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COFACTOR result for job id 76671

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>76671 (1291 residues)
MAYKIRKINRNVERRDYTKVSMNLSLPNLIGIQTETFEWFKTKGIQEVLDEFFPILSFDG
SSVLTLENWGFKEPRLSVRQAREESKIYDAPIYANLKLSVNKTEEIQKEFDGVALDDTLK
ILTNWLEEKTVSKNITFKQQSQNSYFFELTIKKSDKPDLIQIDIIEDKKTSLICNVSIYK
SGEVFLGDFPLMTEAGTFIINGSQKVIVSQLVRSPGAYFNKELNRKTGEMIYFADIIPSR
GTWLEYETDSKKTGADAINPLYVKIDKSRKTTATSLLLAFGISKDDILDIFDNDEVLVET
LQQDSIVGDFKIDWSNQVQEIYKKIRQGETATSEGASKFINSILFDKRKYDLTKAGRFKL
KQKLSIKNRILNRVIAEDIVDANNNVLVAKDTEVNKHNIKQISEILDQDVMSVDLNYLSD
ILGTRKVQKIKVYKDSELKTDTTCLIGLTSSSNEEFITVADILSTVSYLLNLKYNIGEID
DIDNLGNRRVRTVGELLQNQFRMGLNRIDKNVKEKLATSDLYKVKTSTIINAKPLTAIIG
EFFNLSQLSQFMDQINPLSELTNKRRLTALGPGGLSRDRAGLEVRDVHPSHYGRICPIET
PEGPNIGLINNLSTYARVNEYGFITTPYRKVINGIIQNDQVEYLTADQEKNFIIAQSNVN
QDENGKILDEIIVSRFNGDDYMAKVEEIDYIDVSPKQIVSVATSGIPFLENDDANRALMG
ANMQRQAVPLIKPESPIVATGIEFEAARDSGEAIVAKEDAIVKYVDSKTIITDGESGIRT
YILSDYERSNNGTSLTQSPIVKVGDVVKKGEIIADGPSMDQGELAIGQNVVVAFSTYNGY
NFEDAIVMSERIVIDDRFTSIHIDEYTLEVRNTKQGQEEVTREIPNMSEQAKRHLDAEGI
VAIGTEVKVGDVLVGKVTPKGQVQLSPEDKLLHAIFGEKSRNVKDNSLRVPNGGEGIVQS
IKRFKAKSALNPDGIELPADIIEVIKVYVVQKRKIQEGDKMSGRHGNKGIISRILPIEDM
PHLEDGTPVDIILNPQGVPSRMNIGQILEIHLGMAAKKLNQKVITPVFEGLNEKELEEIM
AEAGMTNYGKVTLIDGQTGEPFDKPIAVGVMYMLKLSHMVDDKIHARNVGPYSLITQQPL
GGKAQNGGQRFGEMEVWALEAYGAAHTLREILTIKSDDIKGRSKTYEAIVRSKRIPEPGI
PESFNVLSKEIMGLGFNMYMIDETGEKSVINAYDKKDFDADNYEDDEILVKTDTLYIDDE
DVDAEFEDLTYVDENDILRSFESENDIDEEE

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	6govX	0.80	1.94	0.508	0.820	Download
2	1zyrM	0.79	2.66	0.477	0.819	Download
3	5tw1C	0.78	2.20	0.516	0.802	Download
4	3iydC	0.75	3.62	0.479	0.811	Download
5	5flmB	0.66	3.51	0.236	0.704	Download
6	6gykB	0.65	3.95	0.223	0.709	Download
7	3h0gB	0.65	3.95	0.229	0.708	Download
8	3hkzJ	0.64	3.62	0.265	0.689	Download
9	5fj8B	0.63	4.32	0.218	0.696	Download
10	4qiwB	0.62	3.58	0.262	0.670	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:0003899	0.99	DNA-directed RNA polymerase activity
GO:1901363	0.55	heterocyclic compound binding
GO:0097159	0.55	organic cyclic compound binding
GO:0003676	0.52	nucleic acid 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	0.97	cellular process
GO:0071704	0.94	organic substance metabolic process
GO:0044237	0.94	cellular metabolic process
GO:0044238	0.93	primary metabolic process
GO:0006807	0.93	nitrogen compound metabolic process
GO:0034641	0.92	cellular nitrogen compound metabolic process
GO:0043170	0.90	macromolecule metabolic process
GO:1901576	0.87	organic substance biosynthetic process
GO:0044260	0.87	cellular macromolecule metabolic process
GO:0044249	0.87	cellular biosynthetic process
GO:0006139	0.87	nucleobase-containing compound metabolic process
GO:0044271	0.86	cellular nitrogen compound biosynthetic process
GO:0090304	0.85	nucleic acid metabolic process
GO:0009059	0.85	macromolecule biosynthetic process
GO:0016070	0.83	RNA metabolic process
GO:0034645	0.82	cellular macromolecule biosynthetic process
GO:0034654	0.80	nucleobase-containing compound biosynthetic process
GO:0032774	0.78	RNA biosynthetic process
GO:0006351	0.75	transcription, DNA-templated

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:0000428	0.99	DNA-directed RNA polymerase complex
GO:0044446	0.88	intracellular organelle part
GO:0044444	0.86	cytoplasmic part
GO:0044428	0.82	nuclear part
GO:0055029	0.81	nuclear DNA-directed RNA polymerase complex
GO:0043229	0.67	intracellular organelle
GO:0044451	0.66	nucleoplasm part
GO:0043231	0.65	intracellular membrane-bounded organelle
GO:0005634	0.56	nucleus

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	0.106	3hkzJ	0.641	3.62	0.265	0.689	2.7.7.6	NA
2	0.087	2vumB	0.625	3.90	0.235	0.678	2.7.7.6	NA
3	0.084	3gtgB	0.637	3.85	0.230	0.692	2.7.7.6	NA
4	0.060	3btaA	0.224	9.38	0.044	0.339	3.4.24.69	NA
5	0.060	1ug9A	0.229	9.76	0.036	0.359	3.2.1.70	194

	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	0.36	2o5iC	0.782	2.75	0.476	0.819	1.14	RQA	Download	547,566,570,601,605,609,726,1008,1140
	2	0.07	1l9u7	0.752	2.82	0.447	0.787	0.66	III	Download	184,185,528,530,531,532,533,871,979,982

	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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