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COFACTOR result for job id 76517

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>76517 (145 residues)
MIDINNDSLLREIIIKHFLNPENKTLTNNKNAIIKELKSQTCADQLIIEILIENKIIKSM
KFDGSACAIATSSIDLLINNLLNLDIKKAIELIKNYQIFLLTGTLINADQLNELVVMKNI
HKQKNRILCASLALNDLLEILNSYE

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	2qq4A	0.93	0.65	0.275	0.952	Download
2	1su0B	0.87	1.28	0.207	0.931	Download
3	5uftA	0.87	2.08	0.113	0.959	Download
4	2z7eB	0.73	2.13	0.218	0.821	Download
5	4eb5C	0.73	1.91	0.188	0.807	Download
6	1xjsA	0.71	3.31	0.211	0.945	Download
7	1wfzA	0.65	2.23	0.174	0.752	Download
8	1q48A	0.57	2.42	0.178	0.690	Download
9	3r07C	0.46	2.70	0.149	0.579	Download
10	1zorA1	0.37	4.85	0.025	0.662	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:0051539	1.00	4 iron, 4 sulfur cluster binding
GO:0051537	1.00	2 iron, 2 sulfur cluster binding
GO:0036455	1.00	iron-sulfur transferase activity
GO:0008198	1.00	ferrous iron 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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[0.9,1.0]

Biological Process (BP)

GO term	Cscore^GO	Name
GO:0071704	1.00	organic substance metabolic process
GO:0065007	1.00	biological regulation
GO:0044238	1.00	primary metabolic process
GO:0016226	1.00	iron-sulfur cluster assembly
GO:0097428	0.99	protein maturation by iron-sulfur cluster transfer
GO:0044571	0.99	[2Fe-2S] cluster assembly
GO:0006879	0.99	cellular iron ion homeostasis
GO:0006807	0.66	nitrogen compound metabolic process
GO:0034641	0.57	cellular nitrogen compound metabolic process
GO:1901360	0.55	organic cyclic compound metabolic process
GO:0046483	0.55	heterocycle metabolic process
GO:0006725	0.54	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:0044424	1.00	intracellular part
GO:0044444	0.85	cytoplasmic part
GO:0005737	0.78	cytoplasm
GO:0044446	0.58	intracellular organelle 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	1vlbA	0.478	3.84	0.074	0.648	1.2.99.7	NA
2	0.060	1f8wA	0.510	3.41	0.060	0.697	1.11.1.1	NA
3	0.060	1lvlA	0.483	3.34	0.027	0.662	1.8.1.4	NA
4	0.060	2w2dA	0.362	5.34	0.073	0.683	3.4.24.69	NA
5	0.060	1xdiA	0.487	3.04	0.092	0.648	1.6.5.2	70

	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	0.03	2ckjD	0.503	3.88	0.078	0.745	0.74	FES	Download	45,46,47,63,64,65,67,74
	2	0.02	2ckjD	0.503	3.88	0.078	0.745	0.67	FES	Download	42,43,45,65,66,67

	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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