I-TASSER results

I-TASSER results for job id Rv1883c

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

Input Sequence in FASTA format

>protein (153 residues)
MCLDQVMEGSATVHMAAPPDKIWTLIADVRNTGRFSPETFEAEWLDGATGPALGARFRGH
VRRNGIGPVYWTVCEPGREFGFAVLLGDRPVNNWHYRLTPTADGTEVTESFRLPPSVLTT
VYYRVFGGWLRQRRNIRDMTKTLQRIKDLVEAG

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MCLDQVMEGSATVHMAAPPDKIWTLIADVRNTGRFSPETFEAEWLDGATGPALGARFRGHVRRNGIGPVYWTVCEPGREFGFAVLLGDRPVNNWHYRLTPTADGTEVTESFRLPPSVLTTVYYRVFGGWLRQRRNIRDMTKTLQRIKDLVEAG
Prediction	CCCCCCEEEEEEEEHCCCHHHHHHHHHCHHHCCCCCCCCEEEEEHCCCCCCCCCEEEEEEHCCCCEEEEEEEEEHCCEEEEEEHCCCCCCCEEEEEEEEHCCCEEEEEEEEEHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
Conf.Score	999987699999999599999999986776676678875799996688888888899999668755689999997997999998578876569999999859958999999986875577888876555678999999999999999999979
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MCLDQVMEGSATVHMAAPPDKIWTLIADVRNTGRFSPETFEAEWLDGATGPALGARFRGHVRRNGIGPVYWTVCEPGREFGFAVLLGDRPVNNWHYRLTPTADGTEVTESFRLPPSVLTTVYYRVFGGWLRQRRNIRDMTKTLQRIKDLVEAG
Prediction	864554151423240613063014002215323503440440422456643322231323144543341201211463401031444644333130203147521301021424442234124412443434532464045105302620568
	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

CCCCCCEEEEEEEEHCCCHHHHHHHHHCHHHCCCCCCCCEEEEEHCCCCCCCCCEEEEEEHCCCCEEEEEEEEEHCCEEEEEEHCCCCCCCEEEEEEEEHCCCEEEEEEEEEHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
MCLDQVMEGSATVHMAAPPDKIWTLIADVRNTGRFSPETFEAEWLDGATGPALGARFRGHVRRNGIGPVYWTVCEPGREFGFAVLLGDRPVNNWHYRLTPTADGTEVTESFRLPPSVLTTVYYRVFGGWLRQRRNIRDMTKTLQRIKDLVEAG

2m47A

0.27

0.25

0.96

2.69

MUSTER

--MPKSLTFEDSINIAAPINQVYALVSDITRTGEWSPVCEKCWWD-EDEGPVVGAHFTGRNVTPEETRSEVIVAEPNRCFGWSVTDG---NVKWIYSMEPLEEGTVLTESWEFTPKGQRFFHDSIEEIEKRRLAAITGIPETLVAIQRILEVE

2m47A

0.27

0.25

0.96

3.39

dPPAS

--MPKSLTFEDSINIAAPINQVYALVSDITRTGEWSPVCEKCWWD-EDEGPVVGAHFTGRNVTPEETRSEVIVAEPNRCFGWSVTDG---NVKWIYSMEPLEEGTVLTESWEFTPKGQRFFHDSIEEIEKRRLAAITGIPETLVAIQRILEVE

2m47A

0.27

0.26

0.96

4.33

wdPPAS

M--PKSLTFEDSINIAAPINQVYALVSDITRTGEWSPVCEKCWWD-EDEGPVVGAHFTGRNVTPEETRSEVIVAEPNRCFGWSVTDG---NVKWIYSMEPLEEGTVLTESWEFTPKGQRFFHDSIEEIEKRRLAAITGIPETLVAIQRILEVE

2m47A

0.27

0.25

0.95

3.58

wMUSTER

---PKSLTFEDSINIAAPINQVYALVSDITRTGEWSPVCEKCWWD-EDEGPVVGAHFTGRNVTPEETRSEVIVAEPNRCFGWSVTDG---NVKWIYSMEPLEEGTVLTESWEFTPKGQRFFHDSIEEIEKRRLAAITGIPETLVAIQRILEVE

2m47A

0.27

0.26

0.96

4.47

wPPAS

M--PKSLTFEDSINIAAPINQVYALVSDITRTGEWSPVCEKCWWD-EDEGPVVGAHFTGRNVTPEETRSEVIVAEPNRCFGWSVTDGN---VKWIYSMEPLEEGTVLTESWEFTPKGQRFFHDSIEEIEKRRLAAITGIPETLVAIQRILEVE

2m47A

0.27

0.25

0.96

6.27

dPPAS2

--MPKSLTFEDSINIAAPINQVYALVSDITRTGEWSPVCEKCWWD-EDEGPVVGAHFTGRNVTPEETRSEVIVAEPNRCFGWSVTDG---NVKWIYSMEPLEEGTVLTESWEFTPKGQRFFHDSIEEIEKRRLAAITGIPETLVAIQRILEVE

