I-TASSER results

Input Sequence in FASTA format

>protein (55 residues)
MGSLAAFKLGWLLSAMAPNVVLLTAFRVPQGLTMLTVFATGQAGQHRCRTFHVTP

Predicted Secondary Structure

Sequence	20 40 \| \| MGSLAAFKLGWLLSAMAPNVVLLTAFRVPQGLTMLTVFATGQAGQHRCRTFHVTP
Prediction	CCCHHHHHHHHHHHHHCCCEEEEEEEHCCCCCEEEEEEEHCCCCCEEEEEHCCCC
Conf.Score	9864568888999985997799875646887568988875667764566655689
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 \| \| MGSLAAFKLGWLLSAMAPNVVLLTAFRVPQGLTMLTVFATGQAGQHRCRTFHVTP
Prediction	7442333322221333343111020343344132120223264354414426358
	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

CCCHHHHHHHHHHHHHCCCEEEEEEEHCCCCCEEEEEEEHCCCCCEEEEEHCCCC
MGSLAAFKLGWLLSAMAPNVVLLTAFRVPQGLTMLTVFATGQAGQHRCRTFHVTP

2yvpA1

0.12

0.09

0.73

1.02

dPPAS

---------------MSPWERILLEEILSEPVRLVKERVRTHTGRELTYVYRPGP

3wdoA1

0.28

0.27

0.96

1.05

wMUSTER

VGGLAVFAAGSVIAALSDSIWGIILGRALQGSGAIA--AAVMAEQNRTKSFGITF

4zowA1

0.22

0.98

1.00

wMUSTER

LAGVVWFIVTCLAILLAQNIEQFTLLRFLQGISLCFIGAVGYAEAVCIKIT-IAP

3wdoA1

0.24

0.98

0.97

MUSTER

VGGLAVFAAGSVIAALSDSIWGIILGRALQGSGAIAAAVMA-REQNRTKSFGITF

4h4nA

0.21

0.18

0.85

0.92

dPPAS

--------KKPIAFKVPPNSKLKVTFFGPYNEVITNVSIINQLSTPKCQTITRYP

4h4nA

0.28

0.24

0.85

0.86

wdPPAS

-KKPIAFKV-------PPNSKLKVTFFGPYNEVITNVSIINQLSTPKCQTITRYP

4zowA

0.22

0.98

0.97

wMUSTER

LAGVVWFIVTCLAILLAQNIEQFTLLRFLQGISLCFIGAVGYAEAVCIKIT-IAP

1jb0I

0.45

0.27

0.60

0.73

wPPAS

MGSYAASFLPWIFIPVVPTVVM--------GL--LFLYIEGEA------------

4h4nA

0.28

0.24

0.85

0.86

dPPAS2

-KKPIAFK-------VPPNSKLKVTFFGPYNEVITNVSIINQLSTPKCQTITRYP

1jb0I

0.45

0.27

0.60

0.84

PPAS

MGSYAASFLPWIFIPVVPTVVM--------GLLFL--YIEGEA------------

(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=-1.89

Estimated TM-score = 0.49±0.15

Estimated RMSD = 6.6±4.0Å

Download Model 2

C-score=-2.64

Download Model 3

C-score=-3.06

Download Model 4

C-score=-3.82

Download Model 5

C-score=-5.00

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	2hlwA	0.529	3.24	0.038	0.964
2	2q0vA	0.526	3.14	0.080	0.909
3	3io1A1	0.521	3.31	0.118	0.927
4	4kamA2	0.512	3.43	0.151	0.927
5	3tx8A	0.508	3.20	0.102	0.855
6	4p7hA	0.505	3.86	0.036	0.873
7	4amqA1	0.503	3.16	0.094	0.946
8	2pwqA	0.503	3.28	0.082	0.891
9	2gmiB	0.501	3.42	0.038	0.946
10	1qgnA2	0.500	3.42	0.113	0.909

(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	0.17	8	4etwD	ZMK	Rep, Mult	3,4
2	0.11	6	4xk8i	CLA	Rep, Mult	6,9
3	0.08	4	4yfkC	4C6	Rep, Mult	9,13
4	0.08	4	1izlM	CLA	Rep, Mult	7,10
5	0.04	2	1aeeA	ANL	Rep, Mult	2,9,34,35,54
6	0.02	1	3llxA	ZN	Rep, Mult	46,48
7	0.02	1	3glgI	BEF	Rep, Mult	33,47
8	0.02	1	1m98A	CL	Rep, Mult	32,54,55

