YRC Public Data Repository - Protein Structure Prediction

Protein:	CHD1
Organism:	Saccharomyces cerevisiae
Length:	1468 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 CHD1.

Description	E-value	Query Range	Subject Range
CHD1 - Nucleosome remodeling factor that functions in regulation of transcription elongation; contains a ch... CHD1_YEAST - Chromo domain-containing protein 1 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=CHD1 ...	0.0	[1..1468]	[1..1468]
CHD2 - chromodomain helicase DNA binding protein 2	0.0	[5..1468]	[95..1563]
hrp3 - ATP-dependent DNA helicase Hrp3 HRP3_SCHPO - Chromodomain helicase hrp3 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=hrp3 PE=1 SV=1	0.0	[7..1463]	[50..1388]
CHD1_MOUSE - Chromodomain-helicase-DNA-binding protein 1 OS=Mus musculus GN=Chd1 PE=1 SV=2	0.0	[5..1467]	[82..1509]
gi\|7507776 - gi\|7507776\|pir\|\|T16867 probable cytochrome P450 T13C5.1 [similarity] - Caenorhabditis elegans	0.0	[5..1467]	[82..1509]
Chd1-PA - The gene Chromodomain-helicase-DNA-binding protein 1 is referred to in FlyBase by the symbol Dmel\Ch...	0.0	[6..1461]	[144..1594]
gi\|45384402, gi\|... - gi\|45384402\|ref\|NP_990272.1\| chromodomain helicase DNA binding protein 1 [Gallus gallus], gi\|2501846...	0.0	[5..1310]	[83..1357]

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Predicted Domain #1

Region A:
Residues: [1-133]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MAAKDISTEV LQNPELYGLR RSHRAAAHQQ NYFNDSDDED DEDNIKQSRR KRMTTIEDDE  60
   61 DEFEDEEGEE DSGEDEDEED FEEDDDYYGS PIKQNRSKPK SRTKSKSKSK PKSQSEKQST 120
  121 VKIPTRFSNR QNK

[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 #2

Region A:
Residues: [134-261]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 TVNYNIDYSD DDLLESEDDY GSEEALSEEN VHEASANPQP EDFHGIDIVI NHRLKTSLEE  60
   61 GKVLEKTVPD LNNCKENYEF LIKWTDESHL HNTWETYESI GQVRGLKRLD NYCKQFIIED 120
  121 QQVRLDPY

[Run NCBI BLAST on this sequence.]

Detection Method:	Pfam
Confidence:	17.065502
Match:	PF00385
Description:	'chromo' (CHRromatin Organisation MOdifier) domain

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 #3

Region A:
Residues: [262-341]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 VTAEDIEIMD MERERRLDEF EEFHVPERII DSQRASLEDG TSQLQYLVKW RRLNYDEATW  60
   61 ENATDIVKLA PEQVKHFQNR

[Run NCBI BLAST on this sequence.]

Detection Method:	ORFEUS
Confidence:	13.61
Match:	1gm5A
Description:	RecG, N-terminal domain; RecG "wedge" domain; RecG helicase domain
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
transcription elongation regulator activity	4.88034936399943	bayes_pls_golite062009
lysine N-acetyltransferase activity	3.7424679735172	bayes_pls_golite062009
histone acetyltransferase activity	3.7424679735172	bayes_pls_golite062009
binding	2.64537357529343	bayes_pls_golite062009
nucleic acid binding	2.51683451033161	bayes_pls_golite062009
N-acetyltransferase activity	2.48980517248425	bayes_pls_golite062009
N-acyltransferase activity	2.27909822963553	bayes_pls_golite062009
DNA binding	2.12258000781149	bayes_pls_golite062009
transcription regulator activity	2.09345198747025	bayes_pls_golite062009
acetyltransferase activity	1.95584629179223	bayes_pls_golite062009
DNA-dependent ATPase activity	1.23094623498843	bayes_pls_golite062009
protein binding	1.22129154759482	bayes_pls_golite062009
motor activity	1.14667913749579	bayes_pls_golite062009
general RNA polymerase II transcription factor activity	1.07968294254548	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
transcription repressor activity	0.862685397469217	bayes_pls_golite062009
DNA helicase activity	0.75415390146713	bayes_pls_golite062009
helicase activity	0.6191010101321	bayes_pls_golite062009
microtubule motor activity	0.60036517876321	bayes_pls_golite062009
sequence-specific DNA binding	0.543891899378373	bayes_pls_golite062009
cytoskeletal protein binding	0.500462538667228	bayes_pls_golite062009
ATP-dependent DNA helicase activity	0.41398614759796	bayes_pls_golite062009
purine NTP-dependent helicase activity	0.29664013896754	bayes_pls_golite062009
ATP-dependent helicase activity	0.29664013896754	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
pyrophosphatase activity	0.133017653323467	bayes_pls_golite062009
ATP-dependent RNA helicase activity	0.13050483816765	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
structural constituent of ribosome	0.089234257580272	bayes_pls_golite062009
actin binding	0.00482938540552702	bayes_pls_golite062009

Predicted Domain #4

Region A:
Residues: [342-560]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 ENSKILPQYS SNYTSQRPRF EKLSVQPPFI KGGELRDFQL TGINWMAFLW SKGDNGILAD  60
   61 EMGLGKTVQT VAFISWLIFA RRQNGPHIIV VPLSTMPAWL DTFEKWAPDL NCICYMGNQK 120
  121 SRDTIREYEF YTNPRAKGKK TMKFNVLLTT YEYILKDRAE LGSIKWQFMA VDEAHRLKNA 180
  181 ESSLYESLNS FKVANRMLIT GTPLQNNIKE LAALVNFLM

[Run NCBI BLAST on this sequence.]

Detection Method:	ORFEUS
Confidence:	13.61
Match:	1gm5A
Description:	RecG, N-terminal domain; RecG "wedge" domain; RecG helicase domain
Matching Structure (courtesy of the PDB):

Predicted Domain #5

Region A:
Residues: [561-626]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 PGRFTIDQEI DFENQDEEQE EYIHDLHRRI QPFILRRLKK DVEKSLPSKT ERILRVELSD  60
   61 VQTEYY

[Run NCBI BLAST on this sequence.]

Detection Method:	ORFEUS
Confidence:	12.85
Match:	1hv8A
Description:	Putative DEAD box RNA helicase
Matching Structure (courtesy of the PDB):

Predicted Domain #6

Region A:
Residues: [627-694]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 KNILTKNYSA LTAGAKGGHF SLLNIMNELK KASNHPYLFD NAEERVLQKF GDGKMTRENV  60
   61 LRGLIMSS

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	7.221849
Match:	1hv8A_
Description:	Putative DEAD box RNA helicase
Matching Structure (courtesy of the PDB):

Predicted Domain #7

Region A:
Residues: [695-927]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 GKMVLLDQLL TRLKKDGHRV LIFSQMVRML DILGDYLSIK GINFQRLDGT VPSAQRRISI  60
   61 DHFNSPDSND FVFLLSTRAG GLGINLMTAD TVVIFDSDWN PQADLQAMAR AHRIGQKNHV 120
  121 MVYRLVSKDT VEEEVLERAR KKMILEYAII SLGVTDGNKY TKKNEPNAGE LSAILKFGAG 180
  181 NMFTATDNQK KLEDLNLDDV LNHAEDHVTT PDLGESHLGG EEFLKQFEVT DYK

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	7.30103
Match:	1d9xA_
Description:	Nucleotide excision repair enzyme UvrB
Matching Structure (courtesy of the PDB):

Predicted Domain #8

Region A:
Residues: [928-1105]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 ADIDWDDIIP EEELKKLQDE EQKRKDEEYV KEQLEMMNRR DNALKKIKNS VNGDGTAANS  60
   61 DSDDDSTSRS SRRRARANDM DSIGESEVRA LYKAILKFGN LKEILDELIA DGTLPVKSFE 120
  121 KYGETYDEMM EAAKDCVHEE EKNRKEILEK LEKHATAYRA KLKSGEIKAE NQPKDNPL

[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.

		MCM Score	GO Score	GO Term	SCOP Match	SCOP Description
View	Download	0.932	N/A	N/A	a.7.2	Enzyme IIa from lactose specific PTS, IIa-lac

Predicted Domain #9

Region A:
Residues: [1106-1266]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 TRLSLKKREK KAVLFNFKGV KSLNAESLLS RVEDLKYLKN LINSNYKDDP LKFSLGNNTP  60
   61 KPVQNWSSNW TKEEDEKLLI GVFKYGYGSW TQIRDDPFLG ITDKIFLNEV HNPVAKKSAS 120
  121 SSDTTPTPSK KGKGITGSSK KVPGAIHLGR RVDYLLSFLR G

[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 #10

Region A:
Residues: [1267-1361]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 GLNTKSPSAD IGSKKLPTGP SKKRQRKPAN HSKSMTPEIT SSEPANGPPS KRMKALPKGP  60
   61 AALINNTRLS PNSPTPPLKS KVSRDNGTRQ SSNPS

[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 #11

Region A:
Residues: [1362-1468]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 SGSAHEKEYD SMDEEDCRHT MSAIRTSLKR LRRGGKSLDR KEWAKILKTE LTTIGNHIES  60
   61 QKGSSRKASP EKYRKHLWSY SANFWPADVK STKLMAMYDK ITESQKK

[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.

		MCM Score	GO Score	GO Term	SCOP Match	SCOP Description
View	Download	0.932	0.005	RNA elongation from RNA polymerase II promoter	a.7.2	Enzyme IIa from lactose specific PTS, IIa-lac

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: