I-TASSER results

Input Sequence in FASTA format

>protein (96 residues)
MTAAHGYTQQKDNYAKRLRRVEGQVRGIARMIEEDKYCIDVLTQISAVTSALRSVALNLL
DEHLSHCVTRAVAEGGPGADGKLAEASAAIARLVRS

Predicted Secondary Structure

Sequence	20 40 60 80 \| \| \| \| MTAAHGYTQQKDNYAKRLRRVEGQVRGIARMIEEDKYCIDVLTQISAVTSALRSVALNLLDEHLSHCVTRAVAEGGPGADGKLAEASAAIARLVRS
Prediction	CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHC
Conf.Score	998999968999999999999999999999999799959999999999999999999999999999999889879867999999999999999869
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 \| \| \| \| MTAAHGYTQQKDNYAKRLRRVEGQVRGIARMIEEDKYCIDVLTQISAVTSALRSVALNLLDEHLSHCVTRAVAEGGPGADGKLAEASAAIARLVRS
Prediction	875654457526502520440431152044016675404400301320340054024300441054004513765576245304402500541468
	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

CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHC
MTAAHGYTQQKDNYAKRLRRVEGQVRGIARMIEEDKYCIDVLTQISAVTSALRSVALNLLDEHLSHCVTRAVAEGGPGADGKLAEASAAIARLVRS

4adzA

0.58

0.54

0.94

2.88

MUSTER

------YHKQKAEHLKRLRRIEGQIRGLQRMVDEDVYCIDILTQVSASTKALQSFALQLLEEHLRHCVADAALKGGTEIDAKVEEATKAIGRLLRT

4adzA

0.58

0.54

0.94

3.33

dPPAS

------YHKQKAEHLKRLRRIEGQIRGLQRMVDEDVYCIDILTQVSASTKALQSFALQLLEEHLRHCVADAALKGGTEIDAKVEEATKAIGRLLRT

4adzA

0.58

0.54

0.94

4.31

wdPPAS

------YHKQKAEHLKRLRRIEGQIRGLQRMVDEDVYCIDILTQVSASTKALQSFALQLLEEHLRHCVADAALKGGTEIDAKVEEATKAIGRLLRT

4adzA

0.57

0.53

0.93

3.25

wMUSTER

-------HKQKAEHLKRLRRIEGQIRGLQRMVDEDVYCIDILTQVSASTKALQSFALQLLEEHLRHCVADAALKGGTEIDAKVEEATKAIGRLLRT

4adzA

0.58

0.54

0.94

4.04

wPPAS

------YHKQKAEHLKRLRRIEGQIRGLQRMVDEDVYCIDILTQVSASTKALQSFALQLLEEHLRHCVADAALKGGTEIDAKVEEATKAIGRLLRT

4adzA

0.58

0.54

0.94

7.97

dPPAS2

------YHKQKAEHLKRLRRIEGQIRGLQRMVDEDVYCIDILTQVSASTKALQSFALQLLEEHLRHCVADAALKGGTEIDAKVEEATKAIGRLLRT

4adzA

0.58

0.54

0.94

3.37

PPAS

------YHKQKAEHLKRLRRIEGQIRGLQRMVDEDVYCIDILTQVSASTKALQSFALQLLEEHLRHCVADAALKGGTEIDAKVEEATKAIGRLLRT

4adzA

0.58

0.54

0.94

5.62

Env-PPAS

------YHKQKAEHLKRLRRIEGQIRGLQRMVDEDVYCIDILTQVSASTKALQSFALQLLEEHLRHCVADAALKGGTEIDAKVEEATKAIGRLLRT

4m1pA

0.42

0.41

0.97

2.78

MUSTER

LTMIPRTKEEIENIMKRLKRIEGQVRGVQKMVEDNRYCIDILVQISAIQAALRQVGMQLLERHANHCVAKAIREG--SGEQSLRELMDVIKQFAK-

4m1pA

0.42

0.41

0.97

3.22

dPPAS

GTMIPRTKEEIENIMKRLKRIEGQVRGVQKMVEDNRYCIDILVQISAIQAALRQVGMQLLERHANHCVAKAIREG--SGEQSLRELMDVIKQFAK-

(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 1 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=1.70

Estimated TM-score = 0.95±0.05

Estimated RMSD = 0.8±0.8Å

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	4adzA	0.921	0.48	0.578	0.938
2	4m1pA	0.870	1.25	0.380	0.958
3	5lcyA	0.802	1.38	0.241	0.906
4	2hh7A	0.758	1.66	0.345	0.875
5	3ieeA	0.743	2.10	0.033	0.938
6	3rh3A	0.743	2.39	0.032	0.958
7	1ciiA1	0.734	2.40	0.032	0.938
8	4o6yA	0.732	2.74	0.073	1.000
9	4dvyP3	0.708	2.24	0.056	0.927
10	2cmrA	0.707	2.13	0.092	0.854

