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COFACTOR result for job id 76340

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User Input

>76340 (142 residues)
MSKVRNLDLVYSYLQSTKTPSSLNEIWKSISKDIISQKKDEISVIADLYGDMVLDNRFAL
TTDNLWALSSNSSVENIKKQYDDFINTDHKHRYSDSDEELTIDDEMLLDEDYDSDFTQEL
DDFDEDFDDTDQTYIDDDEYNR

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	2krcA	0.54	2.07	0.189	0.627	Download
2	2va8B	0.49	3.70	0.030	0.676	Download
3	2r8cA	0.48	4.56	0.038	0.831	Download
4	5dfnA	0.48	4.10	0.088	0.739	Download
5	5w1eA3	0.48	3.99	0.099	0.718	Download
6	3feqN	0.48	4.89	0.030	0.852	Download
7	2gaiA	0.48	3.55	0.059	0.648	Download
8	4r8kA	0.48	4.28	0.043	0.761	Download
9	1cy8A3	0.48	3.27	0.089	0.641	Download
10	4ddtA3	0.47	3.45	0.088	0.648	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	1.00	catalytic activity
GO:0016772	0.94	transferase activity, transferring phosphorus-containing groups
GO:0003899	0.74	DNA-directed RNA polymerase 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)

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[0.7,0.8)

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[0.9,1.0]

Biological Process (BP)

GO term	Cscore^GO	Name
GO:0006139	0.99	nucleobase-containing compound metabolic process
GO:0043170	0.96	macromolecule metabolic process
GO:0016070	0.94	RNA metabolic process
GO:0034660	0.93	ncRNA metabolic process
GO:0006364	0.92	rRNA processing
GO:0000448	0.92	cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
GO:1901576	0.57	organic substance biosynthetic process
GO:0044271	0.57	cellular nitrogen compound biosynthetic process
GO:0034654	0.56	nucleobase-containing compound biosynthetic process
GO:0044281	0.55	small molecule metabolic process
GO:1901564	0.54	organonitrogen compound metabolic process
GO:1901135	0.50	carbohydrate derivative 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:0044424	1.00	intracellular part
GO:0043229	0.96	intracellular organelle
GO:0043231	0.95	intracellular membrane-bounded organelle
GO:0044444	0.80	cytoplasmic part
GO:0005634	0.69	nucleus
GO:0032991	0.63	macromolecular complex
GO:0005829	0.54	cytosol
GO:0043234	0.53	protein complex
GO:0005737	0.53	cytoplasm
GO:0009536	0.51	plastid
GO:0009507	0.50	chloroplast

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	2gajB	0.479	3.58	0.059	0.648	5.99.1.2	NA
2	0.060	3ilwA	0.468	4.12	0.038	0.690	5.99.1.3	NA
3	0.060	2wltA	0.453	4.21	0.037	0.704	3.5.1.1	NA
4	0.060	3cirA	0.415	5.38	0.054	0.747	1.3.99.1	NA
5	0.060	3fofA	0.462	4.33	0.045	0.697	5.99.1.-	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:

No Binding sites was predicted

Click to view	Rank	Cscore^LB	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	BS-score	Lig. Name	Download Complex	Predicted binding site residues

	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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