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COFACTOR result for job id 76311

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>76311 (668 residues)
MNTNKQSLYRTYRPKDFNSVAGHNNIKEILEKQIKDNRINHALLFSGQRGTGKTSVARIF
AKTINCLNLTNSTACEQCNNCKLANQNQLIDIIEIDAASNNGVDEIREIKNSVSTLPLNS
KYKVYIIDEVHMLTKQAFNALLKTLEEPPVYAIFILATTEFNKIPQTILSRCQIFNFTKI
DKNSLKNRLQYIANQENYQIEKEVLDEMFYLSEGSLRDAINILEQLMLATDDLITIKTLK
SIFLIATKQEQLQVVHQSLNNNTSFIISYFQKANDQGMNWDVFALGLIEILKEIIEYKLT
NNTEFLNILEKNEVEQFNSVNANNLFILADNLAEAYFKTKAANISFNYLLLSLLKTINSN
NNNLQTVSKTINTKQVEQNQEILKPNDITPEILDEPIIDEPVIQQPIIDEPVLQQPVIDE
PVIQQPVIDNLSLTKDLDDKTLIKNTIENDKPLDSTNLDDPINEFDFYNQKEQTIDEICK
TLSELKIKFNIHISQAINSKVKMLFNEDLISILIETKNYKNQIHNIEQLLEDLFLQDDNQ
LVNAQIASELFMLLDSKIISLTNDVIVLKTQTKAQANLINDSMLDNHVLQQIYNWFKKPY
LIFAIDKMKWDEIKTIFIDLKNKNKLSEYSEINLKQLKEKYLTINDEIDQDLINKAKDLF
NDDFMIGD

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	3glgG	0.51	2.79	0.307	0.551	Download
2	1sxjC	0.41	3.82	0.214	0.463	Download
3	3u5zB	0.40	3.63	0.164	0.452	Download
4	1sxjB	0.40	4.04	0.199	0.460	Download
5	2chvA	0.40	3.98	0.214	0.457	Download
6	1sxjD	0.38	4.32	0.204	0.445	Download
7	1iqpA	0.38	4.40	0.210	0.455	Download
8	1sxjA	0.38	4.67	0.139	0.457	Download
9	5e7pA	0.36	5.01	0.113	0.445	Download
10	3iytA	0.36	6.22	0.057	0.486	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:0003824	1.00	catalytic activity
GO:1901363	0.99	heterocyclic compound binding
GO:0097159	0.99	organic cyclic compound binding
GO:0016787	0.98	hydrolase activity
GO:0003689	0.97	DNA clamp loader activity
GO:0036094	0.73	small molecule binding
GO:0017076	0.72	purine nucleotide binding
GO:0005524	0.71	ATP binding
GO:0016740	0.57	transferase activity
GO:0016772	0.52	transferase activity, transferring phosphorus-containing groups

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:0071704	1.00	organic substance metabolic process
GO:0044238	1.00	primary metabolic process
GO:0044237	1.00	cellular metabolic process
GO:0006807	1.00	nitrogen compound metabolic process
GO:0006259	0.99	DNA metabolic process
GO:0034645	0.98	cellular macromolecule biosynthetic process
GO:0006260	0.97	DNA replication
GO:0006261	0.94	DNA-dependent DNA replication
GO:0016070	0.52	RNA 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:0043234	1.00	protein complex
GO:0044446	0.98	intracellular organelle part
GO:0005663	0.97	DNA replication factor C complex
GO:0044444	0.68	cytoplasmic part
GO:1902494	0.51	catalytic complex
GO:0043229	0.50	intracellular organelle

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	0.087	3glfG	0.509	2.75	0.310	0.551	2.7.7.7	255
2	0.060	2wwyA	0.298	6.69	0.079	0.425	3.6.4.12	NA
3	0.060	2vkzG	0.260	8.32	0.028	0.430	2.3.1.38 3.1.2.14	NA
4	0.060	3fn9C	0.254	8.19	0.046	0.416	3.2.1.23	NA
5	0.060	1e1yA	0.265	7.51	0.057	0.409	2.4.1.1	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	0.79	1njfA	0.350	1.54	0.410	0.358	1.49	ATG	Download	9,12,13,14,20,21,49,50,51,52,53,54,55,159,216,217,220

	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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