(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	0.37	132	3bknC	HEM	Rep, Mult	18,21,22,25,45,49,52,53,55,56
2	0.06	28	3rifD	IVM	Rep, Mult	25,28,32,41,44,45,48,49,52
3	0.06	30	1vlgB	FE	Rep, Mult	17,51,54
4	0.04	14	2r5bA	III	Rep, Mult	20,23,26,27,30,31
5	0.02	9	5d56C	78M	Rep, Mult	59,60,63,64,67
6	0.02	7	1fbmE	RTL	Rep, Mult	49,53,56,60,63
7	0.02	7	3kbkA	HG	Rep, Mult	20,24,47,51
8	0.01	4	3rbcA	FE	Rep, Mult	40,44
9	0.01	5	4hfdA	MBR	Rep, Mult	25,28,29,32,48
10	0.01	3	3qvdA	FE	Rep, Mult	17,20,51
11	0.01	6	5ix6A	AU	Rep, Mult	31,32,36,38,41
12	0.01	4	3re7A	CU	Rep, Mult	28,41,45
13	0.00	1	2q0yA	MG	Rep, Mult	38,40
14	0.00	2	2w6dA	CPL	Rep, Mult	45,49,50
15	0.00	1	2z45A	ZN	Rep, Mult	63,85
16	0.00	1	2no5A	CNR	Rep, Mult	19,22
17	0.00	1	1sumB	FE	Rep, Mult	76,80
18	0.00	1	2a68P	MG	Rep, Mult	85,88

	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	0.210	1urfA	0.560	2.72	0.093	0.740	2.7.11.13	15,18,28
2	0.109	1vp7B	0.508	2.03	0.092	0.615	3.1.11.6	25
3	0.066	2w5jA	0.502	2.59	0.044	0.688	3.6.3.14	NA
4	0.066	3cxhQ	0.496	3.03	0.030	0.688	1.10.2.2	NA
5	0.060	1c3cA	0.636	2.78	0.031	0.906	4.3.2.2	NA
6	0.060	1yfeA	0.613	3.19	0.068	0.906	4.2.1.2	NA
7	0.060	1k7wD	0.599	2.82	0.042	0.823	4.3.2.1	NA
8	0.060	1dcnB	0.642	3.20	0.100	0.906	4.3.2.1	NA
9	0.060	2fenD	0.629	3.46	0.074	0.958	5.5.1.2	NA
10	0.060	1w07B	0.630	3.35	0.022	0.958	1.3.3.6	NA
11	0.060	1w27A	0.666	3.05	0.108	0.948	4.3.1.24	NA
12	0.060	1yisA	0.612	3.11	0.084	0.844	4.3.2.2	NA
13	0.060	3f9mA	0.630	3.18	0.074	0.885	2.7.1.2	NA
14	0.060	2fonB	0.632	3.35	0.022	0.958	1.3.3.6	NA
15	0.060	1h2aL	0.605	3.50	0.042	0.917	1.12.2.1	22
16	0.060	2uxwA	0.619	3.32	0.063	0.885	1.3.99.-	23
17	0.060	1xmeA	0.639	3.40	0.053	0.906	1.9.3.1	95
18	0.060	1k62B	0.668	2.98	0.033	0.927	4.3.2.1	NA
19	0.060	1syyA	0.611	3.69	0.021	0.969	1.17.4.1	NA
20	0.060	1y2mB	0.675	2.91	0.067	0.896	4.3.1.24	NA
21	0.060	3h0gA	0.642	3.44	0.064	0.896	2.7.7.6	59,62,64
22	0.060	1v4tA	0.606	3.65	0.105	0.906	2.7.1.2,2.7.1.1	NA
23	0.060	1dofA	0.626	3.15	0.076	0.896	4.3.2.2	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	0.60	0.875	1.34	0.58	0.94	4uigA	GO:0003677 GO:0006355 GO:0046872
1	0.46	0.870	1.25	0.38	0.96	4m1pA	GO:0003677 GO:0006355 GO:0046872
2	0.39	0.697	1.49	0.31	0.80	3aaiA	GO:0003677 GO:0006355 GO:0046872
3	0.38	0.758	1.66	0.34	0.88	2hh7A	GO:0003677 GO:0005507 GO:0005737 GO:0005886 GO:0006351 GO:0006355 GO:0010272 GO:0046688 GO:0046872 GO:0097077
4	0.15	0.561	2.71	0.03	0.75	3layJ	GO:0008270 GO:0042597
5	0.14	0.537	1.65	0.10	0.62	3p30A
6	0.11	0.506	2.15	0.08	0.62	3cp1A	GO:0005198 GO:0019031
7	0.10	0.734	2.40	0.03	0.94	1ciiA	GO:0005886 GO:0016020 GO:0016021 GO:0019835 GO:0042742 GO:0050829
8	0.10	0.622	3.15	0.10	0.97	2xraA	GO:0000139 GO:0002223 GO:0005198 GO:0005789 GO:0005829 GO:0016020 GO:0016021 GO:0016032 GO:0019012 GO:0019031 GO:0019058 GO:0019062 GO:0019064 GO:0019068 GO:0019082 GO:0020002 GO:0030260 GO:0030683 GO:0033644 GO:0039654 GO:0039663 GO:0044174 GO:0044175 GO:0046718 GO:0055036 GO:0075509 GO:0075512 GO:0090527 GO:1903905 GO:1903908 GO:1903911
9	0.08	0.544	2.81	0.04	0.73	3wfvA	GO:0005198 GO:0016020 GO:0016021 GO:0016032 GO:0019012 GO:0019031 GO:0019062 GO:0020002 GO:0033644 GO:0039663 GO:0044174 GO:0044175 GO:0046718 GO:0055036
10	0.07	0.558	2.26	0.04	0.71	1s94B	GO:0000149 GO:0005484 GO:0005622 GO:0006886 GO:0016020 GO:0016021 GO:0016192 GO:0017157 GO:0061025
11	0.07	0.454	4.13	0.11	0.80	4ggvA	GO:0004497 GO:0005506 GO:0016491 GO:0016705 GO:0020037 GO:0046872 GO:0055114
12	0.07	0.513	3.20	0.09	0.70	1rh1A	GO:0005886 GO:0009405 GO:0016020 GO:0016021 GO:0019835 GO:0042742 GO:0050829
13	0.07	0.480	3.46	0.04	0.69	4we8A	GO:0016020 GO:0016021 GO:0016032 GO:0019012 GO:0019031 GO:0019062 GO:0019064 GO:0019065 GO:0020002 GO:0033644 GO:0039654 GO:0039663 GO:0046718 GO:0046789 GO:0055036 GO:0075509 GO:0075512
14	0.07	0.489	3.59	0.04	0.71	1colA	GO:0005886 GO:0016020 GO:0016021 GO:0019835 GO:0042742 GO:0050829
15	0.07	0.474	4.06	0.07	0.72	1a87A	GO:0005886 GO:0016020 GO:0016021 GO:0019835 GO:0042742 GO:0050829
16	0.07	0.476	3.32	0.08	0.70	1ha0A	GO:0016020 GO:0016021 GO:0016032 GO:0019012 GO:0019031 GO:0019062 GO:0019064 GO:0019065 GO:0020002 GO:0033644 GO:0039654 GO:0039663 GO:0046718 GO:0046789 GO:0055036 GO:0075509 GO:0075512
17	0.07	0.439	3.88	0.06	0.71	3eyjB	GO:0016020 GO:0016021 GO:0016032 GO:0019012 GO:0019031 GO:0019062 GO:0019064 GO:0019065 GO:0020002 GO:0033644 GO:0039654 GO:0039663 GO:0046718 GO:0046789 GO:0055036 GO:0075509 GO:0075512
18	0.07	0.490	3.43	0.07	0.70	3fewX	GO:0016020 GO:0016021 GO:0019835 GO:0050829
19	0.06	0.508	3.52	0.06	0.82	5c16A	GO:0004438 GO:0004725 GO:0005737 GO:0005829 GO:0005886 GO:0006629 GO:0006661 GO:0016020 GO:0016311 GO:0016787 GO:0016791 GO:0035335 GO:0042803 GO:0046856 GO:0052629
20	0.06	0.355	4.18	0.07	0.59	1xmxA	GO:0003676 GO:0004518 GO:0090305
21	0.06	0.421	4.48	0.06	0.74	1llwA	GO:0003824 GO:0005737 GO:0006537 GO:0006541 GO:0006807 GO:0008152 GO:0008652 GO:0015930 GO:0016041 GO:0016491 GO:0016638 GO:0019676 GO:0046872 GO:0051536 GO:0051538 GO:0055114 GO:0097054
22	0.06	0.474	4.32	0.04	0.81	1u2zC	GO:0000077 GO:0000725 GO:0000781 GO:0003677 GO:0005634 GO:0006281 GO:0006289 GO:0006301 GO:0006348 GO:0006351 GO:0006355 GO:0008168 GO:0016568 GO:0016740 GO:0018024 GO:0031151 GO:0031493 GO:0031573 GO:0032259 GO:0034729 GO:0044783 GO:0051598 GO:0051726 GO:0070911

Consensus prediction of GO terms

Molecular Function	GO:0003677	GO:0097077
GO-Score	0.92	0.38
Biological Processes	GO:0006355	GO:0010272	GO:0046688
GO-Score	0.92	0.38	0.38
Cellular Component	GO:0005886	GO:0005737
GO-Score	0.38	0.38

(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 Rv0190

[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]