I-TASSER results

Input Sequence in FASTA format

>protein (80 residues)
MHAKVGDYLVVKGTTTERHDQHAEIIEVRSADGSPPYVVRWLVNGHETTVYPGSDAVVVT
ATEHAEAEKRAAARAGHAAT

Predicted Secondary Structure

Sequence	20 40 60 80 \| \| \| \| MHAKVGDYLVVKGTTTERHDQHAEIIEVRSADGSPPYVVRWLVNGHETTVYPGSDAVVVTATEHAEAEKRAAARAGHAAT
Prediction	CCCCCCEEEEEHCCCCCCCCEEEEEEEEHCCCCCCCEEEEHCCCCCEEEEHCCCCEEEHCCCCHHHHHHHHHHHCCCCCC
Conf.Score	98889969999867788875679999998799999879998589968998669985998698757788766555567789
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 \| \| \| \| MHAKVGDYLVVKGTTTERHDQHAEIIEVRSADGSPPYVVRWLVNGHETTVYPGSDAVVVTATEHAEAEKRAAARAGHAAT
Prediction	76153423020435436445340302203278452203021365434020112320314355656566554555455558
	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

                   |                   |                   |                   |

Sec.Str
Seq

CCCCCCEEEEEHCCCCCCCCEEEEEEEEHCCCCCCCEEEEHCCCCCEEEEHCCCCEEEHCCCCHHHHHHHHHHHCCCCCC
MHAKVGDYLVVKGTTTERHDQHAEIIEVRSADGSPPYVVRWLVNGHETTVYPGSDAVVVTATEHAEAEKRAAARAGHAAT

2a7yA

1.00

4.26

MUSTER

MHAKVGDYLVVKGTTTERHDQHAEIIEVRSADGSPPYVVRWLVNGHETTVYPGSDAVVVTATEHAEAEKRAAARAGHAAT

2a7yA

1.00

5.88

dPPAS

MHAKVGDYLVVKGTTTERHDQHAEIIEVRSADGSPPYVVRWLVNGHETTVYPGSDAVVVTATEHAEAEKRAAARAGHAAT

2a7yA

1.00

5.63

wdPPAS

MHAKVGDYLVVKGTTTERHDQHAEIIEVRSADGSPPYVVRWLVNGHETTVYPGSDAVVVTATEHAEAEKRAAARAGHAAT

2a7yA

1.00

0.99

4.55

wMUSTER

-HAKVGDYLVVKGTTTERHDQHAEIIEVRSADGSPPYVVRWLVNGHETTVYPGSDAVVVTATEHAEAEKRAAARAGHAAT

2a7yA

1.00

5.15

wPPAS

MHAKVGDYLVVKGTTTERHDQHAEIIEVRSADGSPPYVVRWLVNGHETTVYPGSDAVVVTATEHAEAEKRAAARAGHAAT

2a7yA

1.00

10.83

dPPAS2

MHAKVGDYLVVKGTTTERHDQHAEIIEVRSADGSPPYVVRWLVNGHETTVYPGSDAVVVTATEHAEAEKRAAARAGHAAT

2a7yA

1.00

5.24

PPAS

MHAKVGDYLVVKGTTTERHDQHAEIIEVRSADGSPPYVVRWLVNGHETTVYPGSDAVVVTATEHAEAEKRAAARAGHAAT

2a7yA

1.00

5.61

Env-PPAS

MHAKVGDYLVVKGTTTERHDQHAEIIEVRSADGSPPYVVRWLVNGHETTVYPGSDAVVVTATEHAEAEKRAAARAGHAAT

2ldmA

0.17

0.15

0.88

0.98

MUSTER

SEFQINEQVLASWS--DSRFYPAKVTAVN-KDGT--YTVKF-YDGVVQTVKH----HVKAFSKDQNIVGNARGSRAHSSH

2lrqA

0.08

0.07

0.94

1.09

dPPAS

TLFVDGERVLCFH---GPLIYEAKVLKTKPDATPVEYYIHYAGWSKNWDEWVPENRVLKYNDDNVKRRQELARQCGER--

(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=1.60

Estimated TM-score = 0.94±0.05

Estimated RMSD = 0.7±0.7Å

Download Model 2

C-score=-1.60

Download Model 3

C-score=-2.70

Download Model 4

C-score=-4.59

Download Model 5

C-score=-4.04

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	2a7yA	0.905	1.14	1.000	1.000
2	5aj3j	0.584	3.36	0.091	0.900
3	3j7aF	0.518	3.84	0.093	0.850
4	3j38E	0.515	3.98	0.027	0.863
5	4ru5A	0.511	3.35	0.129	0.762
6	4bb7A	0.505	3.43	0.087	0.800
7	2xzmW	0.505	3.82	0.067	0.838
8	3iz6D	0.503	3.35	0.106	0.787
9	3pt6A	0.501	3.18	0.087	0.762
10	4cgkA2	0.501	2.70	0.143	0.688