	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	1v72A	0.467	3.15	0.167	0.818	4.1.2.26	18
2	0.060	1cl2B	0.494	3.46	0.132	0.927	4.4.1.8	49
3	0.060	3ecdB	0.468	3.07	0.200	0.782	2.1.2.1	NA
4	0.060	1cyfA	0.487	2.78	0.160	0.818	1.11.1.5	NA
5	0.060	1kkhA	0.482	2.92	0.042	0.855	2.7.1.36	NA
6	0.060	1yh2A	0.480	3.42	0.100	0.909	6.3.2.19	NA
7	0.060	2okkA	0.502	3.29	0.100	0.909	4.1.1.15	NA
8	0.060	1j7dA	0.529	3.10	0.039	0.927	6.3.2.19	18
9	0.060	3h7fB	0.469	3.27	0.170	0.855	2.1.2.1	NA
10	0.060	2bffA	0.488	3.66	0.055	0.909	1.2.4.4	NA
11	0.060	1ylaA	0.471	3.25	0.059	0.927	6.3.2.19	NA
12	0.060	2ctzA	0.494	3.47	0.113	0.927	2.5.1.49	NA
13	0.060	1um9C	0.482	3.71	0.091	0.909	1.2.4.4	NA
14	0.060	3ic1A	0.467	2.90	0.078	0.891	3.5.1.18	NA
15	0.060	1gtxA	0.476	2.65	0.163	0.782	2.6.1.19	NA
16	0.060	3e77A	0.471	3.11	0.089	0.818	2.6.1.52	NA
17	0.060	1tteA	0.473	3.00	0.078	0.855	6.3.2.19	12
18	0.060	3exeA	0.473	3.61	0.038	0.873	1.2.4.1	NA
19	0.060	1jqgA	0.472	2.98	0.157	0.855	3.4.17.1	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	0.10	0.456	3.35	0.08	0.89	1zdnA	GO:0000166 GO:0004842 GO:0005524 GO:0005680 GO:0005737 GO:0006464 GO:0007049 GO:0010458 GO:0010994 GO:0016567 GO:0016740 GO:0031145 GO:0031625 GO:0035519 GO:0044314 GO:0051301 GO:0061630 GO:0061631 GO:0070534 GO:0070979 GO:0085020 GO:1904668
1	0.07	0.529	3.24	0.04	0.96	2hlwA	GO:0000151 GO:0000209 GO:0002223 GO:0005634 GO:0005737 GO:0005829 GO:0006282 GO:0006301 GO:0006355 GO:0030154 GO:0031371 GO:0031625 GO:0035370 GO:0038095 GO:0043123 GO:0043234 GO:0045893 GO:0050852 GO:0051092 GO:0061630 GO:0070062 GO:0070423 GO:0070534
2	0.07	0.448	3.59	0.08	0.89	2gmiA	GO:0000166 GO:0000209 GO:0004842 GO:0005524 GO:0005634 GO:0005737 GO:0006301 GO:0006513 GO:0010994 GO:0016567 GO:0016740 GO:0031371 GO:0031625 GO:0061630 GO:0070534
3	0.07	0.459	3.53	0.12	0.91	3bzhA	GO:0000151 GO:0000166 GO:0000209 GO:0004842 GO:0005524 GO:0005634 GO:0005654 GO:0005829 GO:0006511 GO:0010390 GO:0016567 GO:0016740 GO:0031145 GO:0032020 GO:0033523 GO:0042296 GO:0042787 GO:0043161 GO:0051436 GO:0051437 GO:0051439 GO:0061631 GO:0070936
4	0.07	0.501	3.42	0.04	0.95	2gmiB	GO:0000209 GO:0004842 GO:0005634 GO:0005737 GO:0006301 GO:0010994 GO:0016874 GO:0031371 GO:0031625 GO:0061630 GO:0070534
5	0.07	0.455	3.38	0.08	0.89	4mdkA	GO:0000082 GO:0000166 GO:0000209 GO:0004842 GO:0005524 GO:0005634 GO:0005654 GO:0005737 GO:0006270 GO:0006464 GO:0007049 GO:0016567 GO:0016740 GO:0031625 GO:0035458 GO:0043161 GO:0043525 GO:0043951 GO:0061630 GO:0061631 GO:0070848 GO:0070936 GO:0090261
6	0.07	0.453	3.35	0.08	0.93	1ayzA	GO:0000166 GO:0000209 GO:0000502 GO:0000722 GO:0000724 GO:0000781 GO:0000790 GO:0003697 GO:0004842 GO:0005524 GO:0005634 GO:0005737 GO:0006281 GO:0006348 GO:0006351 GO:0006353 GO:0006355 GO:0006366 GO:0006513 GO:0006974 GO:0010390 GO:0016567 GO:0016568 GO:0016740 GO:0030433 GO:0030435 GO:0031571 GO:0031625 GO:0033503 GO:0042138 GO:0042275 GO:0042276 GO:0042787 GO:0043142 GO:0061630 GO:0070534 GO:0070987 GO:0071596 GO:0071629 GO:0090089 GO:0097505 GO:1990304
