I-TASSER results

Input Sequence in FASTA format

>protein (54 residues)
MSTKSDHGEIGDVEPLADSTASQARRVVAAYANDADECRIFLSMLGIGPAKLES

Predicted Secondary Structure

Sequence	20 40 \| \| MSTKSDHGEIGDVEPLADSTASQARRVVAAYANDADECRIFLSMLGIGPAKLES
Prediction	CCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCHHHHHHHHHHCCCCCCCCC
Conf.Score	999998555566655557999999999999975756889999998898888889
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 \| \| MSTKSDHGEIGDVEPLADSTASQARRVVAAYANDADECRIFLSMLGIGPAKLES
Prediction	856556554254154346643540442133226435403311312233455478
	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

CCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCHHHHHHHHHHCCCCCCCCC
MSTKSDHGEIGDVEPLADSTASQARRVVAAYANDADECRIFLSMLGIGPAKLES

2mi6A

0.14

0.13

0.91

1.05

Env-PPAS

RPVVEVDYEVGEMDPFATLPA-----TISEVNAEQQKLKVLVSIFGLTFGQVSK

1nppA2

0.24

0.20

0.83

1.02

Env-PPAS

---KVE-FEKGDIEPFMNFTG-----TVEEVHPEKRKLTVMISIFGLDFDQVEK

2md0A

0.20

0.19

0.93

0.88

MUSTER

----NDIRTAADMEHCADEKNFDCRRSLRNGDCDNDDKLLEMGYYPVTCGFCEP

2md0A

0.20

0.19

0.93

0.78

dPPAS

----NDIRTAADMEHCADEKNFDCRRSLRNGDCDNDDKLLEMGYYPVTCGFCEP

2kkeA

0.29

0.26

0.89

0.82

wdPPAS

MVGRRPGGGLKDTKPVVDEIEALKSRVPANTSMSAYIRRIILNHL-----EDE-

1z0kB

0.18

0.17

0.91

0.83

wMUSTER

LPLSGGQGQSEDSDPL-LQQIHNITSFIRQAKAAGDEVRTLQENL----RQLQD

2kkeA

0.29

0.26

0.89

0.84

wPPAS

MVGRRPGGGLKDTKPVVDEIEALKSRVPANTSMSAYIRRIILNHL-----EDE-

2hguK3

0.22

0.15

0.69

0.74

dPPAS2

-------ATESNLKALEARIRAQAKRLAERKAE-AERLKKILENL---------

2kkeA

0.29

0.26

0.89

0.96

PPAS

MVGRRPGGGLKDTKPVVDEIEALKSRVPANTSMSAYIRRIILNHL-----EDE-

2eqfA

0.26

0.22

0.85

1.00

Env-PPAS

GSSGSSGPKQRCRAPACDHFGNAKCN---GY---CNECFQFKQMYGSGPSSG--

(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=-2.08

Estimated TM-score = 0.47±0.15

Estimated RMSD = 7.0±4.1Å

Download Model 2

C-score=-3.47

Download Model 3

C-score=-3.50

Download Model 4

C-score=-4.04

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	3o7hA	0.610	2.53	0.040	0.926
2	5iz2B	0.592	3.15	0.019	0.963
3	3p0kA	0.592	3.21	0.057	0.982
4	3netA	0.584	2.65	0.074	0.870
5	4l7tA	0.581	3.07	0.115	0.963
6	4g84A	0.574	2.83	0.130	0.889
7	3f1xA1	0.571	2.95	0.102	0.889
8	4eqyA2	0.571	2.73	0.200	0.889
9	2hwgA	0.569	2.73	0.085	0.815
10	3eenA2	0.566	2.39	0.111	0.870

(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	0.29	17	3tceB	LYZ	Rep, Mult	33,37
2	0.06	4	1s56B	XE	Rep, Mult	20,24,42,44,46
3	0.06	4	3mmhA	MG	Rep, Mult	27,38,41
4	0.05	3	4ilbA	UNL	Rep, Mult	28,31
5	0.05	3	1iruK	MG	Rep, Mult	36,39
6	0.02	1	4eneA	DMU	Rep, Mult	40,44

