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COFACTOR result for job id 76554

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>76554 (350 residues)
MIEQLNEILNNFKVKLELVKDLNSWEELKKEFIGKDSSLTTILKSIKTISSDKKQEIGKL
ANQIRVEIINQLNEKQEQLKNKELLVKLEKEKIDVTLTNSSLKFGSKHVLNIVIEEISDI
FTEIGFEMVSGTEIESDLYNFQKLNLPVDHPARDMQDTFYLDNNLVLRTHCTNMTSRMLT
KLASLKTEDNNLAVISYGNVYRRDDDDATHSHQFMQIDGFVVGNKISFANLKWILKYMCQ
RLFNKDINIRLRPSYFPFTEPSVEVDVSCFKCDSKGCFICKKTGWIEILGAGMINEHVLK
LNGLDPTKCSGLAFGIGIERIAMLKFNISNIRNFYENNVKFLEQFKFYSE

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	1eiyA	0.88	1.62	0.358	0.917	Download
2	2rhsC	0.75	1.05	0.537	0.766	Download
3	4p75D	0.67	1.39	0.412	0.694	Download
4	3l4gC	0.67	2.60	0.235	0.734	Download
5	3pcoA	0.65	2.09	0.434	0.691	Download
6	2du3A	0.64	3.71	0.200	0.766	Download
7	2du7A	0.62	3.47	0.180	0.729	Download
8	2odrA	0.62	3.35	0.191	0.714	Download
9	3hfvA	0.60	1.99	0.271	0.640	Download
10	6ezdA	0.54	3.09	0.110	0.614	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:0004826	1.00	phenylalanine-tRNA ligase activity
GO:1901363	0.72	heterocyclic compound binding
GO:0097159	0.72	organic cyclic compound binding
GO:0003676	0.70	nucleic acid binding
GO:0003723	0.68	RNA binding
GO:0036094	0.63	small molecule binding
GO:0000166	0.62	nucleotide binding
GO:0005524	0.61	ATP binding
GO:0000049	0.61	tRNA binding
GO:0043167	0.53	ion binding
GO:0043169	0.50	cation binding

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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[0.8,0.9)

[0.9,1.0]

Biological Process (BP)

GO term	Cscore^GO	Name
GO:0006432	1.00	phenylalanyl-tRNA aminoacylation

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:0044444	0.90	cytoplasmic part
GO:0005737	0.87	cytoplasm
GO:0032991	0.66	macromolecular complex
GO:0043226	0.53	organelle
GO:1902494	0.52	catalytic complex
GO:0043229	0.52	intracellular organelle
GO:0043231	0.50	intracellular membrane-bounded organelle

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	0.598	1eiyA	0.880	1.62	0.358	0.917	6.1.1.20	202,313
2	0.241	2rhsC	0.749	1.05	0.537	0.766	6.1.1.20	202,313
3	0.133	3cmqA	0.603	1.95	0.271	0.640	6.1.1.20	202,313
4	0.074	2e3cA	0.530	3.04	0.147	0.606	6.1.1.26	202
5	0.067	3ig2B	0.452	2.91	0.133	0.514	6.1.1.20	130

	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	0.48	2rhqA	0.739	1.31	0.543	0.763	0.99	GAX	Download	144,172,175,179,216,218,256,257,258,259,290,291,298,313,315
2	0.45	1b7yA	0.660	1.66	0.398	0.689	1.12	FYA	Download	170,172,202,214,216,218,256,258,259,288,289,290,291,313,314,315,317,320
3	0.45	1b70A	0.660	1.65	0.398	0.689	1.06	PHE	Download	170,172,202,216,218,290,291,313,314,315

	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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