YRC Public Data Repository - Protein Structure Prediction

Protein:	SNF2
Organism:	Saccharomyces cerevisiae
Length:	1703 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 SNF2.

Description	E-value	Query Range	Subject Range
SNF2 - Catalytic subunit of the SWI/SNF chromatin remodeling complex involved in transcriptional regulation... SNF2_YEAST - Transcription regulatory protein SNF2 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=SN...	0.0	[1..1703]	[1..1703]
gi\|447739 - gi\|447739\|prf\|\|1915304A nylB upstream ORF	0.0	[1..1703]	[1..1703]
gi\|13603721 - gi\|13603721\|gb\|AAK31908.1\|AF247809_1 putative chromatin remodeling protein SYD [Arabidopsis thaliana...	0.0	[66..1529]	[64..1529]
gi\|45384078, gi\|... - gi\|996020\|emb\|CAA62832.1\| BRM protein [Gallus gallus], gi\|45384078\|ref\|NP_990470.1\| SWI/SNF related,...	0.0	[76..1500]	[6..1444]
gi\|7507776 - gi\|7507776\|pir\|\|T16867 probable cytochrome P450 T13C5.1 [similarity] - Caenorhabditis elegans	0.0	[64..1182]	[256..1282]
SMARCA2 - SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2	0.0	[76..1500]	[6..1462]
SNF21_SCHPO - Chromatin structure-remodeling complex subunit snf21 OS=Schizosaccharomyces pombe (strain 972 / ATCC... snf21 - ATP-dependent DNA helicase Snf21	0.0	[443..1476]	[103..1113]

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Predicted Domain #1

Region A:
Residues: [1-404]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MNIPQRQFSN EEVNRCYLRW QHLRNEHGMN APSVPEFIYL TKVLQFAAKQ RQELQMQRQQ  60
   61 QGISGSQQNI VPNSSDQAEL PNNASSHISA SASPHLAPNM QLNGNETFST SAHQSPIMQT 120
  121 QMPLNSNGGN NMLPQRQSSV GSLNATNFSP TPANNGENAA EKPDNSNHNN LNLNNSELQP 180
  181 QNRSLQEHNI QDSNVMPGSQ INSPMPQQAQ MQQAQFQAQQ AQQAQQAQQA QQAQARLQQG 240
  241 RRLPMTMFTA EQSELLKAQI TSLKCLVNRK PIPFEFQAVI QKSINHPPDF KRMLLSLSEF 300
  301 ARRRQPTDQN NQSNLNGGNN TQQPGTNSHY NNTNTDNVSG LTRNAPLDSK DENFASVSPA 360
  361 GPSSVHNAKN GTLDKNSQTV SGTPITQTES KKEENETISN VAKT

[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.

Predicted Domain #2

Region A:
Residues: [405-708]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 APNSNKTHTE QNNPPKPQKP VPLNVLQDQY KEGIKVVDID DPDMMVDSFT MPNISHSNID  60
   61 YQTLLANSDH AKFTIEPGVL PVGIDTHTAT DIYQTLIALN LDTTVNDCLD KLLNDECTES 120
  121 TRENALYDYY ALQLLPLQKA VRGHVLQFEW HQNSLLTNTH PNFLSKIRNI NVQDALLTNQ 180
  181 LYKNHELLKL ERKKTEAVAR LKSMNKSAIN QYNRRQDKKN KRLKFGHRLI ATHTNLERDE 240
  241 QKRAEKKAKE RLQALKANDE EAYIKLLDQT KDTRITHLLR QTNAFLDSLT RAVKDQQKYT 300
  301 KEMI

[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 #3

Region A:
Residues: [709-962]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 DSHIKEASEE VDDLSMVPKM KDEEYDDDDD NSNVDYYNVA HRIKEDIKKQ PSILVGGTLK  60
   61 DYQIKGLQWM VSLFNNHLNG ILADEMGLGK TIQTISLLTY LYEMKNIRGP YLVIVPLSTL 120
  121 SNWSSEFAKW APTLRTISFK GSPNERKAKQ AKIRAGEFDV VLTTFEYIIK ERALLSKVKW 180
  181 VHMIIDEGHR MKNAQSKLSL TLNTHYHADY RLILTGTPLQ NNLPELWALL NFVLPKIFNS 240
  241 VKSFDEWFNT PFAN

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	7.221849
Match:	1gm5A_
Description:	RecG, N-terminal domain; RecG "wedge" domain; RecG helicase domain
Matching Structure (courtesy of the PDB):

Predicted Domain #4

Region A:
Residues: [963-1014]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 TGGQDKIELS EEETLLVIRR LHKVLRPFLL RRLKKDVEKE LPDKVEKVVK CK

