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COFACTOR result for job id 76338

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>76338 (483 residues)
MSFRLRYAPSPTGFLHIGNTRTALMNYLFAKHYNGSFIVRIEDTDLTRNVDGAIESQFEN
LNWLGIFPDESIFNVGDQKYGKYMQSQKFDRYKQLAEQLVDQNKAYRCFCTSEELEKDYE
EQTSKGIIATKYSQKCLFLTQDQIQKNLENKKEYSIRFKVPENKTWTINDIVRGDVSFDS
KDLGDFVILKSNGVATYNFAVVIDDYDMQITHVLRGEEHISNTPRQMMIYDAFNWNYPKF
GHLTLIVDNTGKKLSKRSGNALFFIEQYKKQGYLSQAIFNYIALLGWSPPGEQEILSQNE
LIKIFDEKRFSKSPSTFDMVKMKWINSVYMKKLDDDKYLEFVKSFINTNKFDITSKSEAW
LNHLLLLYKKELEYAEQINDHLDLFFNKNTLDNNTIDVLNNLTNYKNVVEIFKNQINDLK
DWTIENIKQIIKNTSTLANVKGKDLFMPIRIFATKSEHGPSLADVIYLLGKTTVLNNINS
LER

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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	1g59A	0.95	0.98	0.315	0.967	Download
2	2cfoB	0.93	1.88	0.343	0.971	Download
3	2ja2A	0.91	2.51	0.286	0.981	Download
4	6b1zA	0.90	2.53	0.350	0.977	Download
5	4griA	0.89	2.56	0.343	0.965	Download
6	2o5rA	0.88	2.48	0.400	0.938	Download
7	3afhA	0.86	2.83	0.347	0.948	Download
8	6b1pA	0.83	2.28	0.343	0.888	Download
9	5h4vA	0.82	3.21	0.320	0.932	Download
10	4g6zA	0.71	2.61	0.344	0.776	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:0003723	1.00	RNA binding
GO:0004818	0.96	glutamate-tRNA ligase activity
GO:0043167	0.86	ion binding
GO:0046872	0.85	metal ion binding
GO:0035639	0.85	purine ribonucleoside triphosphate binding
GO:0032555	0.85	purine ribonucleotide binding
GO:0030554	0.85	adenyl nucleotide binding
GO:0008270	0.84	zinc ion binding
GO:0005524	0.84	ATP binding
GO:0000049	0.84	tRNA 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:

[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:0006418	1.00	tRNA aminoacylation for protein translation
GO:0006424	0.96	glutamyl-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:0005737	1.00	cytoplasm
GO:0044444	0.98	cytoplasmic part
GO:0005829	0.77	cytosol
GO:0043229	0.75	intracellular organelle
GO:0043231	0.74	intracellular membrane-bounded organelle
GO:0005739	0.69	mitochondrion

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	0.565	2cfoB	0.926	1.88	0.343	0.971	6.1.1.17	256
2	0.538	1g59A	0.952	0.98	0.315	0.967	6.1.1.17	256
3	0.217	2ja2A	0.908	2.51	0.286	0.981	6.1.1.17	256
4	0.110	2o5rA	0.903	2.43	0.391	0.965	6.1.1.17	256
5	0.060	1irxB	0.579	5.30	0.108	0.764	6.1.1.6	16,18,45

	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	0.79	3akzC	0.883	2.32	0.339	0.946	1.39	GSU	Download	6,7,8,9,10,18,22,42,197,215,216,218,219,245,246,253
	2	0.54	2cv1A	0.953	0.96	0.317	0.967	1.36	ATP	Download	7,9,10,12,16,18,19,22,48,216,219,245,246,254

	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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