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COFACTOR result for job id 76483

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>76483 (456 residues)
MSKSIEKMISHLKNQGFVFQGSEIYGGLANSWDYGPLGCEVKNKLKKVWWDFFVKKNPLN
VGLDSSIILNSKVWKASGHIDGFNDPLIDCKNCKSRWRADKLIEEFDSSINTGIMTSAQL
EDYIKQNNILCKKCQKKDFTQIRKFALMFKTNQGVLEDDSSIVYLRPETAQGIFINFKNV
QRSMRKKLPFGIGQIGKSFRNEITPGNFIFRTREFEQMELEFFFDPNDQRDWFKYWLDQI
ELFLTKKICLDKSNYKIRENLKDELAHYALKTSDIEFNFPFGWGELWGISHRSDFDLKVH
QNLSKEDLTVLKEETNQKVLANVIEPSVGVERLMLAIFWQAYTEEQLEENNSRTVLKLPY
NLAPYQVAITPLSKQLNQNANQLFLDLLNDFDAVYDETGNIGKRYRRQDAIGTPFVITYD
FQTLEDQKVTIRYRDTMKQERILISQLKDFLNSQFN

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	2zt6A	0.97	0.86	0.340	0.980	Download
2	1b76A	0.87	1.48	0.439	0.903	Download
3	5z5eA	0.80	1.63	0.424	0.833	Download
4	1nj1A	0.74	2.49	0.142	0.800	Download
5	1nj8A	0.73	2.67	0.177	0.805	Download
6	1nyqB	0.73	2.49	0.194	0.792	Download
7	3ialB	0.73	2.82	0.154	0.809	Download
8	3ugqA	0.73	2.61	0.209	0.798	Download
9	1g5hD	0.73	2.55	0.226	0.783	Download
10	1qf6A	0.72	2.53	0.156	0.785	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:0004812	1.00	aminoacyl-tRNA ligase activity
GO:0004820	0.99	glycine-tRNA ligase activity
GO:0046983	0.73	protein dimerization 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:0071704	1.00	organic substance metabolic process
GO:0044237	1.00	cellular metabolic process
GO:1901564	0.99	organonitrogen compound metabolic process
GO:0044281	0.99	small molecule metabolic process
GO:0043170	0.99	macromolecule metabolic process
GO:0006139	0.99	nucleobase-containing compound metabolic process
GO:0019752	0.98	carboxylic acid metabolic process
GO:0016070	0.98	RNA metabolic process
GO:0006418	0.97	tRNA aminoacylation for protein translation
GO:0006426	0.74	glycyl-tRNA aminoacylation
GO:0009058	0.62	biosynthetic process
GO:1901576	0.61	organic substance biosynthetic process
GO:0044249	0.61	cellular biosynthetic process
GO:0044271	0.56	cellular nitrogen compound biosynthetic 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:0005737	0.98	cytoplasm
GO:0044444	0.74	cytoplasmic part
GO:0043229	0.54	intracellular organelle
GO:0043227	0.51	membrane-bounded 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	0.590	2zt5A	0.969	0.87	0.340	0.980	6.1.1.14	200
2	0.412	1h4sA	0.715	2.93	0.162	0.800	6.1.1.15	200
3	0.411	2j3lB	0.696	2.97	0.175	0.781	6.1.1.15	200
4	0.401	1nj1A	0.736	2.49	0.142	0.800	6.1.1.15	200
5	0.399	2i4nB	0.704	2.65	0.191	0.774	6.1.1.15	200

	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:

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
	1	0.24	1b76B	0.854	2.08	0.443	0.897	0.92	ATP	Download	210,211,212,215,217,327,329,332
	2	0.11	1nj80	0.733	2.67	0.177	0.805	0.86	III	Download	18,20,21,23,31,32,33,34,35,36,39,43,61,62,63,64,65,66,67,69,148,149,150,151,152,163,165,172,175,197,199,201,214,216

	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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