YRC Public Data Repository - Protein Structure Prediction

Protein:	gi\|53734604
Organism:	Xenopus laevis
Length:	356 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|53734604.

Description	E-value	Query Range	Subject Range
gi\|5453854, gi\|4... - gi\|5453854\|ref\|NP_006187.1\| poly(rC) binding protein 1 [Homo sapiens], gi\|460771\|emb\|CAA55016.1\| hnR...	2.0E-73	[1..356]	[1..356]
gi\|57093423 - gi\|57093423\|ref\|XP_538537.1\| PREDICTED: similar to Poly(rC)-binding protein 1 (Alpha-CP1) (hnRNP-E1)...	2.0E-73	[1..356]	[1..356]
gi\|109065037 - gi\|109065037\|ref\|XP_001099433.1\| PREDICTED: similar to poly(rC) binding protein 3 isoform 3 [Macaca ... gi\|114684791 - gi\|114684791\|ref\|XP_001157797.1\| PREDICTED: hypothetical protein isoform 6 [Pan troglodytes]	1.0E-65	[1..354]	[33..391]
gi\|114577926 - gi\|114577926\|ref\|XP_001140593.1\| PREDICTED: poly(rC) binding protein 1 isoform 2 [Pan troglodytes]	2.0E-65	[1..356]	[1..333]
PCBP2 - poly(rC) binding protein 2 gi\|61557337, gi\|... - gi\|61557337\|ref\|NP_001013241.1\| poly(rC) binding protein 2 [Rattus norvegicus], gi\|50926841\|gb\|AAH78...	3.0E-64	[1..353]	[1..361]

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Predicted Domain #1

Region A:
Residues: [1-89]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MDAGVTESGL NVTLTIRLLM HGKEVGSIIG KKGESVKRIR EESGARINIS EGNCPERIIT  60
   61 LTGPTNAIFK AFAMIIDKLE EDINSSMTN

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	10.69897
Match:	2axyA
Description:	Crystal Structure of KH1 domain of human Poly(C)-binding protein-2 with C-rich strand of human telomeric DNA
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
RNA binding	5.18414740305744	bayes_pls_golite062009
nucleic acid binding	4.78650555542715	bayes_pls_golite062009
mRNA binding	3.82977088614136	bayes_pls_golite062009
binding	3.45962790790935	bayes_pls_golite062009
transcription regulator activity	2.28364833275102	bayes_pls_golite062009
DNA binding	2.03207983673692	bayes_pls_golite062009
transcription factor activity	1.30278154718684	bayes_pls_golite062009
protein binding	1.16541072642796	bayes_pls_golite062009
	1.02980840568405	bayes_pls_golite062009
poly-pyrimidine tract binding	0.63404501189528	bayes_pls_golite062009
mRNA 3'-UTR binding	0.489176583045793	bayes_pls_golite062009
transcription repressor activity	0.392035003865213	bayes_pls_golite062009
transcription activator activity	0.324382863054631	bayes_pls_golite062009
transcription factor binding	0.254024117548226	bayes_pls_golite062009
catalytic activity	0.113112541746059	bayes_pls_golite062009
sequence-specific DNA binding	0.0321875054165348	bayes_pls_golite062009

Predicted Domain #2

Region A:
Residues: [90-183]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 STAASRPPVT LRLVVPATQC GSLIGKGGCK IKEIRESTGA QVQVAGDMLP NSTERAITIA  60
   61 GVPQSVTECV KQICLVMLET LSQSPQGRVM TIPY

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	9.0
Match:	1x4mA
Description:	Solution structure of KH domain in Far upstream element binding protein 1
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
RNA binding	5.18414740305744	bayes_pls_golite062009
nucleic acid binding	4.78650555542715	bayes_pls_golite062009
mRNA binding	3.82977088614136	bayes_pls_golite062009
binding	3.45962790790935	bayes_pls_golite062009
transcription regulator activity	2.28364833275102	bayes_pls_golite062009
DNA binding	2.03207983673692	bayes_pls_golite062009
transcription factor activity	1.30278154718684	bayes_pls_golite062009
protein binding	1.16541072642796	bayes_pls_golite062009
	1.02980840568405	bayes_pls_golite062009
poly-pyrimidine tract binding	0.63404501189528	bayes_pls_golite062009
mRNA 3'-UTR binding	0.489176583045793	bayes_pls_golite062009
transcription repressor activity	0.392035003865213	bayes_pls_golite062009
transcription activator activity	0.324382863054631	bayes_pls_golite062009
transcription factor binding	0.254024117548226	bayes_pls_golite062009
catalytic activity	0.113112541746059	bayes_pls_golite062009
sequence-specific DNA binding	0.0321875054165348	bayes_pls_golite062009

Predicted Domain #3

Region A:
Residues: [184-269]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 QPMPASSPVI CAGGQDRCSD AAGYPHATHD LEGPPLDAYS IQGQHTISPL DLAKLNQVAR  60
   61 QQSHFAMMHG GTGFAGIDSS SPEVKG

[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	0.205	a.56.1	CO dehydrogenase ISP C-domain like
View	Download	0.317	d.226.1	GIY-YIG endonuclease
View	Download	0.265	c.58.1	Aminoacid dehydrogenase-like, N-terminal domain

Predicted Domain #4

Region A:
Residues: [270-356]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 YWASLDASTQ TTHELTIPNN LIGCIIGRQG ANINEIRQMS GAQIKIANPV EGSSGRQVTI  60
   61 TGSAASISLA QYLINARLSS EKGMGCS

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	17.522879
Match:	1wvnA
Description:	Crsytal Structure of domain 3 of human alpha polyC binding protein
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
RNA binding	5.18414740305744	bayes_pls_golite062009
nucleic acid binding	4.78650555542715	bayes_pls_golite062009
mRNA binding	3.82977088614136	bayes_pls_golite062009
binding	3.45962790790935	bayes_pls_golite062009
transcription regulator activity	2.28364833275102	bayes_pls_golite062009
DNA binding	2.03207983673692	bayes_pls_golite062009
transcription factor activity	1.30278154718684	bayes_pls_golite062009
protein binding	1.16541072642796	bayes_pls_golite062009
	1.02980840568405	bayes_pls_golite062009
poly-pyrimidine tract binding	0.63404501189528	bayes_pls_golite062009
mRNA 3'-UTR binding	0.489176583045793	bayes_pls_golite062009
transcription repressor activity	0.392035003865213	bayes_pls_golite062009
transcription activator activity	0.324382863054631	bayes_pls_golite062009
transcription factor binding	0.254024117548226	bayes_pls_golite062009
catalytic activity	0.113112541746059	bayes_pls_golite062009
sequence-specific DNA binding	0.0321875054165348	bayes_pls_golite062009

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:

Predicted functions: