YRC Public Data Repository - Protein Structure Prediction

Protein:	gi\|168277836, gi...
Organism:	synthetic construct
Length:	548 amino acids
Reference:	Drew K, et al. (2011) The proteome folding project: Proteome-scale prediction of structure and function. Genome Res. 2011 Sep 16

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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 gi|168277836, gi....

Description	E-value	Query Range	Subject Range
gi\|30584247, gi\|... - gi\|60653005\|gb\|AAX29197.1\| general transcription factor IIH polypeptide 1 62kDa [synthetic construct...	0.0	[1..548]	[1..548]
gi\|10440006 - gi\|10440006\|dbj\|BAB15621.1\| unnamed protein product [Homo sapiens]	0.0	[1..548]	[1..548]
gi\|114636459, gi... - gi\|114636461\|ref\|XP_001173127.1\| PREDICTED: general transcription factor IIH, polypeptide 1, 62kDa i...	0.0	[1..548]	[1..548]
gi\|57102734 - gi\|57102734\|ref\|XP_534083.1\| PREDICTED: similar to TFIIH basal transcription factor complex p62 subu...	0.0	[1..548]	[1..548]
gi\|34856117, gi\|... - gi\|34856117\|ref\|XP_341864.1\| PREDICTED: similar to TFIIH basal transcription factor complex p62 subu...	0.0	[1..548]	[1..547]
gi\|12836734, gi\|... - gi\|31982313\|ref\|NP_032212.2\| general transcription factor II H, polypeptide 1 [Mus musculus], gi\|128...	0.0	[1..548]	[1..547]
gi\|67972274 - gi\|67972274\|dbj\|BAE02479.1\| unnamed protein product [Macaca fascicularis]	0.0	[1..523]	[1..523]

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Predicted Domain #1

Region A:
Residues: [1-108]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MATSSEEVLL IVKKVRQKKQ DGALYLMAER IAWAPEGKDR FTISHMYADI KCQKISPEGK  60
   61 AKIQLQLVLH AGDTTNFHFS NESTAVKERD AVKDLLQQLL PKFKRKAN

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	46.0
Match:	1pfjA
Description:	Solution structure of the N-terminal PH/PTB domain of the TFIIH P62 subunit
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
general RNA polymerase II transcription factor activity	6.19860786133833	bayes_pls_golite062009
binding	3.29080729281876	bayes_pls_golite062009
protein binding	3.17213698546013	bayes_pls_golite062009
transcription regulator activity	2.10584700564436	bayes_pls_golite062009
transferase activity, transferring phosphorus-containing groups	2.05456820914801	bayes_pls_golite062009
nucleic acid binding	1.85794418941003	bayes_pls_golite062009
DNA binding	1.77960272183811	bayes_pls_golite062009
transcription elongation regulator activity	1.38051627844132	bayes_pls_golite062009
enzyme binding	0.977337620102034	bayes_pls_golite062009
RNA polymerase II transcription factor activity	0.704949129344961	bayes_pls_golite062009
protein kinase activity	0.565124275151513	bayes_pls_golite062009
structure-specific DNA binding	0.361321073558889	bayes_pls_golite062009
hydrolase activity	0.354215977182915	bayes_pls_golite062009
cytoskeletal protein binding	0.268141992393579	bayes_pls_golite062009
phosphotransferase activity, alcohol group as acceptor	0.242734483980252	bayes_pls_golite062009
protein domain specific binding	0.236765394237244	bayes_pls_golite062009
kinase activity	0.206532566781865	bayes_pls_golite062009
kinase binding	0.144753921529348	bayes_pls_golite062009
protein serine/threonine kinase activity	0.0735802149531289	bayes_pls_golite062009
actin binding	0.0485598963526399	bayes_pls_golite062009

Predicted Domain #2

Region A:
Residues: [109-298]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 KELEEKNRML QEDPVLFQLY KDLVVSQVIS AEEFWANRLN VNATDSSSTS NHKQDVGISA  60
   61 AFLADVRPQT DGCNGLRYNL TSDIIESIFR TYPAVKMKYA ENVPHNMTEK EFWTRFFQSH 120
  121 YFHRDRLNTG SKDLFAECAK IDEKGLKTMV SLGVKNPLLD LTALEDKPLD EGYGISSVPS 180
  181 ASNSKSIKEN

[Run NCBI BLAST on this sequence.]

Detection Method:	Pfam
Confidence:	18.008774
Match:	PF03909.8
Description:	No description for PF03909.8 was found.

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: [299-435]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 SNAAIIKRFN HHSAMVLAAG LRKQEAQNEQ TSEPSNMDGN SGDADCFQPA VKRAKLQESI  60
   61 EYEDLGKNNS VKTIALNLKK SDRYYHGPTP IQSLQYATSQ DIINSFQSIR QEMEAYTPKL 120
  121 TQVLSSSAAS STITALS

[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 #4

Region A:
Residues: [436-548]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 PGGALMQGGT QQAINQMVPN DIQSELKHLY VAVGELLRHF WSCFPVNTPF LEEKVVKMKS  60
   61 NLERFQVTKL CPFQEKIRRQ YLSTNLVSHI EEMLQTAYNK LHTWQSRRLM KKT

[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	0.947	0.027	regulation of transcription, DNA-dependent	a.24.10	Histidine-containing phosphotransfer domain, HPT 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: