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COFACTOR result for job id 76309

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>76309 (213 residues)
MFITFEGMDGSGKTTALLKVKEELERLNYKVLITREPGGEAIAEQIRQIILDNKNKDMDA
WTEALLFIASRNQHLQKVIKPALEKNIIVISDRFIDSTSAYQGSARNIGVDVVSEVQQIV
LKNCLPDLTLFFDVSFSEAEKRMQIRGESSKNRLDKEKSDFKQKVYQGYLELVKNNPKRI
KVIDANQDIDQVYNQAIKIILEKLKENEKRTSN

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	4tmkA	0.93	0.97	0.387	0.958	Download
2	3lv8A	0.92	0.86	0.340	0.939	Download
3	3uwkA	0.92	0.97	0.368	0.944	Download
4	2ccgA	0.86	2.31	0.413	0.944	Download
5	2pbrA	0.86	1.56	0.364	0.915	Download
6	3hjnA	0.86	1.06	0.397	0.887	Download
7	2wwfA	0.85	1.83	0.294	0.925	Download
8	1e2fA	0.83	2.18	0.234	0.944	Download
9	3tmkA	0.83	2.15	0.220	0.939	Download
10	1mrsA	0.82	2.01	0.219	0.901	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:0019205	1.00	nucleobase-containing compound kinase activity
GO:0016776	1.00	phosphotransferase activity, phosphate group as acceptor
GO:0009041	0.99	uridylate kinase activity
GO:0004798	0.99	thymidylate kinase activity
GO:1901363	0.90	heterocyclic compound binding
GO:0097159	0.90	organic cyclic compound binding
GO:0035639	0.89	purine ribonucleoside triphosphate binding
GO:0032555	0.89	purine ribonucleotide binding
GO:0030554	0.89	adenyl nucleotide binding
GO:0005524	0.88	ATP 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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[0.5,0.6)

[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:1901566	1.00	organonitrogen compound biosynthetic process
GO:1901137	1.00	carbohydrate derivative biosynthetic process
GO:0009142	1.00	nucleoside triphosphate biosynthetic process
GO:0009132	1.00	nucleoside diphosphate metabolic process
GO:0006220	1.00	pyrimidine nucleotide metabolic process
GO:0006235	0.99	dTTP biosynthetic process
GO:0006233	0.99	dTDP biosynthetic process
GO:0006227	0.99	dUDP biosynthetic process
GO:0016310	0.89	phosphorylation
GO:0009123	0.89	nucleoside monophosphate metabolic process
GO:0046940	0.88	nucleoside monophosphate phosphorylation

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	0.89	cytoplasmic part
GO:0005829	0.82	cytosol
GO:0043226	0.74	organelle
GO:0043229	0.73	intracellular organelle
GO:0043227	0.73	membrane-bounded organelle
GO:0043231	0.72	intracellular membrane-bounded organelle
GO:0005634	0.64	nucleus
GO:0005739	0.61	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	0.534	3hjnA	0.857	1.06	0.397	0.887	2.7.4.9	9,35,37,39,66,92,97,101
2	0.492	3ld9A	0.786	1.33	0.415	0.826	2.7.4.9	10,14,35,37,47,67,93,95,97,101,134
3	0.429	1jagA	0.731	3.46	0.127	0.925	2.7.1.113	36,93
4	0.396	2v54A	0.811	2.27	0.235	0.920	2.7.4.9	12,14,93,97,101,105
5	0.360	1gtvB	0.822	2.02	0.219	0.901	2.7.4.9	12,37,67,92,97,101,134

	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	0.57	2ccgA	0.862	2.31	0.413	0.944	1.42	TMP	Download	9,13,35,36,47,67,71,93,97,98,101,102
2	0.52	5tmpA	0.929	0.98	0.387	0.958	1.54	Z5A	Download	9,10,11,12,13,14,36,47,67,71,92,93,97,98,101,102,142,146,152,154,155,162
3	0.43	3lv8A	0.917	0.86	0.340	0.939	1.19	ADP	Download	10,11,12,13,14,142,187,188,189,192
4	0.10	3qejA	0.745	3.25	0.145	0.939	0.80	UDP	Download	9,12,13,14,15,188,189,190
5	0.08	2cck0	0.814	2.29	0.419	0.897	1.04	III	Download	42,45,49,58,59,61,62,64,65,66,68,69,72,73,108,112,116,119,120,122

	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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