NP_346967.1\| recombination factor protein RarA [Clostridium acetobutylicum ATCC 824]...	0.0	[133..585]	[15..437]
gi\|25329891 - gi\|25329891\|pir\|\|G85614 probable polynucleotide enzyme ycaJ [imported] - Escherichia coli (strain O1... gi\|12514054, gi\|... - gi\|15800755\|ref\|NP_286769.1\| recombination factor protein RarA [Escherichia coli O157:H7 EDL933], gi...	0.0	[133..586]	[14..447]
YCAJ_ECOLI - Hypothetical protein ycaJ - Escherichia coli gi\|83585835, gi\|... - gi\|83585835\|ref\|ZP_00924475.1\| COG2256: ATPase related to the helicase subunit of the Holliday junct... gi\|157160415, gi... - gi\|75195080\|ref\|ZP_00705150.1\| COG2256: ATPase related to the helicase subunit of the Holliday junct... gi\|190907651, gi... - gi\|75240969\|ref\|ZP_00724858.1\| COG2256: ATPase related to the helicase subunit of the Holliday junct... gi\|82777586, gi\|... - gi\|82777586\|ref\|YP_403935.1\| recombination factor protein RarA [Shigella dysenteriae Sd197], gi\|8124... gi\|168783802, gi... - gi\|188998918\|gb\|EDU67904.1\| putative DNA recombination-associated ATPase RarA [Escherichia coli O157... gi\|254591492, gi... - gi\|254792092\|ref\|YP_003076929.1\| recombination protein [Escherichia coli O157:H7 str. TW14359], gi\|2... gi\|168787320, gi... - gi\|189372743\|gb\|EDU91159.1\| putative DNA recombination-associated ATPase RarA [Escherichia coli O157... gi\|253972907, gi... - gi\|254161006\|ref\|YP_003044114.1\| recombination protein [Escherichia coli B str. REL606], gi\|25397290... gi\|189376426, gi... - gi\|189376426\|gb\|EDU94842.1\| putative DNA recombination-associated ATPase RarA [Escherichia coli O157... gi\|253977121, gi... - gi\|254287814\|ref\|YP_003053562.1\| recombination protein [Escherichia coli BL21(DE3)], gi\|253977121\|gb... gi\|169888385, gi... - gi\|170080550\|ref\|YP_001729870.1\| recombination protein [Escherichia coli str. K-12 substr. DH10B], g... gi\|242376707, gi... - gi\|251784434\|ref\|YP_002998738.1\| hypothetical protein B21_00903 [Escherichia coli BL21], gi\|24237670... gi\|170520218, gi... - gi\|170682500\|ref\|YP_001744278.1\| putative DNA recombination-associated ATPase RarA [Escherichia coli... gi\|238863427, gi... - gi\|238900150\|ref\|YP_002925946.1\| recombination protein [Escherichia coli BW2952], gi\|238863427\|gb\|AC... RARA_ECOL6 - Replication-associated recombination protein A OS=Escherichia coli O6:H1 (strain CFT073 / ATCC 70092... gi\|192955956, gi... - gi\|193070763\|ref\|ZP_03051698.1\| putative DNA recombination-associated ATPase RarA [Escherichia coli ... gi\|227884141, gi... - gi\|227884141\|ref\|ZP_04001946.1\| recombination ATPase [Escherichia coli 83972], gi\|227838893\|gb\|EEJ49... gi\|195939555 - gi\|195939555\|ref\|ZP_03084937.1\| recombination factor protein RarA [Escherichia coli O157:H7 str. EC4... gi\|208732375, gi... - gi\|208815727\|ref\|ZP_03256906.1\| putative DNA recombination-associated ATPase RarA [Escherichia coli ... EG12690 - recombination intermediate processing DNA-dependent ATPase / DNA-dependent ATPase involved in proces... RARA_ECO57 - Replication-associated recombination protein A OS=Escherichia coli O157:H7 GN=rarA PE=3 SV=1 EG12690 - recombination intermediate processing DNA-dependent ATPase / DNA-dependent ATPase involved in proces... gi\|89107742, gi\|... - gi\|89107742\|ref\|AP_001522.1\| recombination protein [Escherichia coli str. K-12 substr. W3110], gi\|40... gi\|168752126, gi... - gi\|188013952\|gb\|EDU52074.1\| putative DNA recombination-associated ATPase RarA [Escherichia coli O157... gi\|189355914, gi... - gi\|189355914\|gb\|EDU74333.1\| putative DNA recombination-associated ATPase RarA [Escherichia coli O157... gi\|168762974, gi... - gi\|189366832\|gb\|EDU85248.1\| putative DNA recombination-associated ATPase RarA [Escherichia coli O157... gi\|189361172, gi... - gi\|189361172\|gb\|EDU79591.1\| putative DNA recombination-associated ATPase RarA [Escherichia coli O157... gi\|187768384, gi... - gi\|187768384\|gb\|EDU32228.1\| putative DNA recombination-associated ATPase RarA [Escherichia coli O157... YCAJ_ECOL6, RARA... - Uncharacterized protein ycaJ - Escherichia coli O6, Replication-associated recombination protein A O... gi\|13360436, gi\|... - gi\|15830231\|ref\|NP_309004.1\| recombination factor protein RarA [Escherichia coli O157:H7 str. Sakai]... gi\|110342684, gi... - gi\|110641092\|ref\|YP_668822.1\| recombination factor protein RarA [Escherichia coli 536], gi\|110342684... gi\|208737596, gi... - gi\|208822111\|ref\|ZP_03262430.1\| putative DNA recombination-associated ATPase RarA [Escherichia coli ... gi\|209397045, gi... - gi\|209397045\|ref\|YP_002269565.1\| putative DNA recombination-associated ATPase RarA [Escherichia coli... gi\|209918141, gi... - gi\|209918141\|ref\|YP_002292225.1\| recombination factor protein RarA [Escherichia coli SE11], gi\|20991... gi\|217320733, gi... - gi\|217324512\|ref\|ZP_03440596.1\| putative DNA recombination-associated ATPase RarA [Escherichia coli ... gi\|218548414, gi... - gi\|218548414\|ref\|YP_002382205.1\| recombination factor protein RarA [Escherichia fergusonii ATCC 3546... gi\|218688680, gi... - gi\|218688680\|ref\|YP_002396892.1\| recombination factor protein RarA [Escherichia coli ED1a], gi\|21842... gi\|218704321, gi... - gi\|218704321\|ref\|YP_002411840.1\| recombination factor protein RarA [Escherichia coli UMN026], gi\|218...	0.0	[133..586]	[14..447]
