I-TASSER results

I-TASSER results for job id Rv0603

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

Input Sequence in FASTA format

>protein (103 residues)
MNRIVQFGVSAVAAAAIGIGAGSGIAAAFDGEDEVTGPDADRARAAAVQAVPGGTAGEVE
TETGEGAAAYGVLVTRPDGTRVEVHLDRDFRVLDTEPADGDGG

Predicted Secondary Structure

Sequence	20 40 60 80 100 \| \| \| \| \| MNRIVQFGVSAVAAAAIGIGAGSGIAAAFDGEDEVTGPDADRARAAAVQAVPGGTAGEVETETGEGAAAYGVLVTRPDGTRVEVHLDRDFRVLDTEPADGDGG
Prediction	CCCCHHHCHHHHHHHHHHHHCCCCCEHCCCCCCCCCHHHHHHHHHHHHHHCCCCEEEEEEHCCCCCCCEEEEEEHCCCCCEEEEEHCCCCEEEEHCCCCCCCC
Conf.Score	9853444467888888887555444434689887885799999999998658957878997688997579999986999989999779957998567899999
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 \| \| \| \| \| MNRIVQFGVSAVAAAAIGIGAGSGIAAAFDGEDEVTGPDADRARAAAVQAVPGGTAGEVETETGEGAAAYGVLVTRPDGTRVEVHLDRDFRVLDTEPADGDGG
Prediction	7531252314221120211233321122245655244642542343125424634245344547644531413033554451324136514123344577778
	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

                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCCHHHCHHHHHHHHHHHHCCCCCEHCCCCCCCCCHHHHHHHHHHHHHHCCCCEEEEEEHCCCCCCCEEEEEEHCCCCCEEEEEHCCCCEEEEHCCCCCCCC
MNRIVQFGVSAVAAAAIGIGAGSGIAAAFDGEDEVTGPDADRARAAAVQAVPGGTAGEVETETGEGAAAYGVLVTRPDGTRVEVHLDRDFRVLDTEPADGDGG

2kgyA

0.81

0.72

0.88

1.79

MUSTER

-DYDIPTTENLYFQGAMAF-----------GEDEVTGPDADRARAAAVQAVPGGTAGEVETETGEGAAAYGVLVTRPDGTRVEVHLDRDFRVLDTEPADGDGG

2kgyA

0.80

0.72

0.89

1.84

dPPAS

-DYDIPTTENLYFQGAMAFD----------GEDEVTGPDADRARAAAVQAVPGGTAGEVETETGEGAAAYGVLVTRPDGTRVEVHLDRDFRVLDTEPADGDGG

2kgyA

0.85

0.76

0.89

2.43

wdPPAS

-----DYDIPT-TENLYFQG-----AMAFDGEDEVTGPDADRARAAAVQAVPGGTAGEVETETGEGAAAYGVLVTRPDGTRVEVHLDRDFRVLDTEPADGDGG

2kgyA

0.85

0.76

0.89

2.22

wMUSTER

-----DYDIPT-TENLYFQG-----AMAFDGEDEVTGPDADRARAAAVQAVPGGTAGEVETETGEGAAAYGVLVTRPDGTRVEVHLDRDFRVLDTEPADGDGG

2kgyA

0.85

0.76

0.89

2.60

wPPAS

-----DYDIPT-TENLYFQG-----AMAFDGEDEVTGPDADRARAAAVQAVPGGTAGEVETETGEGAAAYGVLVTRPDGTRVEVHLDRDFRVLDTEPADGDGG

2kgyA

0.95

0.76

0.80

2.08

dPPAS2

---------------------DYDIAMAFDGEDEVTGPDADRARAAAVQAVPGGTAGEVETETGEGAAAYGVLVTRPDGTRVEVHLDRDFRVLDTEPADGDGG

2kgyA

0.85

0.76

0.89

2.56

PPAS

-----DYDIPT-TENLYFQG-----AMAFDGEDEVTGPDADRARAAAVQAVPGGTAGEVETETGEGAAAYGVLVTRPDGTRVEVHLDRDFRVLDTEPADGDGG

2kgyA

0.85

0.76

0.89

2.41

Env-PPAS

-----DYDIPTT-ENLYFQG-----AMAFDGEDEVTGPDADRARAAAVQAVPGGTAGEVETETGEGAAAYGVLVTRPDGTRVEVHLDRDFRVLDTEPADGDGG

5kpeA

0.20

0.19

0.98

0.83

MUSTER

MQDIVEA-AKQAAIAIFQLWKNPTDPEAQE-NKILSPDVLDQVREHARELQKQGEVKRVEVTTDGNTVNVTVELEETTGTTYELRFEVDGDTIRRVTVTQNGG

3e1tA2

0.13

0.11

0.81

dPPAS

I--VIGGGPGGSTLASFVAMRGHRVLLLEREAFPRERARFDDMLLRNSERKGRHEVIDVLFEGER---AVGVRYRNTEGVELMAHARF---------------

(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=-0.31

Estimated TM-score = 0.67±0.12

Estimated RMSD = 4.6±3.0Å

Download Model 2

C-score=-2.55

Download Model 3

C-score=-3.31

Download Model 4

C-score=-3.38

Download Model 5

C-score=-0.41

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	2kgyA	0.783	1.94	0.837	0.893
2	1n9wB	0.575	3.31	0.062	0.845
3	4j15A2	0.557	3.25	0.052	0.825
4	1asyA2	0.549	3.61	0.021	0.845
5	3i7fA	0.548	3.58	0.051	0.854
6	5amqA2	0.540	3.68	0.062	0.874
7	4lnsA	0.535	3.31	0.071	0.816
8	1x54A2	0.533	3.81	0.040	0.883
9	4wrtA	0.532	3.90	0.107	0.874
10	1nnhA	0.528	3.69	0.042	0.825

(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	0.08	4	3q2wA	MAN	Rep, Mult	82,95
2	0.08	4	2iwvA	CA	Rep, Mult	62,83,85
3	0.06	3	4gf4A	C8E	Rep, Mult	31,56,57,74,84,93
4	0.06	3	1dk4B	ZN	Rep, Mult	33,58
5	0.06	3	1eyjA	PO4	Rep, Mult	60,75,77,78,79,80
6	0.06	3	2vqiB	C8E	Rep, Mult	60,73
7	0.04	2	2j7qA	GVE	Rep, Mult	41,42,45,73
8	0.02	1	1qprA	MN	Rep, Mult	60,87
9	0.02	1	2erpA	GM6	Rep, Mult	40,43,44,47,79,99,100,102
10	0.02	1	3ujoB	ADE	Rep, Mult	72,74,82,95
11	0.02	1	3zzvB	GAL	Rep, Mult	14,86

	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	0.060	1ks0A	0.299	3.58	0.061	0.466	3.4.24.24	NA
2	0.060	1j7mA	0.228	4.73	0.053	0.427	3.4.24.24	81
3	0.060	1ui7A	0.492	4.25	0.053	0.816	1.4.3.21	33
4	0.060	1wniA	0.500	4.37	0.088	0.893	3.4.24.53	NA
5	0.060	2e3xA	0.491	4.44	0.129	0.893	3.4.24.58	54
6	0.060	2p0uA	0.491	4.19	0.099	0.825	2.3.1.74	NA
7	0.060	12asA	0.523	3.63	0.081	0.825	6.3.1.1	NA
8	0.060	1r56C	0.458	4.02	0.039	0.767	1.7.3.3	NA
9	0.060	3aboB	0.495	4.43	0.084	0.922	4.3.1.7	64,66
10	0.060	1eakD	0.494	3.73	0.118	0.786	3.4.24.24	NA
11	0.060	1ub7A	0.496	4.07	0.129	0.835	2.3.1.41	NA
12	0.060	1htdA	0.494	4.04	0.069	0.854	3.4.24.42	NA
13	0.060	1afwB	0.491	3.68	0.041	0.777	2.3.1.16	NA
14	0.060	3i7fA	0.548	3.58	0.051	0.854	6.1.1.12	NA
15	0.060	3il3A	0.489	4.05	0.074	0.845	2.3.1.180	NA
16	0.060	1x54A	0.533	3.81	0.040	0.883	6.1.1.22	NA
17	0.060	1hovA	0.448	4.20	0.115	0.786	3.4.24.24	NA
18	0.060	1gxdA	0.491	3.76	0.094	0.786	3.4.24.24	16
19	0.060	1kfqB	0.489	4.07	0.054	0.796	5.4.2.2	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	0.15	0.573	3.18	0.06	0.83	3kfuC	GO:0000166 GO:0003676 GO:0004812 GO:0004815 GO:0005524 GO:0005737 GO:0006412 GO:0006418 GO:0006422 GO:0016874 GO:0050560
1	0.07	0.533	3.81	0.04	0.88	1x54A	GO:0000166 GO:0003676 GO:0004812 GO:0004816 GO:0005524 GO:0005737 GO:0006412 GO:0006418 GO:0006421 GO:0016874
2	0.07	0.513	3.83	0.06	0.83	3p8tA	GO:0000166 GO:0004812 GO:0005524 GO:0006418
3	0.07	0.493	3.87	0.04	0.84	3a5yA	GO:0000166 GO:0004812 GO:0004824 GO:0005524 GO:0005737 GO:0005829 GO:0006418 GO:0006430 GO:0016874 GO:0016880 GO:0043687 GO:0052868 GO:0071915 GO:0072581
4	0.07	0.466	3.77	0.09	0.78	1e1tA	GO:0000166 GO:0000287 GO:0003676 GO:0004812 GO:0004824 GO:0005524 GO:0005737 GO:0005829 GO:0006412 GO:0006418 GO:0006430 GO:0016020 GO:0016874 GO:0046872
5	0.07	0.466	3.80	0.08	0.76	3a5zC	GO:0000166 GO:0004812 GO:0004824 GO:0005524 GO:0005737 GO:0005829 GO:0006418 GO:0006430 GO:0016874 GO:0016880 GO:0043687 GO:0052868 GO:0071915 GO:0072581
6	0.07	0.392	5.02	0.07	0.83	1q7tA	GO:0005886 GO:0008270 GO:0010125 GO:0016787 GO:0016811 GO:0019213 GO:0035595 GO:0046872
7	0.07	0.434	3.97	0.07	0.70	4igbB	GO:0016020 GO:0016021
8	0.07	0.458	3.89	0.08	0.78	3a74A	GO:0000166 GO:0000287 GO:0003676 GO:0004812 GO:0004824 GO:0005524 GO:0005737 GO:0006412 GO:0006418 GO:0006430 GO:0016874 GO:0046872
9	0.06	0.420	4.90	0.07	0.83	4almA	GO:0004318 GO:0006633 GO:0016491 GO:0047117 GO:0055114
10	0.06	0.499	3.95	0.04	0.83	1efwA	GO:0000166 GO:0003676 GO:0004812 GO:0004815 GO:0005524 GO:0005737 GO:0006412 GO:0006418 GO:0016874
11	0.06	0.528	3.69	0.04	0.83	1nnhA	GO:0000166 GO:0004812 GO:0004816 GO:0005524 GO:0005737 GO:0006418 GO:0006421
12	0.06	0.405	4.78	0.07	0.79	3czmB	GO:0003824 GO:0004459 GO:0005975 GO:0016491 GO:0016616 GO:0019752 GO:0055114
13	0.06	0.547	3.50	0.04	0.83	1asyA	GO:0000166 GO:0003676 GO:0003723 GO:0004812 GO:0004815 GO:0005524 GO:0005634 GO:0005737 GO:0006412 GO:0006418 GO:0006422 GO:0016874
14	0.06	0.339	4.62	0.06	0.65	1v5sA	GO:0000166 GO:0004672 GO:0004674 GO:0005524 GO:0005886 GO:0006468 GO:0016020 GO:0016301 GO:0016310 GO:0016740 GO:0070062
15	0.06	0.531	3.90	0.05	0.86	2xgtB
16	0.06	0.511	4.09	0.07	0.83	4o2dB	GO:0000166 GO:0003676 GO:0004812 GO:0005524 GO:0005737 GO:0006412 GO:0006418 GO:0016874 GO:0050560
17	0.06	0.497	3.75	0.01	0.79	4o2dA	GO:0000166 GO:0003676 GO:0004812 GO:0005524 GO:0005737 GO:0006412 GO:0006418 GO:0016874 GO:0050560
18	0.06	0.466	3.94	0.08	0.78	4ex5A	GO:0000166 GO:0000287 GO:0003676 GO:0004812 GO:0004824 GO:0005524 GO:0005737 GO:0006412 GO:0006418 GO:0006430 GO:0016874 GO:0046872

Consensus prediction of GO terms

Molecular Function	GO:0005524	GO:0004812
GO-Score	0.35	0.35
Biological Processes	GO:0006418
GO-Score	0.35
Cellular Component	GO:0005737
GO-Score	0.30

(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.