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COFACTOR result for job id 76502

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>76502 (696 residues)
MLFKKITNNVQFRMIKQKKETSFVCLKSIIITLTIFVLLALVILLGFVMIKTNVLFNKQS
FFEFVFGKNWSPDSKQFGILTITLMTLILIFISMLIAVPLTIFTSFFISEYLTLKSQKVT
ITIIKLLAGIPSVVFGLFAREQIGALFKLMGASSNDNLMVASLTMAFMAIPIMISLSYDA
IKSVPFIYRDASLALGISKEKTTFNIIRKSATPKIISAVILGMARVIGETMAIMMIAGNS
TAWFDTNNGVSGFLFSSIRTLSSTIGLEMLENSSSLHESALYAIGMFLFILVFIINLLIL
FVSNKNSISKKIHLVLFKNKKTHKIKHVKLYQKQTLDQIITNRTENKLFKKIYSTIMLVL
MWLSISFVIMFTFWIVFTTIFNGLSSLKYSEAFLTIEGEDGIFAAILTTLLLILCTLLFA
IPLALACAIYLSEFANKNSYFAKFFRFLLNLAASTPSIIFGIFGLSVFIIYLKLPFSIFS
ASITMTIVVLPMLIKNFEDALTSVPLSYREAAIALGLSKTKTLFKIVLPNALQAIITGTI
LAMARIIGESAPIYLTLGTAIKYPDRGFLSSGSTLTTGIYKIASESAPGQGNDIAWLMSL
ITIIFVLTLNLSSSKLSLLLVKTNKKVKFEFKQIYKNFINKQFYKTQFNLFKNSLKQFIK
SLKKYLNITNLFKEIKKTIKYKKEYKKLKKRDNNYE

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	4av3A	0.74	4.10	0.083	0.852	Download
2	4a01A	0.72	4.32	0.079	0.845	Download
3	5twvB	0.39	7.91	0.046	0.608	Download
4	5u71A	0.39	7.53	0.048	0.576	Download
5	5tsiA	0.38	7.59	0.046	0.568	Download
6	5uj9A	0.38	7.26	0.055	0.546	Download
7	3g61A	0.37	7.59	0.056	0.556	Download
8	4f4cA	0.36	7.26	0.027	0.522	Download
9	5a22A	0.34	7.85	0.047	0.522	Download
10	3ayfA	0.34	8.24	0.050	0.550	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:0005215	1.00	transporter activity
GO:0022857	0.96	transmembrane transporter activity
GO:0022892	0.93	substrate-specific transporter activity
GO:0022891	0.92	substrate-specific transmembrane transporter activity
GO:0003824	0.91	catalytic activity
GO:0016787	0.82	hydrolase activity
GO:0016462	0.79	pyrophosphatase activity
GO:0022804	0.77	active transmembrane transporter activity
GO:0015405	0.76	P-P-bond-hydrolysis-driven transmembrane transporter activity
GO:0015075	0.75	ion transmembrane transporter activity
GO:0017111	0.71	nucleoside-triphosphatase activity
GO:0016887	0.70	ATPase activity
GO:0042623	0.69	ATPase activity, coupled
GO:0042626	0.67	ATPase activity, coupled to transmembrane movement of substances
GO:0008509	0.54	anion transmembrane transporter activity
GO:0042625	0.53	ATPase coupled ion transmembrane transporter activity
GO:0043225	0.52	anion transmembrane-transporting ATPase activity
GO:0015103	0.52	inorganic anion transmembrane transporter activity

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:0006810	0.98	transport
GO:0009987	0.75	cellular process
GO:0006811	0.66	ion transport
GO:0008152	0.52	metabolic process
GO:0071704	0.50	organic substance 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:0044425	0.85	membrane part
GO:0044424	0.84	intracellular part
GO:0016020	0.82	membrane
GO:0044459	0.75	plasma membrane part
GO:0016021	0.74	integral component of membrane
GO:0005886	0.66	plasma membrane
GO:0032991	0.63	macromolecular complex
GO:0044444	0.60	cytoplasmic part
GO:0005887	0.53	integral component of plasma membrane
GO:1902494	0.50	catalytic complex

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	3ig5A	0.300	8.03	0.037	0.476	6.3.2.2	220,271
2	0.060	1b0pA	0.310	7.48	0.049	0.467	1.2.7.1	NA
3	0.060	1yq2A	0.311	8.00	0.025	0.488	3.2.1.23	NA
4	0.060	2e1qA	0.320	8.35	0.051	0.527	1.17.3.2 1.17.1.4	NA
5	0.060	2ckjA	0.304	8.48	0.044	0.506	1.17.1.4 1.17.3.2	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	0.01	3nvvC	0.294	7.85	0.079	0.451	0.16	UUU	Download	230,261,263,264,265
2	0.01	1n1hA	0.290	8.71	0.022	0.488	0.14	QNA	Download	87,162,285,286
3	0.01	3nvwC	0.288	7.51	0.065	0.430	0.19	GUN	Download	150,229,263,264
4	0.01	2ckjD	0.307	8.70	0.029	0.522	0.38	FES	Download	80,82,83
5	0.01	3eubU	0.292	7.83	0.073	0.447	0.15	UUU	Download	228,229,285
6	0.01	2yajA	0.328	8.15	0.043	0.526	0.16	4HP	Download	140,219,220,231
7	0.01	3ns1K	0.163	6.61	0.040	0.231	0.12	FAD	Download	77,78,79,85,162,168,169,227
8	0.01	2e1qA	0.320	8.35	0.051	0.527	0.15	UUU	Download	140,229,263
9	0.01	3g60A	0.367	7.55	0.050	0.542	0.14	0JZ	Download	78,81,82,85
10	0.01	1n1hA	0.290	8.71	0.022	0.488	0.18	CH1	Download	163,171,228

	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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