gi\|168822938, gi... - gi\|205340727\|gb\|EDZ27491.1\| putative DNA recombination-associated ATPase RarA [Salmonella enterica s... gi\|168466546, gi... - gi\|195630930\|gb\|EDX49516.1\| putative DNA recombination-associated ATPase RarA [Salmonella enterica s... gi\|194406019, gi... - gi\|194447715\|ref\|YP_002044955.1\| recombination factor protein RarA [Salmonella enterica subsp. enter... gi\|194446297, gi... - gi\|194446297\|ref\|YP_002040161.1\| putative DNA recombination-associated ATPase RarA [Salmonella enter... gi\|205334719, gi... - gi\|205334719\|gb\|EDZ21483.1\| putative DNA recombination-associated ATPase RarA [Salmonella enterica s... gi\|167994703, gi... - gi\|205327462\|gb\|EDZ14226.1\| ATPase, AAA family [Salmonella enterica subsp. enterica serovar 4,[5],12... gi\|56413986, gi\|... - gi\|56413986\|ref\|YP_151061.1\| recombination factor protein RarA [Salmonella enterica subsp. enterica ... gi\|205347729, gi... - gi\|205347729\|gb\|EDZ34360.1\| ATPase, AAA family [Salmonella enterica subsp. enterica serovar Hadar st... gi\|205339853, gi... - gi\|205339853\|gb\|EDZ26617.1\| ATPase, AAA family [Salmonella enterica subsp. enterica serovar Heidelbe... gi\|238913263 - gi\|238913263\|ref\|ZP_04657100.1\| recombination factor protein RarA [Salmonella enterica subsp. enteri... gi\|161364172, gi... - gi\|161614808\|ref\|YP_001588773.1\| recombination factor protein RarA [Salmonella enterica subsp. enter... lcl\|NC_016856.1_... - [gene=ycaJ] [protein=recombination factor protein RarA] [protein_id=YP_005236676.1] [location=100054... gi\|16502126, gi\|... - gi\|25329900\|pir\|\|AH0611 conserevd hypothetical protein STY0960 [imported] - Salmonella enterica subs... gi\|16759833 - gi\|16759833\|ref\|NP_455450.1\| recombination factor protein RarA [Salmonella enterica subsp. enterica ... gi\|213851471 - gi\|213851471\|ref\|ZP_03381369.1\| recombination factor protein RarA [Salmonella enterica subsp. enteri... gi\|213428592 - gi\|213428592\|ref\|ZP_03361342.1\| recombination factor protein RarA [Salmonella enterica subsp. enteri... gi\|16764323, gi\|... - gi\|16764323\|ref\|NP_459938.1\| recombination factor protein RarA [Salmonella typhimurium LT2], gi\|1641... gi\|29138024, gi\|... - gi\|29142394\|ref\|NP_805736.1\| recombination factor protein RarA [Salmonella enterica subsp. enterica ... gi\|214003462 - gi\|214003462\|ref\|ZP_03414197.1\| recombination factor protein RarA [Salmonella enterica subsp. enteri... gi\|197263317, gi... - gi\|197263317\|ref\|ZP_03163391.1\| ATPase, AAA family [Salmonella enterica subsp. enterica serovar Sain... gi\|194457508, gi... - gi\|194471144\|ref\|ZP_03077128.1\| putative DNA recombination-associated ATPase RarA [Salmonella enteri... gi\|199603472, gi... - gi\|200391027\|ref\|ZP_03217638.1\| ATPase, AAA family [Salmonella enterica subsp. enterica serovar Virc... gi\|197094386, gi... - gi\|197362909\|ref\|YP_002142546.1\| recombination factor protein RarA [Salmonella enterica subsp. enter...	0.0	[133..586]	[14..447]

