COFACTOR results for job id CF000002

Download the Query structure file (PDB format)

Evolutionarily conserved residues in query protein

Sequence	20 40 60 80 100 \| \| \| \| \| LLPEIFRQTVEHAPIAISITDLKANILYANRAFRTITGYGSEEVLGKNESILSNGTTPRLVYQALWGRLAQKKPWSGVLVNRRKDKTLYLAELTVAPVLNEAGETIYYLGMHRDTSELH
Cons.Score	00000000342010039002900709009900900479900397293010050000000000004200500000600300029999008500000044040090000410100999000
	Values range from 0 (non-conserved residue) to 9 (highly conserved residue)

Proteins with highly similar structure in PDB (as identified by TM-align)

Top 10 Identified stuctural analogs in PDB

Rank	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	Download Alignment
1	2gj3A	1.000	0.00	1.000	1.000	Download
2	3lyxA	0.860	1.91	0.203	0.983	Download
3	2wkpA1	0.833	1.76	0.228	0.941	Download
4	2z6dA	0.830	1.92	0.278	0.958	Download
5	2wkrA	0.827	1.77	0.221	0.933	Download
6	1n9lA	0.791	1.68	0.283	0.882	Download
7	3rh8B	0.788	2.67	0.254	0.941	Download
8	3ewkA	0.786	1.48	0.337	0.866	Download
9	3p7nA1	0.786	2.16	0.259	0.916	Download
10	2z6cA	0.784	1.51	0.263	0.866	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 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	0.576	2gj3A	0.882	0.00	1.000	1.000	2.7.13.3	NA
2	0.218	1d06A	0.642	2.85	0.223	0.941	2.7.13.3	NA
3	0.212	1s67L	0.625	2.66	0.216	0.924	3.1.4.52	NA
4	0.190	1xj6B	0.576	2.80	0.188	0.824	2.7.13.3	NA
5	0.183	2bydA	0.417	3.86	0.092	0.781	1.2.1.31	95

	Click on the radio buttons to visualize predicted active site residues.
(a)	Cscore^EC is the confidence score for the Enzyme Classification (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 GO terms

Rank	Cscore^GO	TMscore	RMSD^a	IDEN^a	Cov.	PDB Hit	Associated GO Terms
1	1.00	1.0000	0.00	1.00	1.00	2gj3A	GO:0000155 GO:0000160 GO:0004871 GO:0006355 GO:0007165
2	0.35	0.8431	2.30	0.20	0.98	3lyxB	GO:0000155 GO:0000160 GO:0004871 GO:0005515 GO:0006355 GO:0007165
3	0.36	0.8332	1.76	0.23	0.94	2wkpA	GO:0030742 GO:0050690 GO:0009611 GO:0006184 GO:0019899 GO:0007264 GO:0007596 GO:0006928 GO:0051056 GO:0000166 GO:0048261 GO:0010592 GO:0006954 GO:0007411 GO:0030168 GO:0016020 GO:0048011 GO:0008624 GO:0051668 GO:0005515 GO:0030041 GO:0031529 GO:0009653 GO:0007160 GO:0030032 GO:0031295 GO:0016032 GO:0060263 GO:0010310 GO:0042470 GO:0003924 GO:0007155 GO:0006915 GO:0048870 GO:0030334 GO:0032707 GO:0005622 GO:0035025 GO:0031996 GO:0005525 GO:0005886 GO:0005829 GO:0035556 GO:0000155 GO:0000160 GO:0004871 GO:0006355 GO:0007165
4	0.35	0.8176	1.81	0.22	0.92	2v0uA	GO:0000155 GO:0000160 GO:0004871 GO:0006355 GO:0007165
5	0.37	0.7915	1.68	0.28	0.88	1n9lA	GO:0000155 GO:0000160 GO:0004871 GO:0005515 GO:0006355 GO:0007165
6	0.40	0.7864	1.48	0.34	0.87	3ewkA	GO:0000155 GO:0000160 GO:0004871 GO:0006355 GO:0007165
7	0.35	0.7859	2.16	0.25	0.92	3p7nA	GO:0006355 GO:0016301 GO:0016310 GO:0003677 GO:0006351 GO:0000155 GO:0000156 GO:0000160 GO:0003700 GO:0004871 GO:0005622 GO:0007165 GO:0043565
8	0.36	0.7838	1.51	0.26	0.87	2z6cA	GO:0000155 GO:0000160 GO:0004871 GO:0006355 GO:0007165
9	0.36	0.7783	2.41	0.28	0.92	3hjkA	GO:0004871 GO:0006355 GO:0007165
10	0.30	0.7622	2.30	0.18	0.88	3oloA	GO:0004871 GO:0006355 GO:0007165

