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COFACTOR result for job id 76505

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>76505 (409 residues)
MGFWAKLKEKLIKKTNQVEQDEPILDQQEQQEEQEQIIEKEIEQEPVVNQDIQVEIIKEN
KIKKTKTSETKKQEKQTETLKEKKKREKQKEKDKKVEKAMLKSAFNFSKDIKKLSKKYKQ
ADDEFFEELEDVLIQTDMGMKMVLKVSNLVRKKTKRDTSFENIKDALVESLYQAYTDNDW
TNKKYRIDFKENRLNIFMLVGVNGTGKTTSLAKMANYYAELGYKVLIAAADTFRAGATQQ
LEEWIKTRLNNKVDLVKTNKLNADPASVVFDAIKKAKEQNYDLLLIDTAGRLQNKTNLMA
ELEKMNKIIQQVEKSAPHEVLLVIDATTGQNGVIQAEEFSKVADVSGIILTKMDSTSKGG
IGLAIKELLNIPIKMIGVGEKVDDLLAFDIDQYIVHLSSGFMQGDEVEK

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	1zu5B	0.75	0.92	0.974	0.758	Download
2	6cy1A	0.72	1.99	0.363	0.760	Download
3	4ak9A	0.69	1.93	0.375	0.731	Download
4	2og2A	0.68	2.20	0.381	0.731	Download
5	2qy9A	0.68	2.19	0.376	0.729	Download
6	1vmaA	0.68	2.18	0.435	0.719	Download
7	2q9bA	0.64	2.80	0.380	0.712	Download
8	3dmdB	0.63	3.20	0.320	0.714	Download
9	3dm5A	0.62	3.29	0.289	0.719	Download
10	5gadi	0.62	3.21	0.259	0.699	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:1901363	0.96	heterocyclic compound binding
GO:0097159	0.96	organic cyclic compound binding
GO:0036094	0.93	small molecule binding
GO:0005525	0.92	GTP binding
GO:0003824	0.90	catalytic activity
GO:0016787	0.82	hydrolase activity
GO:0017111	0.80	nucleoside-triphosphatase activity
GO:0003924	0.77	GTPase activity
GO:0003676	0.54	nucleic acid binding
GO:0043021	0.52	ribonucleoprotein complex binding
GO:0003723	0.52	RNA binding

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:0009987	0.99	cellular process
GO:0015031	0.98	protein transport
GO:0044763	0.96	single-organism cellular process
GO:0034613	0.96	cellular protein localization
GO:0016043	0.96	cellular component organization
GO:0006605	0.96	protein targeting
GO:0072594	0.95	establishment of protein localization to organelle
GO:0044765	0.95	single-organism transport
GO:0033365	0.95	protein localization to organelle
GO:0045047	0.94	protein targeting to ER
GO:0006612	0.94	protein targeting to membrane
GO:0006613	0.93	cotranslational protein targeting to membrane
GO:0006614	0.92	SRP-dependent cotranslational protein targeting to membrane
GO:0008152	0.65	metabolic process
GO:0071704	0.64	organic substance metabolic process
GO:0044237	0.63	cellular metabolic process
GO:0044238	0.60	primary metabolic process
GO:0006807	0.59	nitrogen compound metabolic process
GO:0034641	0.55	cellular nitrogen compound metabolic process
GO:0043170	0.50	macromolecule metabolic 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:0044444	0.98	cytoplasmic part
GO:0032991	0.89	macromolecular complex
GO:1990904	0.81	ribonucleoprotein complex
GO:0048500	0.74	signal recognition particle
GO:0005737	0.68	cytoplasm
GO:0043226	0.66	organelle
GO:0043229	0.63	intracellular organelle
GO:0043227	0.62	membrane-bounded organelle
GO:0044446	0.59	intracellular organelle part
GO:0043231	0.59	intracellular membrane-bounded organelle
GO:0016020	0.56	membrane
GO:0005829	0.51	cytosol
GO:0044425	0.50	membrane part

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	0.060	2vkzG	0.424	6.12	0.052	0.626	2.3.1.38 3.1.2.14	NA
2	0.060	2jkpB	0.391	6.13	0.046	0.587	3.2.1.20	NA
3	0.060	9rubA	0.389	6.66	0.082	0.616	4.1.1.39	NA
4	0.060	1mhsA	0.390	6.66	0.066	0.624	3.6.3.6	NA
5	0.060	1qbaA	0.392	6.51	0.048	0.611	3.2.1.52	NA

	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	0.17	1ng1A	0.629	2.35	0.304	0.685	1.38	GDP	Download	202,204,206,207,208,209,213,352,377,379,380
	2	0.02	3zq6A	0.415	3.48	0.173	0.487	0.54	UUU	Download	140,142,361,363

	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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