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COFACTOR result for job id 76341

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>76341 (532 residues)
MAKFIFVTGGVVSGLGKGITASSIGALLKASGLKVFMQKFDPYLNVDPGTMSPYQHGEVF
VTKDGGETDLDLGHYERFIDEELTKLSSTTSGKIYLSVIQGERKGVNSGKTIQVVPHITD
AIKQKVYQAAEQSQADVIISEIGGTVGDIESQPFIEAIRQIRLEQGKENVMFVHVVLLLW
LAASKEYKTKPIQNSVKAMASLGIQPDVIVCRSDSSSPKDIKEKISLFCNVPITNIIDAI
DQDSIYRVPLALAKQNIQDIIIEQLQLKAKNIDLSLWKQFNKKIDSSTEEIEISFVGKYI
ELQDAYLSVLESLKIAGWEFNKKIKIRWVQADKLDESNYKEILKNSQGILVPGGFGKRGI
EGMMLASRYARENDIPYLGICLGMQIATISIARDLLNWTDADSTEFNKNTTHPIFDYIKG
IDRDNIGGTLRLGTMVTKLEKDSLVSKLYNSDVALERHRHRYEFNNEYKKDLESVGLRFS
GIYEEKNLVEVVEMPSLKFFVASQFHPEFTSRPNKPTPLFRGFIKAIVENNK

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	3nvaA	0.98	1.11	0.470	0.993	Download
2	2ad5B	0.97	1.28	0.509	0.985	Download
3	1vcoA	0.96	1.29	0.467	0.987	Download
4	4zdiA	0.96	1.18	0.483	0.981	Download
5	5u03A	0.96	1.77	0.471	0.994	Download
6	1ce8B2	0.35	3.51	0.191	0.387	Download
7	2a9vD	0.33	2.60	0.176	0.351	Download
8	1gpmA	0.32	3.72	0.158	0.368	Download
9	2d7jA	0.32	2.74	0.188	0.348	Download
10	1wzaA	0.31	6.83	0.076	0.466	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:0003883	1.00	CTP synthase activity
GO:1901363	0.92	heterocyclic compound binding
GO:0097159	0.92	organic cyclic compound binding
GO:0046872	0.90	metal ion binding
GO:0000166	0.90	nucleotide binding
GO:0005524	0.89	ATP binding
GO:0042802	0.81	identical protein 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:0009987	1.00	cellular process
GO:1901564	0.99	organonitrogen compound metabolic process
GO:0006139	0.99	nucleobase-containing compound metabolic process
GO:1901566	0.98	organonitrogen compound biosynthetic process
GO:0044271	0.98	cellular nitrogen compound biosynthetic process
GO:0006220	0.98	pyrimidine nucleotide metabolic process
GO:0009220	0.97	pyrimidine ribonucleotide biosynthetic process
GO:0006241	0.96	CTP biosynthetic process
GO:0019752	0.91	carboxylic acid metabolic process
GO:0006520	0.90	cellular amino acid metabolic process
GO:0044210	0.89	'de novo' CTP biosynthetic process
GO:0006541	0.89	glutamine metabolic process
GO:0019856	0.82	pyrimidine nucleobase 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:0044444	1.00	cytoplasmic part
GO:0005829	0.84	cytosol
GO:0016020	0.52	membrane

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	2ad5B	0.969	1.28	0.509	0.985	6.3.4.2	43,45,47,50,53,56,59,69,431,506,509
2	0.469	1vcoA	0.965	1.29	0.467	0.987	6.3.4.2	43,45,47,50,54,57,67,70
3	0.262	1s1mB	0.968	1.45	0.510	0.987	6.3.4.2	NA
4	0.254	1vcnA	0.930	1.16	0.464	0.947	6.3.4.2	NA
5	0.060	1b0pA	0.367	7.74	0.064	0.618	1.2.7.1	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	0.44	2ad5B	0.969	1.28	0.509	0.985	1.66	ADP	Download	14,15,16,17,18,19,71,141,239,240,241,242,248
	2	0.01	1a9x1	0.441	6.76	0.066	0.667	0.60	III	Download	16,18,19,72,73

	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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