7	0.07	0.472	3.23	0.06	0.93	3e46A	GO:0000166 GO:0004842 GO:0005524 GO:0005634 GO:0005737 GO:0006511 GO:0010800 GO:0010994 GO:0016567 GO:0016740 GO:0031625 GO:0032433 GO:0032434 GO:0034450 GO:0035458 GO:0043161 GO:0060340 GO:0070059 GO:0070062 GO:0070936
8	0.07	0.526	3.14	0.08	0.91	2q0vA	GO:0004842 GO:0005634 GO:0005737 GO:0006301 GO:0006511 GO:0031625 GO:0061630 GO:0070534
9	0.07	0.450	3.85	0.11	0.93	2mt6A	GO:0000166 GO:0004842 GO:0005524 GO:0005634 GO:0005737 GO:0006281 GO:0006513 GO:0006515 GO:0006974 GO:0016567 GO:0016740 GO:0031625 GO:0043161 GO:0061630 GO:0070979 GO:0071218
10	0.07	0.473	3.00	0.08	0.85	1tteA	GO:0000166 GO:0000209 GO:0000502 GO:0004842 GO:0005524 GO:0005634 GO:0005737 GO:0016050 GO:0016567 GO:0016740 GO:0030433 GO:0031625 GO:0042787 GO:0061630
11	0.07	0.460	3.54	0.04	0.91	2aakA	GO:0000166 GO:0000209 GO:0004842 GO:0005524 GO:0005737 GO:0006281 GO:0006511 GO:0010228 GO:0016567 GO:0016740 GO:0031625 GO:0033523 GO:0043161 GO:0061630
12	0.07	0.479	3.10	0.09	0.84	2f4zA
13	0.07	0.458	3.33	0.08	0.91	2awfA	GO:0000166 GO:0004842 GO:0005524 GO:0005737 GO:0006511 GO:0016567 GO:0016740 GO:0031625 GO:0044257 GO:0061630 GO:0061631 GO:0070062 GO:0070534 GO:0070936
14	0.07	0.455	3.48	0.08	0.89	3e95A	GO:0000166 GO:0004842 GO:0005524 GO:0005634 GO:0005737 GO:0006301 GO:0031625 GO:0061630 GO:0070534
15	0.07	0.476	3.36	0.12	0.89	4gprA	GO:0000166 GO:0005524
16	0.07	0.446	3.73	0.10	0.95	2ayvA
17	0.07	0.438	3.78	0.02	0.93	2f4wB	GO:0000151 GO:0000166 GO:0000209 GO:0005524 GO:0005783 GO:0005789 GO:0006986 GO:0016020 GO:0016021 GO:0016567 GO:0016740 GO:0030433 GO:0031625 GO:0061630 GO:0061631 GO:1903955
18	0.07	0.442	3.72	0.12	0.91	4r8pL	GO:0000122 GO:0000151 GO:0000166 GO:0000209 GO:0000278 GO:0000791 GO:0000792 GO:0001702 GO:0001739 GO:0003682 GO:0004842 GO:0005524 GO:0005634 GO:0005654 GO:0005694 GO:0005768 GO:0005829 GO:0005886 GO:0006281 GO:0006351 GO:0006355 GO:0006464 GO:0006511 GO:0006513 GO:0006915 GO:0006974 GO:0007281 GO:0008270 GO:0009948 GO:0010008 GO:0016020 GO:0016567 GO:0016574 GO:0016604 GO:0016740 GO:0016874 GO:0016925 GO:0021510 GO:0030509 GO:0031519 GO:0032526 GO:0035102 GO:0035518 GO:0035666 GO:0036353 GO:0043161 GO:0043433 GO:0046872 GO:0051865 GO:0061418 GO:0061630 GO:0061631 GO:0070062 GO:0070936 GO:0070979 GO:0071339 GO:0071535 GO:1903955

Consensus prediction of GO terms

Molecular Function	GO:0044389	GO:0061659	GO:0004842	GO:0032550	GO:0035639	GO:0032559	GO:0061650
GO-Score	0.54	0.54	0.54	0.43	0.43	0.43	0.32
Biological Processes	GO:0000209	GO:0010993	GO:0051258	GO:0006281	GO:0043161
GO-Score	0.54	0.43	0.43	0.37	0.32
Cellular Component	GO:0043231	GO:1990234
GO-Score	0.48	0.37

(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 Rv1706A

[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]