COFACTOR result for job id MCF5

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>ysgA.b3830 (271 residues)
MATTQQSGFAPAASPLASTIVQTPDDAIVAGFTSIPSQGDNMPAYHARPKQSDGPLPVVI
VVQEIFGVHEHIRDICRRLALEGYLAIAPELYFREGDPNDFADIPTLLSGLVAKVPDSQV
LADLDHVASWASRNGGDVHRLMITGFCWGGRITWLYAAHNPQLKAAVAWYGKLTGDKSLN
SPKQPVDIATDLNAPILGLYGGQDNSIPQESVETMRQALRAANAKAEIIVYPDAGHAFNA
DYRPSYHAASAEDGWQRMLEWFKQYGGKKSL

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	3f67A	0.87	0.46	0.823	0.875	Download
2	4zv9A	0.78	2.25	0.297	0.856	Download
3	1ve6A	0.77	3.08	0.191	0.900	Download
4	4zi5A	0.77	2.24	0.205	0.845	Download
5	1h2xA4	0.75	3.71	0.128	0.930	Download
6	1z68A	0.75	3.15	0.155	0.878	Download
7	2bklB1	0.74	3.62	0.137	0.915	Download
8	1yr2A	0.74	3.33	0.145	0.886	Download
9	1xfdA	0.74	3.46	0.122	0.889	Download
10	4n5iX	0.71	2.98	0.157	0.830	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:0016787	1.00	hydrolase activity
GO:0016788	0.61	hydrolase activity, acting on ester bonds
GO:0052689	0.56	carboxylic ester hydrolase activity
GO:0043167	0.50	ion 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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[0.6,0.7)

[0.7,0.8)

[0.8,0.9)

[0.9,1.0]

Biological Process (BP)

GO term	Cscore^GO	Name
GO:0008152	0.94	metabolic process
GO:0009987	0.90	cellular process
GO:0071704	0.88	organic substance metabolic process
GO:0044237	0.84	cellular metabolic process
GO:0044238	0.73	primary metabolic process
GO:0044699	0.71	single-organism process
GO:0006807	0.69	nitrogen compound metabolic process
GO:1901575	0.64	organic substance catabolic process
GO:0044763	0.64	single-organism cellular process
GO:0034641	0.63	cellular nitrogen compound metabolic process
GO:1901564	0.61	organonitrogen compound metabolic process
GO:0044248	0.61	cellular catabolic process
GO:0044710	0.59	single-organism metabolic process
GO:1901565	0.54	organonitrogen compound catabolic process
GO:1901360	0.53	organic cyclic compound metabolic process
GO:0046483	0.51	heterocycle metabolic process
GO:0006725	0.51	cellular aromatic compound 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:0044464	1.00	cell part
GO:0044424	0.93	intracellular part
GO:0016020	0.77	membrane
GO:0005886	0.73	plasma membrane
GO:0044444	0.71	cytoplasmic part
GO:0005737	0.62	cytoplasm
GO:0043227	0.57	membrane-bounded organelle
GO:0005829	0.55	cytosol
GO:0044425	0.52	membrane part
GO:0016021	0.50	integral component of 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	0.400	1dinA	0.757	2.33	0.262	0.830	3.1.1.45	204,236
2	0.223	2ocgA	0.642	3.01	0.103	0.742	3.1.-.-	149,197,204,236
3	0.205	2h1iA	0.580	3.60	0.131	0.720	3.1.1.1	67,74,79,98
4	0.128	3i6yA	0.735	3.10	0.155	0.856	3.1.1.2	NA
5	0.109	1fj2A	0.630	3.39	0.126	0.760	3.1.4.39	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:

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	3azqB	0.773	3.08	0.137	0.900	0.63	III	Download	64,147,148,172,236
2	0.15	3h0cA	0.751	3.43	0.137	0.897	0.50	PS4	Download	63,67,68,147,148,172,175,205,206,236
3	0.03	2bgnB	0.747	3.44	0.137	0.897	0.61	UUU	Download	143,145,148,151
4	0.03	1tk3B	0.750	3.39	0.137	0.897	0.52	NDG	Download	239,251,252

	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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