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COFACTOR result for job id 76400

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>76400 (583 residues)
MPDIKFTALGGQDERGKNLYVLEIDNDFFILDAGVKYPEKDILGIDTVIPKFDYIKQNKK
KIKGIFLTNPSAYNMGAVPYLLKEIEAPIYCNEITELIAKIKFQKLRLKNKDHILKVVHD
KDILKIGNTKVEIFRTTSSSPQSFGYVFHTELGSIVYAGDYIIDGKEQSYFSTDYTHLSQ
IAKNGVLALISDAEFASRKDFTVPNHKIDKYILAPFKEKKTKIIVAIFEEDIHKLSQICM
AAKENNRKIAVYGRTMDAVLRSNLIHENLVIKPEDLMSIQEYVNSDNGVLIISGTGDDLY
SKLAKIATSNDSLVEFTEKDLIILTNTPVAGVEKRHAQILDELARTDARLLALSDKNIWS
MRASYEDIKMLTSILNPKYFIPVKALYKDFLNAEKAAIEAGVNNQNIGIIDNGEILKLSK
NHLAISEHSAEHGNVYVDGSGIGDVGSIVLNERKQLATDGVIIVGATIDSRNKELISLID
TQMRGVLYIQEDNPIFKILQREITNLILEGQALYKKEPKKYDLNEIKKDITSKIKQLIKQ
ESGKTPIVLVIINESDGKAYVPRNNKKRYNNNNKSTKSKKDKS

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	3zq4A	0.93	0.74	0.296	0.938	Download
2	4xwtA	0.89	1.55	0.233	0.919	Download
3	3bk1A	0.80	3.44	0.241	0.904	Download
4	5a0tA	0.73	1.43	0.250	0.748	Download
5	5haaA	0.68	2.02	0.209	0.714	Download
6	3af5A	0.59	3.78	0.130	0.683	Download
7	2ycbA	0.59	3.78	0.103	0.681	Download
8	2az4B	0.58	3.15	0.142	0.641	Download
9	2xr1A	0.58	3.66	0.131	0.667	Download
10	2dkfA	0.58	3.35	0.129	0.652	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	0.98	catalytic activity
GO:0016787	0.94	hydrolase activity
GO:0004518	0.93	nuclease activity
GO:1901363	0.91	heterocyclic compound binding
GO:0097159	0.91	organic cyclic compound binding
GO:0004527	0.90	exonuclease activity
GO:0003676	0.90	nucleic acid binding
GO:0016796	0.89	exonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters
GO:0008409	0.89	5'-3' exonuclease activity
GO:0004540	0.78	ribonuclease activity
GO:0004519	0.78	endonuclease activity
GO:0004521	0.77	endoribonuclease activity
GO:0003723	0.77	RNA binding
GO:0043167	0.74	ion binding
GO:0004534	0.74	5'-3' exoribonuclease activity
GO:0046872	0.72	metal ion binding
GO:0008270	0.71	zinc ion binding
GO:0042802	0.55	identical protein binding
GO:0004536	0.50	deoxyribonuclease activity
GO:0003677	0.50	DNA 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	1.00	cellular process
GO:1901360	0.99	organic cyclic compound metabolic process
GO:0044238	0.99	primary metabolic process
GO:0043170	0.99	macromolecule metabolic process
GO:0034641	0.99	cellular nitrogen compound metabolic process
GO:0090304	0.98	nucleic acid metabolic process
GO:0044260	0.98	cellular macromolecule metabolic process
GO:0016070	0.89	RNA metabolic process
GO:0006396	0.84	RNA processing
GO:0034660	0.81	ncRNA metabolic process
GO:0034470	0.79	ncRNA processing
GO:0006364	0.76	rRNA processing
GO:0090501	0.73	RNA phosphodiester bond hydrolysis
GO:0090502	0.71	RNA phosphodiester bond hydrolysis, endonucleolytic
GO:0090503	0.70	RNA phosphodiester bond hydrolysis, exonucleolytic
GO:0065007	0.59	biological regulation
GO:0071840	0.58	cellular component organization or biogenesis
GO:0016043	0.56	cellular component organization
GO:0050896	0.54	response to stimulus
GO:0006996	0.54	organelle organization
GO:0006259	0.53	DNA metabolic process
GO:0065008	0.52	regulation of biological quality
GO:0051716	0.51	cellular response to stimulus
GO:0016071	0.51	mRNA metabolic process
GO:0006950	0.51	response to stress
GO:0033554	0.50	cellular response to stress
GO:0006397	0.50	mRNA processing

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:0005737	1.00	cytoplasm
GO:0044446	0.90	intracellular organelle part
GO:0044428	0.85	nuclear part
GO:0044444	0.69	cytoplasmic part
GO:0044427	0.58	chromosomal part
GO:0000784	0.57	nuclear chromosome, telomeric region
GO:0043226	0.52	organelle
GO:0043229	0.51	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	0.060	2i7vA	0.576	3.88	0.114	0.676	3.1.27.-	NA
2	0.060	3itkC	0.330	5.70	0.082	0.439	1.1.1.22	NA
3	0.060	2vkzG	0.389	7.92	0.051	0.645	2.3.1.38 3.1.2.14	NA
4	0.060	3cmmC	0.371	6.93	0.064	0.561	6.3.2.19	10,39,43
5	0.060	1y44A	0.360	3.11	0.163	0.400	3.1.26.11	9,79,81

	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	0.20	3t3nA	0.872	2.33	0.256	0.926	1.02	QNA	Download	15,37,46,72,73,227,228,229,253,254,255,293,295,296,298,305,329,332,358,359,360,361,362
2	0.02	3iemB	0.586	3.34	0.127	0.660	0.72	SSU	Download	5,7,22,52,53,54,55,56,59,84,413
3	0.01	2cbn0	0.364	3.02	0.140	0.403	0.68	III	Download	53,70,71,76,77,79,80,97,98,104,105,106

	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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