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COFACTOR result for job id 76553

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>76553 (794 residues)
MIITRNWLKKYLNLDNISNDQINMALNSLGFEVDSVYDLNSLNSELILGYVEQSKQIPNT
HLKLNQVNIGTKSLQIVCGASNVDVNQFVIIAPINATIANGLTLTSKKIQNYESQGMICA
LNEIGIDLSVINKEDQLKIYNVFDHNLDLKKYIGSDVKQIIGLDDYLFEIDLTLNRSDCL
ASFQILKELANYFDLEIKNLDNNFSDFKKNNLDLKIDLVNQVKDQIKTISYSYFELNNKN
DKLDSKDEIFLKLNQINSSNHLITNLSLISTLSTAQTHILIDLDKLKSSNLKLEFINHDN
KELLCLTNNNKLVNIIGLDTQNEFNVDNNSKNVLNIMLNIEPNLMRKQQKLLNISNTYLQ
RYIKPINPNLFNLANQTFSNLLNDYQLINKAYEVKILKQTFKNKQSLEIKLNEINDLLGT
NLTIKQIKSLFKHLDFKITNKDDLLDFQIDQNRIDITSKNDLCEEVARLYSYDKIDEVPL
SFTSFKKAKNLNLKLENKLTNYLIGLGFNNTKTYSLTSLNEAKYWNLFNISEFINLVSPL
SNLRQTYRTNLSKSLIDVAIFNHSINNKELKLFEIADIYDLNNLKQRHLVFLTSNHIYKN
SLNQQLIENNFYYNKEILENIFNLYNLDLSEIQYQNDLNLIKEIHPYINTTIYYQNQLIG
YLYKLNPKFESENKLNPTFVCEINLDILNQFKNSFIEAKTLSKFQSSSRDLTIDISNDLT
YQKVLFNALSDVKYLKSHKIVDLYLDDNLIKNNTKALTIQFVFNDLDHQLTENEINQEFE
KIIKNIKQMKVVIR

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	4p71A	0.96	0.96	0.189	0.969	Download
2	2rhqB	0.90	2.83	0.239	0.969	Download
3	3pcoB	0.90	2.85	0.204	0.969	Download
4	2iy5B	0.84	3.96	0.171	0.948	Download
5	3l4gB	0.54	4.93	0.141	0.636	Download
6	2odrA1	0.22	3.25	0.096	0.244	Download
7	3hfvA	0.21	3.97	0.052	0.241	Download
8	3ig2B	0.21	2.41	0.215	0.224	Download
9	1fbvA	0.17	7.38	0.056	0.252	Download
10	3cg3A	0.16	7.15	0.029	0.228	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:0004826	1.00	phenylalanine-tRNA ligase activity
GO:1901363	0.64	heterocyclic compound binding
GO:0097159	0.64	organic cyclic compound binding
GO:0003676	0.60	nucleic acid binding
GO:0043167	0.59	ion binding
GO:0003723	0.58	RNA binding
GO:0097367	0.56	carbohydrate derivative binding
GO:0046872	0.56	metal ion binding
GO:0017076	0.56	purine nucleotide binding
GO:0005524	0.55	ATP binding
GO:0000287	0.55	magnesium ion binding
GO:0000049	0.53	tRNA 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:

[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:0006432	1.00	phenylalanyl-tRNA aminoacylation

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:0032991	0.96	macromolecular complex
GO:1902494	0.94	catalytic complex
GO:0009328	0.93	phenylalanine-tRNA ligase complex
GO:0005737	0.81	cytoplasm

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	0.203	2rhqB	0.898	2.83	0.239	0.969	6.1.1.20	NA
2	0.180	2iy5B	0.839	3.96	0.171	0.948	6.1.1.20	NA
3	0.060	2vuaA	0.167	7.87	0.042	0.254	3.4.24.69	NA
4	0.060	3btaA	0.285	8.70	0.034	0.467	3.4.24.69	NA
5	0.060	1llwA	0.269	8.68	0.029	0.436	1.4.7.1	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:

No Binding sites was predicted

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

	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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