2m47A

0.27

0.25

0.96

4.06

PPAS

--MPKSLTFEDSINIAAPINQVYALVSDITRTGEWSPVCEKCWWD-EDEGPVVGAHFTGRNVTPEETRSEVIVAEPNRCFGWSVTDGN---VKWIYSMEPLEEGTVLTESWEFTPKGQRFFHDSIEEIEKRRLAAITGIPETLVAIQRILEVE

2m47A

0.27

0.25

0.96

3.31

Env-PPAS

--MPKSLTFEDSINIAAPINQVYALVSDITRTGEWSPVCEKCWWD-EDEGPVVGAHFTGRNVTPEETRSEVIVAEPNRCFGWSVTDG---NVKWIYSMEPLEEGTVLTESWEFTPKGQRFFHDSIEEIEKRRLAAITGIPETLVAIQRILEVE

2d4rA

0.14

0.13

0.93

2.05

MUSTER

------PEVRAERYIPAPPERVYRLAKDLEGLKPYLKEVESLEVVAREGARTR-SRWVAVAGKKVRWLEEEEWDDENLRNRFFSPEGDFDRYEGTWVFLPEGEGTRVVLTLTYELTI--PIFGGL--LRKLVQKLQENVESLLKGLEERVLAA

2d4rA

0.14

0.13

0.93

2.39

dPPAS

------PEVRAERYIPAPPERVYRLAKDLEGLKPYLKEVESLEVVAREGARTR-SRWVAVAGKKVRWLEEEEWDDENLRNRFFSPEGDFDRYEGTWVFLPEGEGTRVVLTLTYELTIPIFG----GLLRKLVQKLQENVESLLKGLEERVLAA

(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 5 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=0.58

Estimated TM-score = 0.79±0.09

Estimated RMSD = 3.6±2.5Å

Download Model 2

C-score=-0.33

Download Model 3

C-score=-0.19

Download Model 4

C-score=-0.74

Download Model 5

C-score=0.28

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	0.859	2.05	0.259	0.954
2	3ie5B	0.730	3.00	0.062	0.948
3	4xrtA	0.710	3.31	0.131	0.948
4	2leqA	0.709	2.52	0.114	0.863
5	4xrwA	0.704	3.20	0.126	0.928
6	3k3kA	0.700	3.18	0.120	0.902
7	3tfzA	0.698	3.21	0.142	0.908
8	2kf2A	0.698	3.02	0.137	0.908
9	2rezA	0.696	3.49	0.135	0.915
10	3kdhA	0.696	3.17	0.135	0.902

(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.)

Ligand binding sites

Rank	C-score	Cluster size	PDB Hit	Lig Name	Download Complex	Ligand Binding Site Residues
1	0.19	10	3ns2B	PYV	Rep, Mult	69,82,84,134,135,138
2	0.06	3	3tl1A	JRO	Rep, Mult	61,64,65,67,84,89,92,111,130,131,134,135,138
3	0.04	2	4n3eM	2AN	Rep, Mult	11,13,15,22,26,96,98,107,109
4	0.04	2	3gl2A	D3M	Rep, Mult	29,53,81,83,96,129
5	0.02	1	4dkiB	BCT	Rep, Mult	148,151
6	0.02	1	1bv10	III	Rep, Mult	23,29,30,33,34,42,43,44,50,51,52,74
7	0.02	1	2gkdA	NUC	Rep, Mult	120,123,124
8	0.02	1	2g4lA	SO4	Rep, Mult	101,103,104
9	0.02	1	1f8vC	NUC	Rep, Mult	143,147
10	0.02	1	2flhA	ZEA	Rep, Mult	23,28,76,77
11	0.02	1	3c0vC	TBR	Rep, Mult	73,75,79,95
12	0.02	1	2a5vA	SCN	Rep, Mult	80,96
13	0.02	1	5e4mB	HBA	Rep, Mult	8,9,10,108,110,111,112

	Download the all possible binding ligands and detailed prediction summary.
	Download the templates clustering results.
(a)	C-score is the confidence score of the prediction. C-score ranges [0-1], where a higher score indicates a more reliable prediction.
(b)	Cluster size is the total number of templates in a cluster.
(c)	Lig Name is name of possible binding ligand. Click the name to view its information in the BioLiP database.
(d)	Rep is a single complex structure with the most representative ligand in the cluster, i.e., the one listed in the Lig Name column. Mult is the complex structures with all potential binding ligands in the cluster.

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	0.201	2vq5A	0.639	3.60	0.101	0.889	4.2.1.78	41
2	0.060	2cb1A	0.478	4.72	0.072	0.784	4.2.99.10	NA
3	0.060	1zefA	0.476	5.08	0.071	0.837	3.1.3.1	NA
4	0.060	2ii4A	0.478	5.25	0.035	0.843	2.3.1.168	90
5	0.060	3l60A	0.496	5.25	0.035	0.863	2.3.1.12	NA
6	0.060	1q23B	0.494	5.16	0.059	0.850	2.3.1.28	NA
7	0.060	3en1A	0.618	3.52	0.066	0.863	1.14.12.11	28
8	0.060	2cghB	0.495	3.50	0.092	0.673	6.3.4.15	NA
9	0.060	1xl7B	0.476	4.81	0.113	0.745	2.3.1.137	NA
10	0.060	1ciaA	0.482	4.78	0.029	0.797	2.3.1.28	NA
11	0.060	2ewnA	0.499	3.39	0.132	0.686	6.3.4.15	NA
12	0.060	2de6B	0.585	4.25	0.062	0.908	1.14.12.-	NA
13	0.060	2debA	0.487	4.65	0.111	0.765	2.3.1.21	NA
14	0.060	1tlbA	0.476	4.84	0.111	0.758	1.3.3.3	107
15	0.060	2vkzG	0.476	4.89	0.041	0.810	2.3.1.38,3.1.2.14	NA
16	0.060	1z01A	0.591	4.39	0.068	0.922	1.14.13.61	NA
17	0.060	2ihwA	0.476	5.27	0.043	0.843	2.3.1.168	NA
18	0.060	1kfqB	0.507	3.99	0.088	0.732	5.4.2.2	81
19	0.060	1d8hA	0.499	4.11	0.077	0.758	3.1.3.33	NA
20	0.060	2ow6A	0.481	4.78	0.074	0.765	3.2.1.114	NA

(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	0.29	0.677	3.56	0.17	0.88	1xn5A	GO:0006950
1	0.27	0.605	3.01	0.16	0.80	2lcgA	GO:0006950
2	0.26	0.709	2.52	0.11	0.86	2leqA	GO:0006950
3	0.22	0.706	3.19	0.13	0.90	2rerA	GO:0003824 GO:0008152 GO:0008168 GO:0008171 GO:0016740 GO:0017000 GO:0032259
4	0.21	0.658	3.44	0.06	0.92	1e09A	GO:0006952 GO:0009607
5	0.20	0.653	3.69	0.09	0.92	4c9iA	GO:0006952 GO:0009607
6	0.20	0.663	2.74	0.12	0.83	2m89A	GO:0006950
7	0.19	0.657	3.22	0.17	0.84	2nn5A	GO:0006950
8	0.19	0.662	3.14	0.15	0.86	3q63F	GO:0006950
9	0.18	0.660	3.34	0.11	0.91	2flhB	GO:0006952 GO:0009607
10	0.18	0.719	2.89	0.07	0.92	2il5A	GO:0006950
11	0.17	0.668	3.38	0.08	0.92	5c9yA	GO:0006952 GO:0009607
12	0.17	0.677	3.00	0.14	0.86	1xn6A	GO:0006950
13	0.16	0.643	3.54	0.12	0.90	2bk0A	GO:0006952 GO:0009607
14	0.16	0.657	3.44	0.09	0.91	4c94A	GO:0006952 GO:0009607
15	0.16	0.665	3.32	0.13	0.88	1xfsA	GO:0006950
16	0.16	0.673	3.26	0.07	0.90	4q0kA	GO:0006952 GO:0009607 GO:0009740
17	0.15	0.638	3.45	0.12	0.84	2kewA	GO:0006950
18	0.15	0.608	3.26	0.16	0.79	4fpwA	GO:0006950
19	0.12	0.696	3.17	0.14	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
20	0.10	0.688	3.46	0.06	0.94	5i8fA	GO:0006952 GO:0009607
21	0.10	0.651	3.68	0.09	0.92	1ifvA	GO:0006952 GO:0009607 GO:0016787
22	0.09	0.639	3.71	0.08	0.92	5amwA	GO:0006952 GO:0009607
23	0.09	0.636	3.72	0.07	0.92	2k7hA	GO:0004864 GO:0004872 GO:0005634 GO:0005737 GO:0006952 GO:0009607 GO:0009738 GO:0010427 GO:0043086 GO:0080163
24	0.09	0.645	3.82	0.10	0.92	4m9bA	GO:0006952 GO:0009607
25	0.08	0.617	3.26	0.13	0.81	3q6aB	GO:0006950
26	0.08	0.666	3.85	0.11	0.93	4gy9A	GO:0006952 GO:0009607 GO:0009736 GO:0009877
27	0.08	0.653	3.60	0.08	0.90	2vneA	GO:0006952 GO:0009607 GO:0009820 GO:0016829 GO:0050474
28	0.08	0.626	3.94	0.06	0.91	2qimA	GO:0006952 GO:0009607 GO:0046872
29	0.07	0.612	3.32	0.15	0.80	2luzA	GO:0006950

Consensus prediction of GO terms

Molecular Function	GO:0016741
GO-Score	0.43
Biological Processes	GO:0006950	GO:0016999	GO:0044249
GO-Score	0.62	0.43	0.43
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.