YRC Public Data Repository - Protein Structure Prediction

Protein:	MSH6
Organism:	Saccharomyces cerevisiae
Length:	1242 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 MSH6.

Description	E-value	Query Range	Subject Range
MSH6 - Protein required for mismatch repair in mitosis and meiosis, forms a complex with Msh2p to repair bo... MSH6_YEAST - DNA mismatch repair protein MSH6 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=MSH6 PE...	0.0	[1..1242]	[1..1242]
gi\|447739 - gi\|447739\|prf\|\|1915304A nylB upstream ORF	0.0	[1..1242]	[1..1242]
MSH6_MOUSE - DNA mismatch repair protein Msh6 OS=Mus musculus GN=Msh6 PE=1 SV=2	0.0	[51..1185]	[122..1340]
gi\|7507776 - gi\|7507776\|pir\|\|T16867 probable cytochrome P450 T13C5.1 [similarity] - Caenorhabditis elegans	0.0	[51..1198]	[122..1360]
MSH6 - mutS homolog 6 (E. coli) gi\|123987976 - gi\|123987976\|gb\|ABM83824.1\| mutS homolog 6 (E. coli) [synthetic construct]	0.0	[51..1198]	[122..1360]
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	[299..1240]	[3..862]

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Predicted Domain #1

Region A:
Residues: [1-248]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MAPATPKTSK TAHFENGSTS SQKKMKQSSL LSFFSKQVPS GTPSKKVQKP TPATLENTAT  60
   61 DKITKNPQGG KTGKLFVDVD EDNDLTIAEE TVSTVRSDIM HSQEPQSDTM LNSNTTEPKS 120
  121 TTTDEDLSSS QSRRNHKRRV NYAESDDDDS DTTFTAKRKK GKVVDSESDE DEYLPDKNDG 180
  181 DEDDDIADDK EDIKGELAED SGDDDDLISL AETTSKKKFS YNTSHSSSPF TRNISRDNSK 240
  241 KKSRPNQA

[Run NCBI BLAST on this sequence.]

Detection Method:	ORFEUS
Confidence:	10.28
Match:	1ldvA
Description:	No description for 1ldvA was found.

Predicted Domain #2

Region A:
Residues: [249-303]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 PSRSYNPSHS QPSATSKSSK FNKQNEERYQ WLVDERDAQR RPKSDPEYDP RTLYI

[Run NCBI BLAST on this sequence.]

Detection Method:	ORFEUS
Confidence:	8.11
Match:	1k83A
Description:	RBP1
Matching Structure (courtesy of the PDB):

Predicted Domain #3

Region A:
Residues: [304-417]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 PSSAWNKFTP FEKQYWEIKS KMWDCIVFFK KGKFFELYEK DALLANALFD LKIAGGGRAN  60
   61 MQLAGIPEMS FEYWAAQFIQ MGYKVAKVDQ RESMLAKEMR EGSKGIVKRE LQCI

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	1615.228787
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: [418-611]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 LTSGTLTDGD MLHSDLATFC LAIREEPGNF YNETQLDSST IVQKLNTKIF GAAFIDTATG  60
   61 ELQMLEFEDD SECTKLDTLM SQVRPMEVVM ERNNLSTLAN KIVKFNSAPN AIFNEVKAGE 120
  121 EFYDCDKTYA EIISSEYFST EEDWPEVLKS YYDTGKKVGF SAFGGLLYYL KWLKLDKNLI 180
  181 SMKNIKEYDF VKSQ

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	1615.228787
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: [612-637]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 HSMVLDGITL QNLEIFSNSF DGSDKG

[Run NCBI BLAST on this sequence.]

Region B:
Residues: [917-1190]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 YLGAPSCRPT IVDEVDSKTN TQLNGFLKFK SLRHPCFNLG ATTAKDFIPN DIELGKEQPR  60
   61 LGLLTGANAA GKSTILRMAC IAVIMAQMGC YVPCESAVLT PIDRIMTRLG ANDNIMQGKS 120
  121 TFFVELAETK KILDMATNRS LLVVDELGRG GSSSDGFAIA ESVLHHVATH IQSLGFFATH 180
  181 YGTLASSFKH HPQVRPLKMS ILVDEATRNV TFLYKMLEGQ SEGSFGMHVA SMCGISKEII 240
  241 DNAQIAADNL EHTSRLVKER DLAANNLNGE VVSV

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	1615.228787
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: [638-792]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 TLFKLFNRAI TPMGKRMMKK WLMHPLLRKN DIESRLDSVD SLLQDITLRE QLEITFSKLP  60
   61 DLERMLARIH SRTIKVKDFE KVITAFETII ELQDSLKNND LKGDVSKYIS SFPEGLVEAV 120
  121 KSWTNAFERQ KAINENIIVP QRGFDIEFDK SMDRI

[Run NCBI BLAST on this sequence.]

Region B:
Residues: [867-916]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 EAKEIHKTLE EDLKNRLCQK FDAHYNTIWM PTIQAISNID CLLAITRTSE

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	1615.228787
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 #7

Region A:
Residues: [793-866]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 QELEDELMEI LMTYRKQFKC SNIQYKDSGK EIYTIEIPIS ATKNVPSNWV QMAANKTYKR  60
   61 YYSDEVRALA RSMA

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	1615.228787
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 #8

Region A:
Residues: [1191-1242]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 PGGLQSDFVR IAYGDGLKNT KLGSGEGVLN YDWNIKRNVL KSLFSIIDDL QS

[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	0.646	a.4.1	Homeodomain-like
View	Download	0.636	a.4.1	Homeodomain-like
View	Download	0.386	a.4.5	"Winged helix" DNA-binding domain
View	Download	0.359	a.76.1	Iron-dependent represor protein, dimerization domain
View	Download	0.351	a.155.1	H-NS histone-like proteins
View	Download	0.346	a.77.1	DEATH domain
View	Download	0.335	d.42.1	POZ domain
View	Download	0.332	a.36.1	Signal peptide-binding domain
View	Download	0.319	a.50.1	Anaphylotoxins (complement system)
View	Download	0.310	a.23.5	Hemolysin expression modulating protein HHA
View	Download	0.310	a.4.5	"Winged helix" DNA-binding domain
View	Download	0.308	a.159.2	FF domain
View	Download	0.303	a.4.1	Homeodomain-like
View	Download	0.302	a.144.2	Ribosomal protein L20
View	Download	0.293	a.4.1	Homeodomain-like
View	Download	0.292	a.60.1	SAM/Pointed domain
View	Download	0.268	a.4.10	N-terminal Zn binding domain of HIV integrase
View	Download	0.256	a.4.6	C-terminal effector domain of the bipartite response regulators
View	Download	0.244	a.60.2	RuvA domain 2-like
View	Download	0.243	a.4.1	Homeodomain-like
View	Download	0.241	a.4.5	"Winged helix" DNA-binding domain
View	Download	0.233	d.52.5	Probable GTPase Der, C-terminal domain
View	Download	0.222	d.58.23	Probable ACP-binding domain of malonyl-CoA ACP transacylase
View	Download	0.218	a.164.1	C-terminal domain of DFF45/ICAD (DFF-C domain)
View	Download	0.217	a.112.1	Description not found.
View	Download	0.210	a.60.3	C-terminal domain of RNA polymerase alpha subunit

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