Consensus Prediction of Gene Ontology terms

Molecular Function    Biological Process Cellular Location

GO term GO-Score    GO term GO-Score GO term GO-Score

GO:0004871 0.138    GO:0006355 0.176    GO:0044464 0.014

GO:0000155 0.08    GO:0007165 0.144    GO:0005622 0.014

GO:0005515 0.08    GO:0000160 0.084    GO:0016020 0.014

GO:0003677 0.034    GO:0018298 0.018    GO:0005829 0.008

GO:0043565 0.014    GO:0009584 0.012    GO:0042470 0.004

GO:0009881 0.014    GO:0016310 0.008    GO:0005886 0.004

GO:0003700 0.012    GO:0030168 0.008    GO:0005634 0.002

GO:0000156 0.012    GO:0007602 0.008

GO:0008020 0.012    GO:0006954 0.006

GO:0000166 0.006    GO:0046278 0.006

(a) Cscore^GO, which is a combined measure for evaluating global and local similarity between query and template protein. Cscore^GO values range in between [0-1]; where a higher value indicates a better confidence in predicting the function using the template.

(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.

(f) The second table shows a consistence of function (GO terms) amongst top scoring templates. The GO-Score associated with each prediction is defined as the average weight of the GO term, where the weights are assigned based on Cscore^GO of the template from which the GO term is derived.

Predicted 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 in the model

1 0.53 2pr5A 0.759 2.02 0.299 0.866 1.38 FMN Download 18,20,24,48,49,50,52,53,62,65,66,69,81,91,93,95,108,109,110,112

2 0.28 1s66L 0.728 2.69 0.225 0.924 1.09 HEM Download 18,20,49,52,53,54,57,62,70,75,77,79,81,93,95,108,110

3 0.28 2r78A 0.758 1.95 0.234 0.882 0.86 ACT Download 26,49,50,52,53,93

4 0.17 3f1nA 0.723 1.98 0.143 0.849 1.13 EDO Download 18,20,53,80,82,91,93,110,112

5 0.17 3f1nA 0.723 1.98 0.143 0.849 1.05 EDO Download 24,62,65,66,74,76,94,96,110

6 0.07 2p7jA 0.618 3.32 0.105 0.840 0.84 SO4 Download 16,49,52,81,82,93,112

7 0.05 1kouA 0.711 2.40 0.171 0.857 1.16 DHC Download 29,33,37,39,49,51,52,53,54,81,83

8 0.03 2qkpB 0.624 3.15 0.143 0.849 0.91 EDO Download 14,16,32,37,112,113

9 0.02 1oj5A 0.535 3.47 0.109 0.765 0.96 PEP Download 26,27,28,29,31,39

10 0.02 3oovA 0.571 3.55 0.089 0.807 0.88 GOL Download 11,14,30,32,33

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 >1.1 reflects a very good 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.

(a)	Cscore^GO, which is a combined measure for evaluating global and local similarity between query and template protein. Cscore^GO values range in between [0-1]; where a higher value indicates a better confidence in predicting the function using the template.
(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.
(f)	The second table shows a consistence of function (GO terms) amongst top scoring templates. The GO-Score associated with each prediction is defined as the average weight of the GO term, where the weights are assigned based on Cscore^GO of the template from which the GO term is derived.