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Predicted Domain #1

Region A:
Residues: [1-110]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MSNKRTSVEQ LISCPICSRK VFFSLINSHL DICGKEKSKP SSRPQTVSSL LAGPKKRKQA  60
   61 NSEKFIDLEN KDHEIKPGLK SESDDIEIVE NESKRFKAAP STDFAKSIVE

[Run NCBI BLAST on this sequence.]

Detection Method:

deduced

Shown below are all of our de novo (Rosetta) predictions for this domain.
Click here to view only most confident match.

		MCM Score	SCOP Match	SCOP Description
View	Download	0.220	a.118.8	TPR-like
View	Download	0.321	d.129.2	Phosphoglucomutase, C-terminal domain

Predicted functions:

Term	Confidence	Notes
binding	2.64537357529343	bayes_pls_golite062009
nucleic acid binding	2.21184938313192	bayes_pls_golite062009
DNA binding	1.94055378599526	bayes_pls_golite062009
transcription regulator activity	1.83584389083042	bayes_pls_golite062009
pyrophosphatase activity	1.49611313354225	bayes_pls_golite062009
DNA-dependent ATPase activity	1.2155186842031	bayes_pls_golite062009
helicase activity	1.16085745407703	bayes_pls_golite062009
catalytic activity	1.00104173493322	bayes_pls_golite062009
DNA helicase activity	0.72881469450553	bayes_pls_golite062009
structure-specific DNA binding	0.720649395550746	bayes_pls_golite062009
transcription factor activity	0.697256579145077	bayes_pls_golite062009
purine NTP-dependent helicase activity	0.59513742813869	bayes_pls_golite062009
ATP-dependent helicase activity	0.59513742813869	bayes_pls_golite062009
double-stranded DNA binding	0.58862275163252	bayes_pls_golite062009
purine nucleotide binding	0.428373955572763	bayes_pls_golite062009
purine ribonucleotide binding	0.424644011903671	bayes_pls_golite062009
ribonucleotide binding	0.424583288440993	bayes_pls_golite062009
nucleotide binding	0.422354428195324	bayes_pls_golite062009
protein-DNA loading ATPase activity	0.3625050107782	bayes_pls_golite062009
DNA clamp loader activity	0.27925703205288	bayes_pls_golite062009
ATP-dependent DNA helicase activity	0.22150712609541	bayes_pls_golite062009
protein binding	0.170837278876362	bayes_pls_golite062009
ATP binding	0.04834397972685	bayes_pls_golite062009
adenyl ribonucleotide binding	0.0149501427627318	bayes_pls_golite062009
adenyl nucleotide binding	0.00365326483311895	bayes_pls_golite062009
DNA polymerase activity	4.95561462330096E-4	bayes_pls_golite062009

Predicted Domain #2

Region A:
Residues: [111-138]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 PASSRDQLHN DYESRWLQKI SHLPLSEK

[Run NCBI BLAST on this sequence.]

Region B:
Residues: [298-368]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 NVNELCIVLS RGIALLNKCR KQVWNIENPL KLSRSILEYV VDLSVGDTRR ALNMLEMIEV  60
   61 STRERKADEE E

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	169.70927
Match:	1iqpA_
Description:	Replication factor C
Matching Structure (courtesy of the PDB):

Predicted Domain #3

Region A:
Residues: [139-297]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 LRPKELRDYV GQQHILSQDN GTLFKYIKQG TIPSMILWGP PGVGKTSLAR LLTKTATTSS  60
   61 NESNVGSRYF MIETSATKAN TQELRGIFEK SKKEYQLTKR RTVLFIDEIH RFNKVQQDLL 120
  121 LPHVENGDII LIGATTENPS FQLNNALISR CLIFVLEKL

[Run NCBI BLAST on this sequence.]

Region B:
Residues: [369-508]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 LSIDDVRDII KNNSSNGLNT YYDPKGDNHY DTISAFHKSI RGGDENASLY YLARMLQGGE  60
   61 DPLYVARRMI RIASEDIGLR DSSLLPLAVA AHDAVMKVGL PEADLALAQC CVALARAPKS 120
  121 VELYRAWKKL RAMMSENMYS

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	169.70927
Match:	1iqpA_
Description:	Replication factor C
Matching Structure (courtesy of the PDB):

Predicted Domain #4

Region A:
Residues: [509-587]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 LASSEIPMHI RNAPTKLMEE LGYHKGYKYN PDYIEGKVQQ DYFPKEVLEK CPNKTDLKFL  60
   61 DGKHLGDKED PDLRQSYQG

[Run NCBI BLAST on this sequence.]

Detection Method:

MSA

Shown below are all of our structure predictions for this domain.
Click here to view only most confident match.

		MCM Score	GO Score	GO Term	SCOP Match	SCOP Description
View	Download	0.229	0.640	helicase activity	a.60.2	RuvA domain 2-like
View	Download	0.302	0.056	nucleus	d.58.7	RNA-binding domain, RBD
View	Download	0.281	0.018	regulation of DNA replication	a.77.1	DEATH domain
View	Download	0.212	N/A	N/A	d.57.1	DNA damage-inducible protein DinI

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: