I-TASSER results

Input Sequence in FASTA format

>protein (54 residues)
MPGLVPAMPLDALRPARQPTSGLGECATMRRPEAGNEKVAVIWESLDVVPPESL

Predicted Secondary Structure

Sequence	20 40 \| \| MPGLVPAMPLDALRPARQPTSGLGECATMRRPEAGNEKVAVIWESLDVVPPESL
Prediction	CCCCCCCCCHHHCCCCCCCCCCCCHHHHCCCCCCCCCEEEEEEEHCCCCCCCCC
Conf.Score	999888887566566779999865444346888888668998764568998889
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 \| \| MPGLVPAMPLDALRPARQPTSGLGECATMRRPEAGNEKVAVIWESLDVVPPESL
Prediction	754334434253244345435323423434437445530111154144344778
	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

                   |                   |

Sec.Str
Seq

CCCCCCCCCHHHCCCCCCCCCCCCHHHHCCCCCCCCCEEEEEEEHCCCCCCCCC
MPGLVPAMPLDALRPARQPTSGLGECATMRRPEAGNEKVAVIWESLDVVPPESL

1s4kA1

0.28

0.24

0.85

1.12

Env-PPAS

----ANALELQALR---RIFDTIEECTIY-ITQDNNSATWQRWEAGDIISPEII

2octA1

0.35

0.26

0.74

1.05

Env-PPAS

MSG--------APSATQPATAETQHIADQVRSEKYNKKKAVSFKS-QVV-----

1okgA3

0.33

0.31

0.94

0.78

MUSTER

TPSLNPKANLDTLKAPERPDAEVQSAATHLH--AG-EAATVYFKSGRVVVVPNL

1ppjI

0.34

0.26

0.76

0.90

dPPAS

--AAVPATS-------ESPVLSVLCRESLRGQAAGRPLVASV--SLNV--PASV

1ppjI

0.44

0.30

0.67

0.80

wdPPAS

--AAVPATSLSVL--CRESLRGQA----AGRP------VASV--SLNV--PASV

1okgA3

0.35

0.31

0.91

0.82

wMUSTER

TPSL-PKANLDTLKAPERPDAEVQSAATLH---AG-EAATVYFKSGRVVVVPNL

1ppjI

0.49

0.31

0.65

0.83

wPPAS

--AAVPATSLSVL--CRESLRG----A-AGRP------VASV--SLNV--PASV

1ppjI

0.43

0.30

0.69

0.92

dPPAS2

--AAVPATSLSVL--CRESLRGQA----AGRPL-----VASV--SLNV--PASV

1ppjI

0.44

0.30

0.67

0.96

PPAS

--AAVPATSLSVL--CRESLRGQA----AGRP------VASV--SLNV--PASV

2lclA

0.22

0.20

0.94

0.95

Env-PPAS

GPDIVPATPYDKVIITEGAFEGF-Q-AIFTEPD-GEARSMLLLNLINSVKNTEF

(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=-2.23

Estimated TM-score = 0.45±0.15

Estimated RMSD = 7.3±4.2Å

Download Model 2

C-score=-2.49

Download Model 3

C-score=-2.90

Download Model 4

C-score=-2.78

Download Model 5

C-score=-4.30

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	1xv2C	0.519	2.92	0.021	0.870
2	1aqzB	0.508	2.98	0.039	0.870
3	2kaaA	0.504	3.07	0.059	0.907
4	1rmsA	0.499	2.92	0.021	0.833
5	1sqhA	0.482	3.52	0.098	0.833
6	1lqmH	0.478	3.12	0.065	0.833
7	2mqdA	0.475	3.47	0.021	0.852
8	3qhyA	0.474	3.26	0.167	0.870
9	1rtuA	0.471	3.14	0.022	0.833
10	1qsmD	0.471	3.36	0.061	0.815

(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	0.10	5	1txcB	2AN	Rep, Mult	8,30,42,47,48
2	0.07	3	1xrmA	III	Rep, Mult	1,4
3	0.07	3	1ib4B	MAN	Rep, Mult	21,25
4	0.05	2	2o8mB	III	Rep, Mult	34,39
5	0.04	2	1aztB	MG	Rep, Mult	20,47,48
6	0.04	2	4y2nB	MG	Rep, Mult	39,49
7	0.02	1	2m0oA	III	Rep, Mult	12,20,21,23,26,43,44,45,47
8	0.02	1	1zaoA	MN	Rep, Mult	36,47
9	0.02	1	3nmuC	NUC	Rep, Mult	35,36
10	0.02	1	3j0qL	NUC	Rep, Mult	18,19
11	0.02	1	4polA	COM	Rep, Mult	25,26
12	0.02	1	3bwxA	CA	Rep, Mult	9,12
13	0.02	1	2g77A	AF3	Rep, Mult	14,53

	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	1ucyE	0.404	3.50	0.020	0.852	3.4.21.5	43
2	0.060	1bbrH	0.285	3.98	0.063	0.667	3.4.21.5	15
3	0.060	1ah5A	0.440	3.41	0.080	0.852	2.5.1.61,4.3.1.8	NA
4	0.060	1bsgA	0.449	3.64	0.061	0.889	3.5.2.6	NA
5	0.060	1ybqA	0.444	3.50	0.083	0.815	3.4.19.1	9
6	0.060	1f1sA	0.445	3.23	0.000	0.759	4.2.2.1	NA
7	0.060	1jwtA	0.442	3.62	0.019	0.907	3.4.21.5	NA
8	0.060	2c4bA	0.471	3.10	0.041	0.870	3.1.27.3	NA
9	0.060	1ay7A	0.424	3.65	0.061	0.870	3.1.27.3	NA
10	0.060	2puxB	0.436	3.48	0.020	0.889	3.4.21.5	NA
11	0.060	3d5gB	0.446	3.61	0.058	0.889	3.1.4.8	17
12	0.060	1n4oB	0.402	3.64	0.060	0.907	3.5.2.6	NA
13	0.060	1onxA	0.447	3.47	0.083	0.815	3.4.19.-	NA
14	0.060	1bujA	0.462	2.97	0.041	0.870	3.1.27.-	25
15	0.060	3a3iA	0.442	3.36	0.082	0.852	3.4.16.4	38
16	0.060	1madH	0.442	3.31	0.068	0.778	1.4.99.3	9
17	0.060	1cefA	0.465	2.94	0.045	0.815	3.4.16.4	NA
18	0.060	1jqjA	0.432	3.77	0.063	0.870	2.7.7.7	17,28,30,48
19	0.060	1c54A	0.461	3.25	0.096	0.926	3.1.27.3	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	0.14	0.478	3.12	0.07	0.83	1lqmH
1	0.07	0.512	2.94	0.00	0.89	1xv2C	GO:0045151 GO:0047605
2	0.07	0.293	4.06	0.04	0.63	4bt2A	GO:0016829 GO:0016831 GO:0045151 GO:0047605
3	0.07	0.443	3.71	0.02	0.85	1dy6A	GO:0008800 GO:0016787 GO:0030655 GO:0046677
4	0.07	0.431	3.31	0.12	0.80	2wpwA	GO:0008080 GO:0033050
5	0.07	0.301	3.85	0.08	0.63	3dkqB	GO:0005506 GO:0016491 GO:0016705 GO:0016706 GO:0031418 GO:0046872 GO:0051213 GO:0055114
6	0.07	0.415	3.52	0.04	0.83	1fusA	GO:0003723 GO:0004518 GO:0004519 GO:0004521 GO:0004540 GO:0016787 GO:0046589 GO:0090305 GO:0090501 GO:0090502
7	0.07	0.404	3.51	0.04	0.85	3f2oB	GO:0000209 GO:0004842 GO:0005737 GO:0005829 GO:0016567 GO:0035556
8	0.07	0.442	3.33	0.04	0.89	1sqhA	GO:0016740 GO:0016746 GO:0016747
9	0.07	0.318	4.18	0.10	0.67	3dkqA	GO:0005506 GO:0016491 GO:0016705 GO:0016706 GO:0031418 GO:0046872 GO:0051213 GO:0055114
10	0.07	0.412	3.57	0.12	0.89	2blmA	GO:0005886 GO:0008800 GO:0016020 GO:0016787 GO:0030655 GO:0046677
11	0.07	0.389	3.92	0.10	0.91	4yfmA	GO:0008800 GO:0016787 GO:0030655 GO:0046677
12	0.07	0.402	3.64	0.06	0.91	1n4oB	GO:0008800 GO:0016787 GO:0030655 GO:0046677
13	0.06	0.504	3.07	0.06	0.91	2kaaA	GO:0003723 GO:0004540 GO:0090501
14	0.06	0.429	3.25	0.09	0.81	3whoA	GO:0003723 GO:0004518 GO:0004519 GO:0004521 GO:0004540 GO:0016787 GO:0046589 GO:0090305 GO:0090501 GO:0090502
15	0.06	0.409	3.68	0.06	0.89	3lezA	GO:0008800 GO:0016787 GO:0030655 GO:0046677 GO:0046872
16	0.06	0.321	4.07	0.10	0.67	1y44A	GO:0004518 GO:0004519 GO:0008033 GO:0008270 GO:0016787 GO:0016891 GO:0034414 GO:0042779 GO:0042781 GO:0046872 GO:0090502
17	0.06	0.269	4.42	0.07	0.70	4d2oB	GO:0008800 GO:0016787 GO:0030655 GO:0046677
18	0.06	0.312	4.37	0.06	0.78	1iuzA	GO:0005507 GO:0009055 GO:0009507 GO:0009535 GO:0009536 GO:0009579 GO:0016020 GO:0046872 GO:0051607 GO:0055114

Consensus prediction of GO terms

Molecular Function	GO:0047605	GO:0008800	GO:0008080
GO-Score	0.13	0.07	0.07
Biological Processes	GO:0045151	GO:0046677	GO:0033050	GO:0030655
GO-Score	0.13	0.07	0.07	0.07
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.

I-TASSER results for job id Rv2395B

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

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