(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	3quiA	ADP	Rep, Mult	10,57,59
2	0.08	4	3ll6A	MG	Rep, Mult	26,38,40,47
3	0.04	2	2wx5H	NA	Rep, Mult	3,4,25
4	0.04	2	3lxvN	CO3	Rep, Mult	40,45
5	0.04	2	4p1vA	FUC	Rep, Mult	8,22,24,60
6	0.04	2	3quiC	ANP	Rep, Mult	11,23,50
7	0.02	1	2hg3H	CDL	Rep, Mult	9,41,46
8	0.02	1	2g4lA	SO4	Rep, Mult	30,32,33
9	0.02	1	2j8cH	CDL	Rep, Mult	68,69,72,73
10	0.02	1	3zt6A	ACX	Rep, Mult	52,53
11	0.02	1	2gkdA	NUC	Rep, Mult	45,74,75
12	0.02	1	4hxeB	MG	Rep, Mult	7,24
13	0.02	1	2p9i3	III	Rep, Mult	35,36,38,39,41
14	0.02	1	3jcmU	NUC	Rep, Mult	19,55
15	0.02	1	1xu25	III	Rep, Mult	7,9,11,28,29,34

	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	2b2cA	0.433	3.26	0.027	0.675	2.5.1.16	NA
2	0.060	1nb3A	0.438	3.50	0.047	0.725	3.4.22.16	NA
3	0.060	2rnzA	0.438	3.25	0.087	0.650	2.3.1.48	24
4	0.060	3k2iA	0.446	4.35	0.051	0.800	3.1.2.2	51
5	0.060	3ehbB	0.438	3.59	0.125	0.725	1.9.3.1	50
6	0.060	2cf6A	0.442	3.67	0.127	0.713	1.1.1.195	NA
7	0.060	1ynnD	0.468	3.55	0.172	0.787	2.7.7.6	NA
8	0.060	3k2lA	0.438	2.98	0.043	0.613	2.7.12.1	12,54
9	0.060	1p58A	0.436	3.73	0.066	0.725	2.7.7.48	NA
10	0.060	3exmA	0.433	3.66	0.043	0.787	3.6.1.6	NA
11	0.060	1z57A	0.433	2.97	0.129	0.613	2.7.12.1,	12
12	0.060	1ynnJ	0.330	4.18	0.069	0.625	2.7.7.6	NA
13	0.060	3eqlD	0.461	3.53	0.156	0.787	2.7.7.6	NA
14	0.060	1cruB	0.459	3.79	0.074	0.787	1.1.5.2	NA
15	0.060	1nu3B	0.441	4.06	0.097	0.762	3.3.2.8	NA
16	0.060	1ugrB	0.433	3.38	0.133	0.700	4.2.1.84	24,26
17	0.060	3h0gA	0.466	3.77	0.119	0.775	2.7.7.6	NA
18	0.060	1uzgA	0.309	3.98	0.056	0.537	2.1.1.56,2.7.7.48,3.4.21.91	NA
19	0.060	1i8qA	0.440	4.25	0.038	0.838	4.2.2.1	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	0.86	0.905	1.14	1.00	1.00	2a7yA	GO:0005618
1	0.07	0.592	3.51	0.12	0.91	3j9mA0	GO:0003735 GO:0005739 GO:0005743 GO:0005840 GO:0030529 GO:0032543 GO:0070125 GO:0070126
2	0.07	0.515	3.98	0.03	0.86	4v6wAE	GO:0000022 GO:0003723 GO:0003735 GO:0005622 GO:0005840 GO:0006412 GO:0007052 GO:0019843 GO:0022627 GO:0030529 GO:0051297 GO:0051298
3	0.07	0.517	3.93	0.11	0.85	4kzxE	GO:0003723 GO:0003735 GO:0005622 GO:0005840 GO:0006412 GO:0019843 GO:0030529
4	0.07	0.520	3.83	0.09	0.84	5it9E	GO:0003723 GO:0003735 GO:0005622 GO:0005840 GO:0006412 GO:0019843 GO:0030529
5	0.07	0.515	3.66	0.08	0.82	4btsAW	GO:0003723 GO:0003735 GO:0005622 GO:0005840 GO:0006412 GO:0019843 GO:0030529
6	0.07	0.494	3.86	0.10	0.84	4v8mA1	GO:0003723 GO:0003735 GO:0005622 GO:0005840 GO:0006412 GO:0019843 GO:0022627 GO:0030529 GO:0032403
7	0.07	0.518	3.84	0.09	0.85	3j7aF	GO:0003723 GO:0003735 GO:0005622 GO:0005840 GO:0006412 GO:0015935 GO:0019843 GO:0022627 GO:0030529
8	0.06	0.374	4.29	0.04	0.72	1u17A	GO:0005576 GO:0042311 GO:0046872 GO:0050880 GO:0051381 GO:0070026
9	0.06	0.361	4.04	0.07	0.62	3oheA	GO:0003824
10	0.06	0.364	4.08	0.05	0.65	3aqqA	GO:0000177 GO:0000932 GO:0003676 GO:0003677 GO:0003723 GO:0003730 GO:0005737 GO:0005829 GO:0006355 GO:0019902 GO:0035556 GO:0043186 GO:0043488 GO:0070062
11	0.06	0.307	4.80	0.07	0.69	3b8fB	GO:0003824 GO:0004126 GO:0009972 GO:0016787 GO:0016814 GO:0017001
12	0.06	0.251	5.28	0.11	0.61	2petA	GO:0004888 GO:0005055 GO:0005886 GO:0005887 GO:0007155 GO:0007160 GO:0007165 GO:0008022 GO:0009897 GO:0009986 GO:0016020 GO:0016021 GO:0043236 GO:0070062
13	0.06	0.343	4.74	0.06	0.76	2agdA	GO:0000138 GO:0000139 GO:0002064 GO:0002526 GO:0003831 GO:0003945 GO:0004461 GO:0005576 GO:0005615 GO:0005794 GO:0005886 GO:0005975 GO:0005989 GO:0006012 GO:0006486 GO:0006487 GO:0007155 GO:0007339 GO:0007341 GO:0008092 GO:0008285 GO:0008378 GO:0009101 GO:0009312 GO:0009611 GO:0009897 GO:0009986 GO:0016020 GO:0016021 GO:0016323 GO:0016740 GO:0016757 GO:0018146 GO:0019901 GO:0030057 GO:0030112 GO:0030145 GO:0030175 GO:0030198 GO:0030879 GO:0031526 GO:0032580 GO:0035250 GO:0042060 GO:0042127 GO:0042803 GO:0042995 GO:0043014 GO:0043065 GO:0045136 GO:0046872 GO:0048487 GO:0048754 GO:0050900 GO:0051270 GO:0060046 GO:0060054 GO:0060055 GO:0060058 GO:0070062
14	0.06	0.443	3.28	0.07	0.64	3kbgA	GO:0003723 GO:0003735 GO:0005622 GO:0005840 GO:0006412 GO:0019843 GO:0030529
15	0.06	0.345	4.43	0.09	0.74	1fgxB	GO:0000138 GO:0002064 GO:0002526 GO:0003831 GO:0003945 GO:0004461 GO:0005576 GO:0005615 GO:0005794 GO:0005886 GO:0005975 GO:0005989 GO:0006012 GO:0006486 GO:0006487 GO:0007155 GO:0007339 GO:0007341 GO:0008092 GO:0008285 GO:0008378 GO:0009101 GO:0009312 GO:0009897 GO:0009986 GO:0016020 GO:0016021 GO:0016323 GO:0016740 GO:0016757 GO:0030057 GO:0030112 GO:0030145 GO:0030175 GO:0030198 GO:0030879 GO:0031526 GO:0032580 GO:0035250 GO:0042060 GO:0042127 GO:0042803 GO:0042995 GO:0043014 GO:0043065 GO:0045136 GO:0046872 GO:0048487 GO:0048754 GO:0050900 GO:0051270 GO:0060046 GO:0060054 GO:0060055 GO:0060058 GO:0070062
16	0.06	0.280	4.52	0.07	0.55	2om5A	GO:0000226 GO:0001764 GO:0001948 GO:0005886 GO:0005887 GO:0007155 GO:0007160 GO:0007409 GO:0007411 GO:0007413 GO:0007417 GO:0007612 GO:0007628 GO:0008076 GO:0009986 GO:0010769 GO:0010954 GO:0016020 GO:0021853 GO:0022010 GO:0030246 GO:0030424 GO:0031133 GO:0031175 GO:0031225 GO:0031623 GO:0033268 GO:0042802 GO:0043005 GO:0043025 GO:0043209 GO:0043621 GO:0044224 GO:0045163 GO:0045202 GO:0045665 GO:0048168 GO:0048710 GO:0060168 GO:0071205 GO:0071206 GO:0097090
17	0.06	0.576	3.22	0.09	0.88	5aj3j	GO:0003735 GO:0005739 GO:0032543
18	0.06	0.259	4.32	0.10	0.51	2myjA	GO:0009268 GO:0033554 GO:0042597 GO:0051082

Consensus prediction of GO terms

Molecular Function	GO:0005198	GO:0003723
GO-Score	0.48	0.37
Biological Processes	GO:0010467	GO:0034645	GO:0044267	GO:0043043
GO-Score	0.37	0.37	0.37	0.37
Cellular Component	GO:0005618	GO:0044444	GO:0030529	GO:0043232
GO-Score	0.86	0.48	0.48	0.48

(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 Rv2302

[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]