	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	2jguA	0.528	3.23	0.104	0.889	2.7.7.7	NA
2	0.060	2vdcL	0.544	2.79	0.040	0.870	1.4.1.13	26
3	0.060	1gehA	0.529	3.18	0.096	0.926	4.1.1.39	NA
4	0.060	2wdqA	0.540	3.04	0.082	0.907	1.3.99.1	NA
5	0.060	1gehC	0.529	3.19	0.096	0.926	4.1.1.39	NA
6	0.060	3hriA	0.445	3.10	0.047	0.741	6.1.1.21	NA
7	0.060	3netA	0.584	2.65	0.074	0.870	6.1.1.21	48
8	0.060	3fhgA	0.525	2.58	0.130	0.907	4.2.99.18	37
9	0.060	1rblA	0.364	4.02	0.058	0.759	4.1.1.39	NA
10	0.060	2hvgA	0.526	3.64	0.132	0.982	4.3.2.2	NA
11	0.060	2hwgA	0.569	2.73	0.085	0.815	2.7.3.9	NA
12	0.060	1gk8A	0.534	3.11	0.058	0.926	4.1.1.39	NA
13	0.060	3im9A	0.557	2.85	0.056	0.889	2.3.1.39	17,22
14	0.060	1zxiC	0.528	2.65	0.120	0.852	1.2.99.2	NA
15	0.060	2jf2A	0.554	3.08	0.096	0.907	2.3.1.129	NA
16	0.060	1nm2A	0.539	3.20	0.111	0.907	2.3.1.39	NA
17	0.060	1zq9A	0.554	2.93	0.120	0.926	2.1.1.-	NA
18	0.060	1knpA	0.527	3.24	0.041	0.907	1.4.3.16	NA
19	0.060	1svdA	0.368	4.03	0.077	0.759	4.1.1.39	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	0.07	0.559	2.80	0.13	0.89	4phcA	GO:0000166 GO:0004812 GO:0004821 GO:0005524 GO:0005737 GO:0005739 GO:0005829 GO:0006412 GO:0006418 GO:0006427 GO:0016874 GO:0032543
1	0.07	0.552	2.58	0.11	0.85	4yrcA	GO:0004812 GO:0004821 GO:0005524 GO:0005737 GO:0006418 GO:0006427 GO:0016874
2	0.07	0.525	2.22	0.07	0.78	2q37A	GO:0001560 GO:0003824 GO:0005777 GO:0005829 GO:0005886 GO:0006144 GO:0008152 GO:0009742 GO:0016020 GO:0016787 GO:0016829 GO:0016831 GO:0019428 GO:0019628 GO:0031234 GO:0033971 GO:0051289 GO:0051997
3	0.07	0.391	3.48	0.00	0.78	3s9vB	GO:0000287 GO:0003824 GO:0008152 GO:0009507 GO:0009536 GO:0010333 GO:0016829 GO:0016853 GO:0046872 GO:0050554 GO:0050559
4	0.07	0.504	2.87	0.12	0.87	3racA	GO:0004821 GO:0005737 GO:0016874
5	0.07	0.454	2.96	0.07	0.78	1qe0A	GO:0000166 GO:0004812 GO:0004821 GO:0005524 GO:0005737 GO:0006412 GO:0006418 GO:0006427 GO:0016874
6	0.07	0.506	2.85	0.11	0.83	1wu7A	GO:0000166 GO:0004812 GO:0004821 GO:0005524 GO:0005737 GO:0006412 GO:0006418 GO:0006427 GO:0016874
7	0.07	0.455	3.08	0.05	0.74	3hriF	GO:0004812 GO:0004821 GO:0005524 GO:0005737 GO:0006418 GO:0006427 GO:0016874
8	0.07	0.482	3.22	0.07	0.80	4e51A	GO:0000166 GO:0004812 GO:0004821 GO:0005524 GO:0005737 GO:0006412 GO:0006418 GO:0006427 GO:0016874
9	0.07	0.452	2.97	0.07	0.78	1qe0B	GO:0000166 GO:0004812 GO:0004821 GO:0005524 GO:0005737 GO:0006412 GO:0006418 GO:0006427 GO:0016874
10	0.07	0.472	3.07	0.06	0.85	2o70F	GO:0005777 GO:0006144 GO:0016829 GO:0016831 GO:0019428 GO:0019628
11	0.07	0.457	3.09	0.04	0.76	1httA	GO:0000166 GO:0004812 GO:0004821 GO:0005524 GO:0005737 GO:0005829 GO:0006412 GO:0006418 GO:0006427 GO:0016874
12	0.07	0.450	3.16	0.04	0.76	1kmmC	GO:0000166 GO:0004812 GO:0004821 GO:0005524 GO:0005737 GO:0005829 GO:0006412 GO:0006418 GO:0006427 GO:0016874
13	0.07	0.483	2.96	0.10	0.87	3mopK	GO:0000166 GO:0000187 GO:0001959 GO:0002224 GO:0002755 GO:0004672 GO:0004674 GO:0005524 GO:0005634 GO:0005737 GO:0005829 GO:0005886 GO:0006468 GO:0006954 GO:0007165 GO:0007249 GO:0007254 GO:0010008 GO:0031663 GO:0032088 GO:0034162 GO:0042803 GO:0043433 GO:0046982 GO:0051092 GO:0070423 GO:0070498 GO:0070555
14	0.07	0.457	2.65	0.10	0.80	2o8iA	GO:0019428
15	0.07	0.472	4.14	0.04	0.89	3hjbA	GO:0004347 GO:0005737 GO:0006094 GO:0006096 GO:0016853
16	0.07	0.449	3.18	0.07	0.76	1adjA	GO:0000166 GO:0004812 GO:0004821 GO:0005524 GO:0005737 GO:0006412 GO:0006418 GO:0006427 GO:0016874
17	0.07	0.358	3.24	0.08	0.67	3rc1A	GO:0000166 GO:0016491 GO:0055114
18	0.06	0.445	3.10	0.05	0.74	3hriA	GO:0004812 GO:0004821 GO:0005524 GO:0005737 GO:0006418 GO:0006427 GO:0016874

Consensus prediction of GO terms

Molecular Function	GO:0004812
GO-Score	0.37
Biological Processes	GO:0006427	GO:0032543	GO:0019628	GO:0001560	GO:0019428	GO:0009742	GO:0051289	GO:0006144
GO-Score	0.13	0.07	0.07	0.07	0.07	0.07	0.07	0.07
Cellular Component	GO:0044424
GO-Score	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 Rv3489

[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]