[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
binding	2.64537357529343	bayes_pls_golite062009
nucleic acid binding	2.51683451033161	bayes_pls_golite062009
ATP-dependent DNA helicase activity	2.4348680404207	bayes_pls_golite062009
pyrophosphatase activity	2.13284212711072	bayes_pls_golite062009
DNA binding	2.12258000781149	bayes_pls_golite062009
transcription regulator activity	2.09345198747025	bayes_pls_golite062009
helicase activity	1.70242731830224	bayes_pls_golite062009
structure-specific DNA binding	1.2539059700735	bayes_pls_golite062009
protein binding	1.22129154759482	bayes_pls_golite062009
DNA-dependent ATPase activity	1.2155186842031	bayes_pls_golite062009
purine NTP-dependent helicase activity	1.19311444180077	bayes_pls_golite062009
ATP-dependent helicase activity	1.19311444180077	bayes_pls_golite062009
double-stranded DNA binding	1.117585097627	bayes_pls_golite062009
general RNA polymerase II transcription factor activity	1.07968294254548	bayes_pls_golite062009
histone acetyltransferase activity	1.05990253628867	bayes_pls_golite062009
lysine N-acetyltransferase activity	1.05990253628867	bayes_pls_golite062009
catalytic activity	1.00104173493322	bayes_pls_golite062009
transcription activator activity	0.889929694023098	bayes_pls_golite062009
transcription factor activity	0.887108427603557	bayes_pls_golite062009
DNA helicase activity	0.72881469450553	bayes_pls_golite062009
motor activity	0.677658554107	bayes_pls_golite062009
single-stranded DNA binding	0.568457189190858	bayes_pls_golite062009
sequence-specific DNA binding	0.543891899378373	bayes_pls_golite062009
mismatched DNA binding	0.31144582840038	bayes_pls_golite062009
RNA polymerase II transcription factor activity	0.243902356228423	bayes_pls_golite062009
RNA helicase activity	0.18426050934025	bayes_pls_golite062009
nucleoside-triphosphatase activity	0.147579541298736	bayes_pls_golite062009
RNA-dependent ATPase activity	0.14606996093053	bayes_pls_golite062009
ATP-dependent RNA helicase activity	0.13050483816765	bayes_pls_golite062009
microtubule motor activity	0.11674780318211	bayes_pls_golite062009
nucleotide binding	0.114848452385726	bayes_pls_golite062009
hydrolase activity, acting on acid anhydrides	0.113504049290503	bayes_pls_golite062009
hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides	0.111293884322157	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

Predicted Domain #5

Region A:
Residues: [1015-1086]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MSALQQIMYQ QMLKYRRLFI GDQNNKKMVG LRGFNNQIMQ LKKICNHPFV FEEVEDQINP  60
   61 TRETNDDIWR VA

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	7.39794
Match:	1hv8A_
Description:	Putative DEAD box RNA helicase
Matching Structure (courtesy of the PDB):

Predicted Domain #6

Region A:
Residues: [1087-1347]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 GKFELLDRIL PKLKATGHRV LIFFQMTQIM DIMEDFLRYI NIKYLRLDGH TKSDERSELL  60
   61 RLFNAPDSEY LCFILSTRAG GLGLNLQTAD TVIIFDTDWN PHQDLQAQDR AHRIGQKNEV 120
  121 RILRLITTNS VEEVILERAY KKLDIDGKVI QAGKFDNKST SEEQEALLRS LLDAEEERRK 180
  181 KRESGVEEEE ELKDSEINEI LARNDEEMAV LTRMDEDRSK KEEELGVKSR LLEKSELPDI 240
  241 YSRDIGAELK REESESAAVY N

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	5.39794
Match:	1d9xA_
Description:	Nucleotide excision repair enzyme UvrB
Matching Structure (courtesy of the PDB):

Predicted Domain #7

Region A:
Residues: [1348-1510]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 GRGARERKTA TYNDNMSEEQ WLRQFEVSDD EKNDKQARKQ RTKKEDKSEA IDGNGEIKGE  60
   61 NIDADNDGPR INNISAEDRA DTDLAMNDDD FLSKKRKAGR PRGRPKKVKL EGSENSEPPA 120
  121 LESSPVTGDN SPSEDFMDIP KPRTAGKTSV KSARTSTRGR GRG

[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 #8

Region A:
Residues: [1511-1703]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 RGRGRGRGRG RGRPPKARNG LDYVRTPAAA TSPIDIREKV AKQALDLYHF ALNYENEAGR  60
   61 KLSDIFLSKP SKALYPDYYM IIKYPVAFDN INTHIETLAY NSLKETLQDF HLIFSNARIY 120
  121 NTEGSVVYED SLELEKVVTK KYCEIMGDNS QLDFTEFDEQ YGTRPLVLPP VVTSSVAESF 180
  181 TDEADSSMTE ASV

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	87.10721
Match:	1e6iA_
Description:	GCN5
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: