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COFACTOR result for job id 76468

[Download result.tar.bz2 for all prediction results]

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>76468 (212 residues)
MRIAIFGTTGAGKTTLLENLKKLLDSSYVFINETSLDCPYFNKAYDDTNKNVQDYNYKLD
LWMLTDRMKTFIKYKDHQNVIYDRSILDSMVFSQTDHMYNRLSDTDYNVFKDYFLTCILP
NIFDIKNNWKTFDVVIYLKVDPYKAIQRINKRSRDVELDTNDLFWLNLTNAYEFWYNIYK
EVVPFWVIDANVDDPNYIATSIANMIKNIDNK

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	2jasC	0.91	0.58	0.361	0.915	Download
2	2ocpA	0.86	2.01	0.188	0.953	Download
3	1p60A	0.85	1.96	0.184	0.948	Download
4	5xtcw	0.81	2.59	0.179	0.948	Download
5	1p7cB	0.80	2.65	0.146	0.934	Download
6	1p6xA	0.77	2.82	0.141	0.924	Download
7	1zm7B	0.77	1.89	0.200	0.849	Download
8	1osnA1	0.66	2.75	0.162	0.788	Download
9	1z83A	0.65	3.11	0.135	0.802	Download
10	2cdnA	0.64	3.25	0.159	0.802	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	0.99	catalytic activity
GO:0016301	0.98	kinase activity
GO:0019205	0.97	nucleobase-containing compound kinase activity
GO:0005524	0.90	ATP binding
GO:0019206	0.80	nucleoside kinase activity
GO:0009041	0.73	uridylate kinase activity
GO:0004798	0.73	thymidylate kinase activity
GO:0019136	0.68	deoxynucleoside kinase activity
GO:0004138	0.54	deoxyguanosine kinase activity
GO:0004797	0.53	thymidine kinase activity

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 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:0044237	1.00	cellular metabolic process
GO:0006139	0.99	nucleobase-containing compound metabolic process
GO:0055086	0.93	nucleobase-containing small molecule metabolic process
GO:0034654	0.92	nucleobase-containing compound biosynthetic process
GO:1901564	0.91	organonitrogen compound metabolic process
GO:1901135	0.91	carbohydrate derivative metabolic process
GO:0044711	0.91	single-organism biosynthetic process
GO:0006796	0.91	phosphate-containing compound metabolic process
GO:1901566	0.90	organonitrogen compound biosynthetic process
GO:1901137	0.90	carbohydrate derivative biosynthetic process
GO:0072527	0.85	pyrimidine-containing compound metabolic process
GO:0016310	0.85	phosphorylation
GO:0072528	0.84	pyrimidine-containing compound biosynthetic process
GO:0006753	0.79	nucleoside phosphate metabolic process
GO:1901293	0.77	nucleoside phosphate biosynthetic process
GO:0009117	0.76	nucleotide metabolic process
GO:0006220	0.75	pyrimidine nucleotide metabolic process
GO:0009221	0.74	pyrimidine deoxyribonucleotide biosynthetic process
GO:0009211	0.74	pyrimidine deoxyribonucleoside triphosphate metabolic process
GO:0006235	0.73	dTTP biosynthetic process
GO:0006233	0.73	dTDP biosynthetic process
GO:0006227	0.73	dUDP biosynthetic process
GO:0009157	0.64	deoxyribonucleoside monophosphate biosynthetic process
GO:0046940	0.58	nucleoside monophosphate phosphorylation
GO:0009130	0.54	pyrimidine nucleoside monophosphate biosynthetic process
GO:0009220	0.53	pyrimidine ribonucleotide biosynthetic process
GO:0009174	0.53	pyrimidine ribonucleoside monophosphate biosynthetic process
GO:0006230	0.52	TMP 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:0005737	1.00	cytoplasm
GO:0044444	0.88	cytoplasmic part
GO:0005829	0.85	cytosol
GO:0043227	0.58	membrane-bounded organelle
GO:0043231	0.56	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	0.548	1p60A	0.851	1.96	0.184	0.948	2.7.1.74	33,84
2	0.364	1jagA	0.856	2.01	0.188	0.953	2.7.1.113	84
3	0.362	3hjnA	0.709	2.54	0.167	0.816	2.7.4.9	NA
4	0.249	2v54A	0.702	3.03	0.122	0.849	2.7.4.9	12,14,32,84
5	0.181	2grjG	0.575	3.03	0.135	0.698	2.7.1.24	10,12,134,168

	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	0.61	2jatA	0.869	1.19	0.363	0.896	1.57	POP	Download	8,10,11,12,13,14,15,152
2	0.27	1p5zB	0.850	1.99	0.189	0.948	1.17	ADP	Download	10,11,12,13,14,15,83,148,151,152,190,192,193
3	0.24	2jasA	0.904	0.60	0.361	0.915	1.42	DTP	Download	9,10,11,12,13,14,33,41,44,45,59,60,63,67,83,84,89,92,157
4	0.10	3qenB	0.844	2.05	0.184	0.948	0.97	5BT	Download	9,33,41,44,45,59,60,67,89,92,160,164

	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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