I-TASSER results

I-TASSER results for job id Rv2778c

[Click on result.tar.bz2 to download the tarball file including all modelling results listed on this page]

Input Sequence in FASTA format

>protein (156 residues)
MPDPDGPSVTVTVEIDANPDLVYGLITDLPTLASLAEEVVAMQLRKGDDVRKGAVFVGRN
ENGGRRWTTTCTVTDADPGRVFAFDVRSGIIPISRWQYGIVATEHGCRVTESTWDRRPSW
FRAVARMATGVKDRASVNTEHIRRTLQRLKDRAEAG

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MPDPDGPSVTVTVEIDANPDLVYGLITDLPTLASLAEEVVAMQLRKGDDVRKGAVFVGRNENGGRRWTTTCTVTDADPGRVFAFDVRSGIIPISRWQYGIVATEHGCRVTESTWDRRPSWFRAVARMATGVKDRASVNTEHIRRTLQRLKDRAEAG
Prediction	CCCCCCCEEEEEEEHCCCHHHHHHHHHCHHHCCCCCCCEEEEEEHCCCCCCCCEEEEEEHCCCCEEEEEEEEEEEEHCCEEEEEEHCCCCCCEEEEEEEEEEHCCEEEEEEEEEHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
Conf.Score	999998779999999599999999985876665668865899996788888888999996678778789999999979979999987898765799999999599699999999768865567888876566689999997999999999999869
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MPDPDGPSVTVTVEIDANPDLVYGLITDLPTLASLAEEVVAMQLRKGDDVRKGAVFVGRNENGGRRWTTTCTVTDADPGRVFAFDVRSGIIPISRWQYGIVATEHGCRVTESTWDRRPSWFRAVARMATGVKDRASVNTEHIRRTLQRLKDRAEAG
Prediction	565474341323241513063014002216324412340441423557423222312333544624142403023124633020314444343131202031476212011223444432242133214324414531464144005302620578
	Values range from 0 (buried residue) to 8 (highly exposed residue)

Predicted Normalized B-facotr

(B-factor is a value to indicate the extent of the inherent thermal mobility of residues/atoms in proteins. In I-TASSER, this value is deduced from threading template proteins from the PDB in combination with the sequence profiles derived from sequence databases. The reported B-factor profile in the figure below corresponds to the normalized B-factor of the target protein, defined by B=(B'-u)/s, where B' is the raw B-factor value, u and s are respectively the mean and standard deviation of the raw B-factors along the sequence. (Click here to read more about predicted normalized B-factor)

Top 10 threading templates used by I-TASSER

Rank

PDB
Hit

Iden1

Iden2

Cov

Norm.
Zscore

Download
Align.

                  20                  40                  60                  80                 100                 120                 140

                   |                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCCCCCEEEEEEEHCCCHHHHHHHHHCHHHCCCCCCCEEEEEEHCCCCCCCCEEEEEEHCCCCEEEEEEEEEEEEHCCEEEEEEHCCCCCCEEEEEEEEEEHCCEEEEEEEEEHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
MPDPDGPSVTVTVEIDANPDLVYGLITDLPTLASLAEEVVAMQLRKGDDVRKGAVFVGRNENGGRRWTTTCTVTDADPGRVFAFDVRSGIIPISRWQYGIVATEHGCRVTESTWDRRPSWFRAVARMATGVKDRASVNTEHIRRTLQRLKDRAEAG

2m47A

0.24

0.23

0.97

2.78

MUSTER

M--PKSLTFEDSINIAAPINQVYALVSDITRTGEWSPVCEKCWWDEDEGPVVGAHFTGRNVTPERTWETRSEVIVAEPNRCFGWSVTDGN---VKWIYSMEPLEEGTVLTESWEFTPKGQRFFHDKSIEEIEKRRLAAITGIPETLVAIQRILEVE

2m47A

0.23

0.22

0.97

3.51

dPPAS

--MPKSLTFEDSINIAAPINQVYALVSDITRTGEWSPVCEKCWWDEDEGPVVGAHFTGRNVTPERTWETRSEVIVAEPNRCFGWSVTDGN---VKWIYSMEPLEEGTVLTESWEFTPKGQRFFHDKSIEEIEKRRLAAITGIPETLVAIQRILEVE

2m47A

0.24

0.23

0.97

4.43

wdPPAS

M--PKSLTFEDSINIAAPINQVYALVSDITRTGEWSPVCEKCWWDEDEGPVVGAHFTGRNVTPERTWETRSEVIVAEPNRCFGWSVTDGN---VKWIYSMEPLEEGTVLTESWEFTPKGQRFFHDKSIEEIEKRRLAAITGIPETLVAIQRILEVE

2m47A

0.23

0.22

0.96

3.85

wMUSTER

---PKSLTFEDSINIAAPINQVYALVSDITRTGEWSPVCEKCWWDEDEGPVVGAHFTGRNVTPERTWETRSEVIVAEPNRCFGWSVTDGN---VKWIYSMEPLEEGTVLTESWEFTPKGQRFFHDKSIEEIEKRRLAAITGIPETLVAIQRILEVE

2m47A

0.24

0.23

0.97

4.80

wPPAS

M--PKSLTFEDSINIAAPINQVYALVSDITRTGEWSPVCEKCWWDEDEGPVVGAHFTGRNVTPERTWETRSEVIVAEPNRCFGWSVTDGN---VKWIYSMEPLEEGTVLTESWEFTPKGQRFFHDKSIEEIEKRRLAAITGIPETLVAIQRILEVE

2m47A

0.23

0.22

0.97

6.23

dPPAS2

--MPKSLTFEDSINIAAPINQVYALVSDITRTGEWSPVCEKCWWDEDEGPVVGAHFTGRNVTPERTWETRSEVIVAEPNRCFGWSVTDGN---VKWIYSMEPLEEGTVLTESWEFTPKGQRFFHDKSIEEIEKRRLAAITGIPETLVAIQRILEVE

2m47A

0.24

0.23

0.97

4.43

PPAS

M--PKSLTFEDSINIAAPINQVYALVSDITRTGEWSPVCEKCWWDEDEGPVVGAHFTGRNVTPERTWETRSEVIVAEPNRCFGWSVTDGN---VKWIYSMEPLEEGTVLTESWEFTPKGQRFFHDKSIEEIEKRRLAAITGIPETLVAIQRILEVE

2m47A

0.24

0.23

0.97

3.60

Env-PPAS

M--PKSLTFEDSINIAAPINQVYALVSDITRTGEWSPVCEKCWWDEDEGPVVGAHFTGRNVTPERTWETRSEVIVAEPNRCFGWSVTDGN---VKWIYSMEPLEEGTVLTESWEFTPKGQRFFHDKSIEEIEKRRLAAITGIPETLVAIQRILEVE

2d4rA

0.18

0.16

0.91

2.05

MUSTER

------PEVRAERYIPAPPERVYRLAKDLEGLKPYLKEVESLEVVAREG---ARTRSRWVAVAGKKVRWLEEEEWDDENLRNRFFSPEGDFDRYEGTWVFLPEGEGTRVVLTLTYELTIPI-----FGGLLRKLVQKLQENVESLLKGLEERVLAA

2d4rA

0.18

0.16

0.91

2.38

dPPAS

------PEVRAERYIPAPPERVYRLAKDLEGLKPYLKEVESLEVVAREG---ARTRSRWVAVAGKKVRWLEEEEWDDENLRNRFFSPEGDFDRYEGTWVFLPEGEGTRVVLTLTYELTIPI-----FGGLLRKLVQKLQENVESLLKGLEERVLAA

(a)	Iden1 is the number of template residues identical to query divided by number of aligned residues.
(b)	Iden2 is the number of template residues identical to query divided by query sequence length.
(c)	Cov is equal the number of aligned template residues divided by query sequence length.
(d)	Norm. Zscore is the normalized Z-score of the threading alignments. A Normalized Z-score >1 means a good alignment.
(e)	Download Align. list the threading program used to identify the template provide the 3D structure of aligned regions of threading templates.

Top 3 final models predicted by I-TASSER

(For each target, I-TASSER simulations generate a large ensemble of structural conformations, called decoys. To select the final models, I-TASSER uses the SPICKER program to cluster all the decoys based on the pair-wise structure similarity, and reports up to five models which corresponds to the five largest structure clusters. The confidence of each model is quantitatively measured by C-score that is calculated based on the significance of threading template alignments and the convergence parameters of the structure assembly simulations. C-score is typically in the range of [-5, 2], where a C-score of higher value signifies a model with a high confidence and vice-versa. TM-score and RMSD are estimated based on C-score and protein length following the correlation observed between these qualities. Since the top 5 models are ranked by the cluster size, it is possible that the lower-rank models have a higher C-score in rare cases. Although the first model has a better quality in most cases, it is also possible that the lower-rank models have a better quality than the higher-rank models as seen in our benchmark tests. If the I-TASSER simulations converge, it is possible to have less than 5 clusters generated. This is usually an indication that the models have a good quality because of the converged simulations.)

More about C-score

Local structure accuracy of first model

Download Model 1

C-score=0.61

Estimated TM-score = 0.80±0.09

Estimated RMSD = 3.6±2.5Å

Download Model 2

C-score=0.06

Download Model 3

C-score=0.64

Proteins structureally close to the target in PDB (as identified by TM-align

(After the structure assembly simulation, I-TASSER uses the TM-align structural alignment program to match the first I-TASSER model to all structures in the PDB library. This section reports the top 10 proteins from the PDB that have the closest structural similarity, i.e. the highest TM-score, to the predicted I-TASSER model. Due to the structural similarity, these proteins often have similar function to the target. However, users are encouraged to use the data in the next section 'Predicted function using COACH' to infer the function of the target protein, since COACH has been extensively trained to derive biological functions from multi-source of sequence and structure features which has on average a higher accuracy than the function annotations derived only from the global structure comparison.)

Top 10 Identified stuctural analogs in PDB

Rank	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov
1	2m47A	0.843	2.10	0.232	0.962
2	3ie5B	0.751	2.85	0.074	0.949
3	4xrtA	0.736	3.20	0.112	0.974
4	4xrwA	0.724	3.17	0.179	0.962
5	3tfzA	0.709	3.13	0.146	0.910
6	3k3kA	0.707	3.07	0.207	0.904
7	3qtjA	0.705	2.92	0.157	0.891
8	3kdhA	0.701	3.05	0.208	0.904
9	3klxA	0.699	2.89	0.134	0.885
10	2il5A	0.699	2.97	0.106	0.885

(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 function using COACH

(This section reports biological annotations of the target protein by COACH based on the I-TASSER structure prediction. COACH is a meta-server approach that combines multiple function annotation results from the COFACTOR, TM-SITE and S-SITE programs.)

Enzyme Commission (EC) numbers and active sites

Rank	Cscore^EC	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov	EC Number	Active Site Residues
1	0.196	2vq5A	0.629	3.53	0.106	0.885	4.2.1.78	32,53,100
2	0.060	1im0A	0.536	3.50	0.033	0.744	3.1.1.32,3.1.1.4	NA
3	0.060	1s4bP	0.488	5.16	0.082	0.840	3.4.24.15	NA
4	0.060	2pmgB	0.347	5.51	0.028	0.641	5.4.2.2	NA
5	0.060	2ewnA	0.503	3.91	0.059	0.705	6.3.4.15	NA
6	0.060	2o36A	0.491	5.10	0.075	0.833	3.4.24.15	14,97,99
7	0.060	1b5sE	0.497	4.62	0.064	0.788	2.3.1.12	9,25,100
8	0.060	3en1A	0.605	3.80	0.065	0.865	1.14.12.11	28
9	0.060	2de6B	0.590	4.08	0.081	0.878	1.14.12.-	NA
10	0.060	1ciaA	0.482	5.07	0.094	0.814	2.3.1.28	NA
11	0.060	1t7nA	0.487	4.96	0.086	0.833	2.3.1.7	NA
12	0.060	2fy3A	0.483	5.00	0.064	0.814	2.3.1.6	NA
13	0.060	1q6xA	0.494	4.88	0.081	0.801	2.3.1.6	NA
14	0.060	2ihwA	0.514	4.55	0.079	0.795	2.3.1.168	NA
15	0.060	1n2lA	0.485	5.00	0.043	0.827	3.1.6.8	NA
16	0.060	1uliC	0.598	3.87	0.073	0.853	1.14.12.18	28
17	0.060	1ndoA	0.570	4.18	0.080	0.859	1.14.12.12	154,155
18	0.060	1b5sA	0.497	4.62	0.064	0.788	2.3.1.12	NA
19	0.060	1wqlA	0.595	3.81	0.065	0.853	1.14.12.-	28
20	0.060	1z01A	0.604	4.29	0.068	0.891	1.14.13.61	28

(a)	Cscore^EC is the confidence score for the 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.

Gene Ontology (GO) terms

Rank	Cscore^GO	TM-score	RMSD^a	IDEN^a	Cov	PDB Hit	Associated GO Terms
Homologous GO templates in PDB
0	0.24	0.659	2.82	0.16	0.81	2m89A	GO:0006950
1	0.24	0.713	3.07	0.13	0.91	2rerA	GO:0003824 GO:0008152 GO:0008168 GO:0008171 GO:0016740 GO:0017000 GO:0032259
2	0.23	0.663	3.04	0.11	0.83	3q63F	GO:0006950
3	0.21	0.667	3.45	0.13	0.92	4gy9A	GO:0006952 GO:0009607 GO:0009736 GO:0009877
4	0.20	0.672	3.28	0.10	0.92	2flhB	GO:0006952 GO:0009607
5	0.19	0.648	3.68	0.10	0.92	5amwA	GO:0006952 GO:0009607
6	0.19	0.680	3.32	0.08	0.92	1e09A	GO:0006952 GO:0009607
7	0.18	0.688	3.23	0.08	0.92	5c9yA	GO:0006952 GO:0009607
8	0.17	0.663	3.38	0.14	0.85	1xn5A	GO:0006950
9	0.17	0.616	3.03	0.16	0.80	2lcgA	GO:0006950
10	0.17	0.669	3.54	0.07	0.92	4c9iA	GO:0006952 GO:0009607
11	0.16	0.649	3.49	0.12	0.92	2bk0A	GO:0006952 GO:0009607
12	0.16	0.648	3.06	0.11	0.81	2nn5A	GO:0006950
13	0.15	0.656	3.53	0.11	0.90	4a80A	GO:0005737 GO:0006952 GO:0009607
14	0.15	0.671	3.43	0.09	0.92	4c94A	GO:0006952 GO:0009607
15	0.14	0.682	3.16	0.11	0.91	4q0kA	GO:0006952 GO:0009607 GO:0009740
16	0.13	0.734	2.95	0.10	0.92	2il5A	GO:0006950
17	0.12	0.701	3.05	0.21	0.90	3kdhA	GO:0004864 GO:0004872 GO:0005634 GO:0005737 GO:0005886 GO:0009738 GO:0010427 GO:0016020 GO:0042803 GO:0043086 GO:0080163
18	0.11	0.629	3.51	0.10	0.82	2kewA	GO:0006950
19	0.11	0.711	3.16	0.08	0.94	5i8fA	GO:0006952 GO:0009607
20	0.09	0.650	3.73	0.08	0.92	4m9bA	GO:0006952 GO:0009607
21	0.09	0.631	3.64	0.10	0.91	2wqlA	GO:0006952 GO:0009607
22	0.09	0.655	3.66	0.08	0.92	1tw0A	GO:0006952 GO:0009607
23	0.09	0.664	3.54	0.07	0.92	1ifvA	GO:0006952 GO:0009607 GO:0016787
24	0.08	0.629	3.83	0.08	0.92	2qimA	GO:0006952 GO:0009607 GO:0046872
25	0.08	0.642	3.68	0.09	0.92	2k7hA	GO:0004864 GO:0004872 GO:0005634 GO:0005737 GO:0006952 GO:0009607 GO:0009738 GO:0010427 GO:0043086 GO:0080163

Consensus prediction of GO terms

Molecular Function	GO:0016741
GO-Score	0.47
Biological Processes	GO:0016999	GO:0044249	GO:0009755	GO:0044403	GO:0071368	GO:0006952	GO:0009607
GO-Score	0.47	0.47	0.42	0.42	0.42	0.37	0.37
Cellular Component
GO-Score

(a)	Cscore^GO is a combined measure for evaluating global and local similarity between query and template protein. It's range is [0-1] and higher values indicate more confident predictions.
(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 consensus GO terms amongst the 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.

[Click on result.tar.bz2 to download the tarball file including all modelling results listed on this page]

Please cite the following articles when you use the I-TASSER server:
1.	J Yang, R Yan, A Roy, D Xu, J Poisson, Y Zhang. The I-TASSER Suite: Protein structure and function prediction. Nature Methods, 12: 7-8, 2015.
2.	J Yang, Y Zhang. I-TASSER server: new development for protein structure and function predictions, Nucleic Acids Research, 43: W174-W181, 2015.
3.	A Roy, A Kucukural, Y Zhang. I-TASSER: a unified platform for automated protein structure and function prediction. Nature Protocols, 5: 725-738, 2010.
4.	Y Zhang. I-TASSER server for protein 3D structure prediction. BMC Bioinformatics, 9: 40, 2008.