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COFACTOR result for job id 76292

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>76292 (325 residues)
MTILFNTSILTWALALVGVLLFASLSSLVSEKAGVVNIAVEGMMIIGALVVSILGTYLTS
NDNKSNYTQIPIVLLAGVITAVFALLHAFPAITLKANQIISGTAINILALGLGIFLSTSN
WFGKQSQVIASGYSSIDVINITKVVNGKTQQVASMLPIWTIIAIILAIGLFVFFKYTKQG
MRYAMVGENPNAIDAAGISVTKYRYLAVILSGFLAGVGGGVFVVTAVSGGGLFSGNMLGY
GFLGIAIMIFGQWRISFIVIGSIIFSWLFALGQQIGTLSTNKTIQAISTLFNTLPFVLTI
LAMVAFSKTSRAPAAVGVPFDKAKR

Download query sequence and structure

Proteins with similar structure

Top 10 structural analogs in PDB (as identified by TM-align)

Rank	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	Download Alignment
1	2nq2A	0.68	3.17	0.119	0.797	Download
2	5b57A	0.67	3.74	0.092	0.825	Download
3	1l7vA	0.66	3.40	0.109	0.791	Download
4	4g1uA	0.66	3.52	0.115	0.797	Download
5	1pw4A	0.47	5.51	0.058	0.699	Download
6	4pypA	0.46	5.58	0.063	0.695	Download
7	4apsA	0.46	5.67	0.094	0.695	Download
8	4gbyA2	0.33	5.21	0.068	0.474	Download
9	4cl4A2	0.32	5.50	0.059	0.471	Download
10	4ikvA1	0.31	5.52	0.063	0.462	Download

(a)	Query structure is shown in cartoon, while the structural analog is displayed using backbone trace.
(b)	Ranking of proteins is based on TM-score of the structural alignment between the query structure and known structures in the PDB library.
(c)	RMSD^a is the RMSD between residues that are structurally aligned by TM-align.
(d)	IDEN^a is the percentage sequence identity in the structurally aligned region.
(e)	Cov. represents the coverage of the alignment by TM-align and is equal to the number of structurally aligned residues divided by length of the query protein.

Predicted Gene Ontology (GO) Terms

Molecular Function (MF)

GO term	Cscore^GO	Name
GO:0005215	1.00	transporter activity
GO:0022857	0.99	transmembrane transporter activity
GO:0022891	0.90	substrate-specific transmembrane transporter activity
GO:0015144	0.85	carbohydrate transmembrane transporter activity
GO:0051119	0.84	sugar transmembrane transporter activity
GO:0015145	0.83	monosaccharide transmembrane transporter activity
GO:0003824	0.82	catalytic activity

Download full result of the above consensus prediction.

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(a)

Cscore^GO is the confidence score of predicted GO terms. Cscore^GO values range in between [0-1]; where a higher value indicates a better confidence in predicting the function using the template.

(b)

The graph shows the predicted terms within the Gene Ontology hierachy for Molecular Function. Confidently predicted terms are color coded by Cscore^GO:

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[0.5,0.6)

[0.6,0.7)

[0.7,0.8)

[0.8,0.9)

[0.9,1.0]

Biological Process (BP)

GO term	Cscore^GO	Name
GO:0051234	0.97	establishment of localization
GO:0006810	0.95	transport
GO:0009987	0.75	cellular process
GO:0071702	0.65	organic substance transport
GO:0008152	0.65	metabolic process
GO:0071704	0.64	organic substance metabolic process
GO:0044237	0.62	cellular metabolic process
GO:0044238	0.60	primary metabolic process
GO:0044699	0.59	single-organism process
GO:0006807	0.58	nitrogen compound metabolic process
GO:0044765	0.56	single-organism transport
GO:1901360	0.54	organic cyclic compound metabolic process
GO:0046483	0.54	heterocycle metabolic process
GO:0034641	0.54	cellular nitrogen compound metabolic process
GO:0008643	0.53	carbohydrate transport
GO:0006139	0.50	nucleobase-containing compound metabolic process

Download full result of the above consensus prediction.

Click the graph to show a high resolution version.

(a)

Cscore^GO is the confidence score of predicted GO terms. Cscore^GO values range in between [0-1]; where a higher value indicates a better confidence in predicting the function using the template.

(b)

The graph shows the predicted terms within the Gene Ontology hierachy for Biological Process. Confidently predicted terms are color coded by Cscore^GO:

[0.4,0.5)

[0.5,0.6)

[0.6,0.7)

[0.7,0.8)

[0.8,0.9)

[0.9,1.0]

Cellular Component (CC)

GO term	Cscore^GO	Name
GO:0016021	1.00	integral component of membrane
GO:0005886	1.00	plasma membrane
GO:0044424	0.75	intracellular part
GO:0044444	0.57	cytoplasmic part

Download full result of the above consensus prediction.

Click the graph to show a high resolution version.

(a)

Cscore^GO is the confidence score of predicted GO terms. Cscore^GO values range in between [0-1]; where a higher value indicates a better confidence in predicting the function using the template.

(b)

The graph shows the predicted terms within the Gene Ontology hierachy for Cellular Component. Confidently predicted terms are color coded by Cscore^GO:

[0.4,0.5)

[0.5,0.6)

[0.6,0.7)

[0.7,0.8)

[0.8,0.9)

[0.9,1.0]

Predicted Enzyme Commission (EC) Numbers

Top 5 enzyme homologs in PDB

Rank	Cscore^EC	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	EC Number	Predicted Active Site Residues
1	0.060	3ii9C	0.364	5.97	0.089	0.575	1.3.99.7	NA
2	0.060	2lgsA	0.372	5.33	0.052	0.538	6.3.1.2	NA
3	0.060	1jqoA	0.364	6.39	0.035	0.594	4.1.1.31	NA
4	0.060	1lgrA	0.372	5.32	0.052	0.538	6.3.1.2	NA
5	0.060	2ix6E	0.363	5.68	0.047	0.535	1.3.3.6	NA

	Click on the radio buttons to visualize predicted active site residues.
(a)	Cscore^EC is the confidence score for the Enzyme Commission (EC) number prediction. Cscore^EC values range in between [0-1]; where a higher score indicates a more reliable EC number prediction.
(b)	TM-score is a measure of global structural similarity between query and template protein.
(c)	RMSD^a is the RMSD between residues that are structurally aligned by TM-align.
(d)	IDEN^a is the percentage sequence identity in the structurally aligned region.
(e)	Cov. represents the coverage of global structural alignment and is equal to the number of structurally aligned residues divided by length of the query protein.

Predicted Ligand Binding Sites

Template proteins with similar binding site:

Rank	Cscore^LB	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	BS-score	Lig. Name	Download Complex	Predicted binding site residues
1	0.03	2nq22	0.676	3.06	0.124	0.788	0.79	III	Download	31,35,175,176,181,182,184,185,187,188,190,191,192,194,195,196,198,252
2	0.01	3gjcB	0.406	5.59	0.061	0.603	0.59	BOG	Download	34,245,250
3	0.01	2q72A	0.384	6.44	0.056	0.637	0.66	IXX	Download	26,43,44,47,222
4	0.01	3gjdA	0.382	6.46	0.059	0.637	0.55	BOG	Download	39,40,42,45
5	0.01	1siwA	0.383	7.01	0.031	0.680	0.57	SF4	Download	41,46,48,80,81,212
6	0.01	2jbsC	0.396	5.79	0.066	0.597	0.54	FMN	Download	212,215,216

	Click on the radio buttons to visualize predicted binding site and residues.
(a)	Cscore^LB is the confidence score of predicted binding site. Cscore^LB values range in between [0-1]; where a higher score indicates a more reliable ligand-binding site prediction.
(b)	BS-score is a measure of local similarity (sequence & structure) between template binding site and predicted binding site in the query structure. Based on large scale benchmarking analysis, we have observed that a BS-score >1 reflects a significant local match between the predicted and template binding site.
(c)	TM-score is a measure of global structural similarity between query and template protein.
(d)	RMSD^a the RMSD between residues that are structurally aligned by TM-align.
(e)	IDEN^a is the percentage sequence identity in the structurally aligned region.
(f)	Cov. represents the coverage of global structural alignment and is equal to the number of structurally aligned residues divided by length of the query protein.

[Download result.tar.bz2 for all prediction results]

Reference:

Chengxin Zhang, Peter L Freddolino, and Yang Zhang. COFACTOR: Improved protein function prediction by combining structure, sequence, and protein-protein interaction information. Nucleic Acids Research, 45: W291-299 (2017)
Ambrish Roy, Jianyi Yang, and Yang Zhang. COFACTOR: An accurate comparative algorithm for structure-based protein function annotation. Nucleic Acids Research, 40:W471-W477 (2012).

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