YRC Public Data Repository - Protein Structure Prediction

Protein:	SNF12
Organism:	Saccharomyces cerevisiae
Length:	566 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 SNF12.

Description	E-value	Query Range	Subject Range
SNF12 - 73 kDa subunit of the SWI/SNF chromatin remodeling complex involved in transcriptional regulation; h... SNF12_YEAST - Transcription regulatory protein SNF12 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=S... gi\|151944551 - gi\|151944551\|gb\|EDN62829.1\| SWI/SNF transcription activation complex 73 kDa subunit [Saccharomyces c...	0.0	[1..566]	[1..566]
tag-246 - D15Kz1 protein homolog status:Confirmed UniProt:Q09646 protein_id:CAA87424.1	0.0	[1..381]	[1..367]
gi\|114644841, gi... - gi\|114644841\|ref\|XP_001155587.1\| PREDICTED: SWI/SNF-related matrix-associated actin-dependent regula... gi\|4566530 - gi\|4566530\|gb\|AAD23390.1\|AF109733_1 SWI/SNF-related, matrix-associated, actin-dependent regulator of... gi\|109096590 - gi\|109096590\|ref\|XP_001110916.1\| PREDICTED: similar to SWI/SNF-related matrix-associated actin-depen... tr\|G3HX65\|G3HX65... - SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1 OS=Cri...	1.0E-85	[266..548]	[194..422]
SNF12_ARATH - SWI/SNF complex component SNF12 homolog OS=Arabidopsis thaliana GN=At5g14170 PE=1 SV=1	1.0E-85	[2..352]	[82..442]
SMRD1_MOUSE, SCD... - SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1 OS=Mus...	2.0E-84	[5..380]	[73..432]
SMRD2_RAT - SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 2 OS=Rat...	1.0E-82	[5..380]	[72..451]

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Predicted Domain #1

Region A:
Residues: [1-204]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MSKVMKPSNG KGSRKSSKAA TPDTKNFFHA KKKDPVNQDK ANNASQITPT VPHSHPSDMV  60
   61 IPDHLAELIP ELYSFQQLVD SEKRLDHFIH LRNLHMKRMV AQWERSKLSQ EFLYPHLNFP 120
  121 NVKFLRIFIS NVSENQPWQM DTNNEADLMA LENATWTMRI EGRLLDNVQA NDPAREKFSS 180
  181 FIESIVVDFK NKENDNVPST KFNA

[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.

Found no structure predictions for this domain.

Predicted Domain #2

Region A:
Residues: [205-263]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 APEENATEGP SDKKLNLNLP LQFSLPNGDN STTTNTDQNN ATMGEETAKK DMSSTTPKL

[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	0.363	a.60.2	RuvA domain 2-like
View	Download	0.351	d.10.1	DNA-binding domain
View	Download	0.343	b.40.6	MOP-like
View	Download	0.335	d.11.1	Penicillin-binding protein 2x (pbp-2x), c-terminal domain

Predicted Domain #3

Region A:
Residues: [264-566]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 ESVKWQYDPN NPVDFDGLDI KRVGSENVEC TISILRKSSP EEPFMSYSPQ LTAIIGLKSG  60
   61 TSHDAIFSIY KYIHLNELLT NDESAFENLM GNRNNHNSNT STSKMLDAAS SQVSIVKLDT 120
  121 QLITLLPSSL KESSPDTMKL TDLLSLINST HLLPLQPIEI DYTVRVDKAS TYGELVLDIE 180
  181 VPDVNALKFN NTQRESQIGA AELNENAREL EQIKPKIALQ DKEITSVLSN LHESNKRYRF 240
  241 FKKISEDPVK ALNECIASTS NALKVLSGDE GYNEDMVRRA NFYKENEAML RENIEVILSN 300
  301 GRM

[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.

Found no structure predictions for this domain.

Predicted functions:

Term	Confidence	Notes
transcription regulator activity	4.01592136607858	bayes_pls_golite062009
basal transcription repressor activity	3.09418413549897	bayes_pls_golite062009
binding	2.67987108623459	bayes_pls_golite062009
transcription coactivator activity	2.58234407051051	bayes_pls_golite062009
general RNA polymerase II transcription factor activity	2.32480271621458	bayes_pls_golite062009
transcription repressor activity	1.98538788872171	bayes_pls_golite062009
transcription activator activity	1.83085389017135	bayes_pls_golite062009
transcription factor binding	1.73032563380905	bayes_pls_golite062009
transcription cofactor activity	1.60414428986898	bayes_pls_golite062009
protein binding	1.58138506346812	bayes_pls_golite062009
structural molecule activity	1.28917299936669	bayes_pls_golite062009
RNA polymerase II transcription factor activity	1.06026105710513	bayes_pls_golite062009
catalytic activity	0.121624777548864	bayes_pls_golite062009

Predicted Domain #4

Region A:
Residues: [305-450]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 EPFMSYSPQL TAIIGLKSGT SHDAIFSIYK YIHLNELLTN DESAFENLMG NRNNHNSNTS  60
   61 TSKMLDAASS QVSIVKLDTQ LITLLPSSLK ESSPDTMKLT DLLSLINSTH LLPLQPIEID 120
  121 YTVRVDKAST YGELVLDIEV PDVNAL

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	22.0
Match:	1uhrA
Description:	Solution structure of the SWIB domain of mouse BRG1-associated factor 60a
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
transcription regulator activity	4.01592136607858	bayes_pls_golite062009
basal transcription repressor activity	3.09418413549897	bayes_pls_golite062009
binding	2.67987108623459	bayes_pls_golite062009
transcription coactivator activity	2.58234407051051	bayes_pls_golite062009
general RNA polymerase II transcription factor activity	2.32480271621458	bayes_pls_golite062009
transcription repressor activity	1.98538788872171	bayes_pls_golite062009
transcription activator activity	1.83085389017135	bayes_pls_golite062009
transcription factor binding	1.73032563380905	bayes_pls_golite062009
transcription cofactor activity	1.60414428986898	bayes_pls_golite062009
protein binding	1.58138506346812	bayes_pls_golite062009
structural molecule activity	1.28917299936669	bayes_pls_golite062009
RNA polymerase II transcription factor activity	1.06026105710513	bayes_pls_golite062009
catalytic activity	0.121624777548864	bayes_pls_golite062009

Predicted Domain #5

Region A:
Residues: [451-566]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 KFNNTQRESQ IGAAELNENA RELEQIKPKI ALQDKEITSV LSNLHESNKR YRFFKKISED  60
   61 PVKALNECIA STSNALKVLS GDEGYNEDMV RRANFYKENE AMLRENIEVI LSNGRM

[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.

Found no 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

Predicted functions:

Predicted functions: