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COFACTOR result for job id 76547

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>76547 (202 residues)
MWIKDKLVETKVFLKNHNYLWKFKLIVCLPIFISLISFDWISKAIVVSHMKLGETKTFIN
GFLNFQYVINLGMAYGKLHDKAYLVIIFATIFSLFLTTIFIFLNNKKWLIVLVIILAGSW
GNLLARLWAPGNENNVYYGVVDFLTWDFSLFNSRDYVFNLADLYVNIAIGLTILFTIIEL
VLYIKSKIKTKKEKIDNEQNNS

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	5dirA	0.71	1.41	0.232	0.748	Download
2	2j8sA3	0.47	5.44	0.081	0.792	Download
3	3perA	0.47	4.91	0.055	0.703	Download
4	1xmgC	0.47	4.91	0.047	0.683	Download
5	2zsmA	0.39	5.79	0.028	0.693	Download
6	4mt1A2	0.35	5.45	0.065	0.569	Download
7	3k07A	0.34	6.13	0.049	0.639	Download
8	2rjqA	0.31	5.85	0.051	0.515	Download
9	4uw2A1	0.31	5.35	0.030	0.530	Download
10	4ntcA1	0.30	5.66	0.075	0.525	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:0003824	0.98	catalytic activity
GO:0016787	0.94	hydrolase activity
GO:0008233	0.87	peptidase 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:

[0.4,0.5)

[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:0009987	0.96	cellular process
GO:0071704	0.94	organic substance metabolic process
GO:0044238	0.94	primary metabolic process
GO:0044237	0.94	cellular metabolic process
GO:0043170	0.91	macromolecule metabolic process
GO:0044267	0.88	cellular protein metabolic process
GO:0006807	0.81	nitrogen compound metabolic process
GO:0034641	0.80	cellular nitrogen compound metabolic process
GO:1901564	0.75	organonitrogen compound metabolic process
GO:0051604	0.62	protein maturation
GO:0006465	0.60	signal peptide processing
GO:0043412	0.51	macromolecule modification
GO:1901360	0.50	organic cyclic 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:0044464	0.99	cell part
GO:0016020	0.95	membrane
GO:0005886	0.91	plasma membrane
GO:0044425	0.80	membrane part
GO:0016021	0.78	integral component of membrane
GO:0044424	0.70	intracellular 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	1mhyD	0.438	4.77	0.021	0.648	1.14.13.25	NA
2	0.060	1rsrB	0.429	5.31	0.067	0.683	1.17.4.1	NA
3	0.060	1yfeA	0.413	4.75	0.062	0.619	4.2.1.2	NA
4	0.060	1qleC	0.448	4.11	0.074	0.614	1.9.3.1	90,92,117
5	0.060	3cmmC	0.410	5.25	0.053	0.614	6.3.2.19	71

	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	0.01	1v54C	0.453	4.68	0.031	0.648	0.42	CDL	Download	114,115,117,118,121,122,125,126,130
2	0.01	3perB	0.469	4.85	0.061	0.698	0.48	PO4	Download	118,121,162
3	0.01	1v54P	0.451	4.58	0.031	0.639	0.42	CDL	Download	1,6,114,117,118,121
4	0.01	3ag1C	0.447	4.38	0.031	0.624	0.46	CDL	Download	114,115,117,118,121,122,125,126,130
5	0.01	2eimC	0.452	4.64	0.031	0.644	0.51	CDL	Download	118,122,125,126
6	0.01	2dysC	0.451	4.65	0.031	0.644	0.41	CDL	Download	41,45,117,120,121,124
7	0.01	3dhhB	0.463	4.54	0.021	0.658	0.46	BML	Download	119,120,123
8	0.01	1v55P	0.452	4.65	0.031	0.644	0.43	CDL	Download	38,42,116,117,121,124,125,128

	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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