I-TASSER results

Input Sequence in FASTA format

>protein (82 residues)
MGRNATAVVSLPVVALSPRAGQAGYLWQSITRGLRVTPICCYHPPCGGGVQKMLSRKLGR
VCPAPSPKDAARGAHNVGANAV

Predicted Secondary Structure

Sequence	20 40 60 80 \| \| \| \| MGRNATAVVSLPVVALSPRAGQAGYLWQSITRGLRVTPICCYHPPCGGGVQKMLSRKLGRVCPAPSPKDAARGAHNVGANAV
Prediction	CCCCCEEEEEEEEEEHCCCCCCCCHHHHHHHCCCEEHCEEHCCCCCCCHHHHHHHHHHCCCCCCCCHHHHHHCCCCCCCCCC
Conf.Score	9976467887667776788887655788876475565556679999977999999987787899996776654555677789
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 \| \| \| \| MGRNATAVVSLPVVALSPRAGQAGYLWQSITRGLRVTPICCYHPPCGGGVQKMLSRKLGRVCPAPSPKDAARGAHNVGANAV
Prediction	8655231313132311334344323124313441422210023241443145215541453153444653353345344648
	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

CCCCCEEEEEEEEEEHCCCCCCCCHHHHHHHCCCEEHCEEHCCCCCCCHHHHHHHHHHCCCCCCCCHHHHHHCCCCCCCCCC
MGRNATAVVSLPVVALSPRAGQAGYLWQSITRGLRVTPICCYHPPCGGGVQKMLSRKLGRVCPAPSPKDAARGAHNVGANAV

5t57A1

0.25

0.21

0.82

0.81

MUSTER

M---------KEKIAL---FGAGGKMGVRLAKNLLKSDYRVSHVEVSEVGKKRLKDELGLEC--VSTEAALDNV-DVVILAV

5t57A1

0.24

0.20

0.82

1.00

dPPAS

---------MKEKIAL---FGAGGKMGVRLAKNLLKSDYRVSHVEVSEVGKKRLKDELGLEC--VSTEAALDNV-DVVILAV

1w0rA2

0.31

0.18

0.59

0.62

wdPPAS

---------------CCPEMGGWS--WGPWEP-------C--SVTCSKGTR---TRR--RACNHPAPK---CGGHCPGQAQE

5t57A1

0.25

0.20

0.78

0.70

wMUSTER

---------MKEKIAL----GAGGKMGVRLAKNLLKSDYRVSHVEVSEVGKKRLKDELGLEC--VSTEAALDNVDVV---AV

5d0kC

0.25

0.16

0.63

0.65

wPPAS

-------VQTIERFTFPHKYKKTD----TI--GVRRLP-CLFHQLC---VDQWLAMS--KKCP--------R--VDIET-QL

5t57A1

0.24

0.20

0.82

0.90

dPPAS2

---------MKEKIAL---FGAGGKMGVRLAKNLLKSDYRVSHVEVSEVGKKRLKDELGLEC--VSTEAALDNV-DVVILAV

5t57A1

0.25

0.20

0.78

0.77

PPAS

---------MKEKIAL----GAGGKMGVRLAKNLLKSDYRVSHVEVSEVGKKRLKDELGLECV--STEAALDNVDVV---AV

1vw4X

0.30

0.22

0.73

0.81

Env-PPAS

---SKNSVIKLLSTAAS------GYSYISIKKGAPLVTQVRYDPV----VKRHKEAKKRKVAERK-PLDFLRTA--------

3hdjA2

0.29

0.24

0.83

0.69

MUSTER

-----TAACTVPVLGL---AGQGAEHAAQLSARFALEAILVHDPYASPEILERIGRRCG--VPAAAPADIAAQADIV----V

3hdjA2

0.21

0.18

0.87

0.72

dPPAS

LARPRSS-----VLGLFGAGTQGAEHAAQLSARFALEAILVHDPYASPEILERIGRRCG--VPAAAPADIAAQADIVV----

(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=-1.83

Estimated TM-score = 0.49±0.15

Estimated RMSD = 7.4±4.2Å

Download Model 2

C-score=-3.06

Download Model 3

C-score=-2.22

Download Model 4

C-score=-2.75

Download Model 5

C-score=-4.48

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	4c3sA2	0.629	3.13	0.101	0.963
2	3k9dC	0.623	3.05	0.087	0.963
3	5j78A	0.613	3.05	0.063	0.963
4	4h04A	0.610	3.44	0.025	0.976
5	3vmnA	0.607	3.12	0.039	0.927
6	3fi9A	0.606	2.99	0.117	0.939
7	3my7A2	0.606	3.11	0.100	0.963
8	2c40A	0.605	2.98	0.055	0.890
9	3g5iA	0.605	2.97	0.055	0.890
10	1ezrA	0.602	3.01	0.055	0.890

(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	3ugvB	MG	Rep, Mult	14,41,67
2	0.04	2	3pipA	MG	Rep, Mult	38,44
3	0.04	2	3ph3B	RB5	Rep, Mult	75,76
4	0.04	2	2wwaI	NUC	Rep, Mult	1,3,6,7,8,10,14,79,80
5	0.02	1	3rbpA	MG	Rep, Mult	39,46
6	0.02	1	1peoA	DCP	Rep, Mult	27,35,39,40
7	0.02	1	1izlM	CLA	Rep, Mult	16,20
8	0.02	1	3pyoX	MG	Rep, Mult	23,28
9	0.02	1	4dlmA	ZN	Rep, Mult	28,57
10	0.02	1	4fe1F	CLA	Rep, Mult	26,30
11	0.02	1	2bq1E	DGT	Rep, Mult	12,13,14,40,68
12	0.02	1	2gk1A	UUU	Rep, Mult	11,12,14
13	0.02	1	1onkB	AZI	Rep, Mult	81,82

	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	1ezrA	0.602	3.01	0.055	0.890	3.2.2.1	NA
2	0.060	2hg2A	0.593	3.51	0.075	0.963	1.2.1.21,1.2.1.22	NA
3	0.060	1yoeA	0.609	3.14	0.053	0.915	3.2.2.8	NA
4	0.060	3dk5A	0.547	3.39	0.082	0.878	2.3.1.157	NA
5	0.060	3ifh6	0.580	3.32	0.063	0.976	1.2.1.16	11
6	0.060	3b4wA	0.600	3.40	0.063	0.963	1.2.1.-	NA
7	0.060	3gvgA	0.581	2.90	0.145	0.878	5.3.1.1	NA
8	0.060	1xi3B	0.577	3.05	0.105	0.878	2.5.1.3	NA
9	0.060	1ky8A	0.588	3.42	0.125	0.976	1.2.1.9	NA
10	0.060	1c7sA	0.596	3.51	0.000	0.988	3.2.1.52	79
11	0.060	3ce6A	0.575	3.37	0.089	0.927	3.3.1.1	NA
12	0.060	1o01C	0.562	3.73	0.025	0.988	1.2.1.3	NA
13	0.060	2zkmX	0.585	3.50	0.037	0.927	3.1.4.11	NA
14	0.060	1wndA	0.579	3.60	0.100	0.939	1.2.1.19	17,20
15	0.060	3fz0B	0.581	3.18	0.068	0.890	3.2.2.1	NA
16	0.060	1js1X	0.578	3.25	0.158	0.915	2.1.3.9	NA
17	0.060	2masA	0.596	2.95	0.082	0.890	3.2.2.1	NA
18	0.060	3jz4A	0.580	3.30	0.013	0.976	1.2.1.16	73
19	0.060	1jwbB	0.595	3.20	0.089	0.963	2.7.7.-	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	0.09	0.619	3.01	0.04	0.96	3my7C	GO:0004022 GO:0006066 GO:0008152 GO:0008774 GO:0015976 GO:0016491 GO:0016620 GO:0046872 GO:0055114
1	0.07	0.564	3.71	0.02	0.99	4lihA	GO:0008152 GO:0016491 GO:0016620 GO:0055114
2	0.07	0.547	3.62	0.07	0.99	3pqaB	GO:0008152 GO:0008911 GO:0016491 GO:0016620 GO:0055114
3	0.07	0.568	3.71	0.07	0.96	4i1wA	GO:0000166 GO:0008152 GO:0016491 GO:0016620 GO:0055114
4	0.07	0.447	3.31	0.00	0.74	4nmkC	GO:0000166 GO:0008152 GO:0016491 GO:0016620 GO:0055114
5	0.07	0.573	3.48	0.06	0.98	4neaA	GO:0008152 GO:0008802 GO:0016491 GO:0016620 GO:0019285 GO:0046872 GO:0055114
6	0.07	0.549	3.87	0.07	0.96	3u4jA	GO:0008152 GO:0016491 GO:0016620 GO:0055114
7	0.07	0.553	3.33	0.04	0.95	1bi9D	GO:0001568 GO:0001758 GO:0001822 GO:0001889 GO:0001936 GO:0002138 GO:0003007 GO:0004028 GO:0004029 GO:0005737 GO:0005829 GO:0007494 GO:0008152 GO:0008284 GO:0008285 GO:0009855 GO:0009952 GO:0009954 GO:0010628 GO:0014032 GO:0016331 GO:0016491 GO:0016620 GO:0016918 GO:0021915 GO:0021983 GO:0030182 GO:0030324 GO:0030326 GO:0030900 GO:0030902 GO:0031016 GO:0031076 GO:0032355 GO:0033189 GO:0034097 GO:0035115 GO:0035799 GO:0042572 GO:0042573 GO:0042574 GO:0042904 GO:0043010 GO:0043065 GO:0048384 GO:0048471 GO:0048566 GO:0048738 GO:0055114 GO:0060324 GO:0071300
8	0.07	0.454	3.24	0.03	0.74	4qyjA	GO:0008152 GO:0016491 GO:0016620 GO:0055114
9	0.07	0.584	3.67	0.05	0.96	3rh9A	GO:0008152 GO:0009013 GO:0016491 GO:0016620 GO:0055114
10	0.07	0.573	3.63	0.05	0.96	4cazA	GO:0008152 GO:0008802 GO:0016491 GO:0016620 GO:0019145 GO:0019285 GO:0046872 GO:0047105 GO:0055114
11	0.07	0.554	3.37	0.06	0.95	3efvA	GO:0000166 GO:0004029 GO:0004777 GO:0008152 GO:0009013 GO:0016491 GO:0016620 GO:0055114
12	0.07	0.586	3.42	0.05	0.95	3lv1A	GO:0000166 GO:0004030 GO:0006081 GO:0008152 GO:0016491 GO:0016620 GO:0018477 GO:0018479 GO:0019596 GO:0055114
13	0.07	0.586	3.27	0.04	0.98	3hazA	GO:0000166 GO:0003842 GO:0004029 GO:0004657 GO:0006561 GO:0008152 GO:0016491 GO:0016620 GO:0055114
14	0.07	0.563	3.36	0.04	0.96	1t90A	GO:0004029 GO:0004491 GO:0008152 GO:0016491 GO:0016620 GO:0018478 GO:0019310 GO:0055114
15	0.07	0.569	3.44	0.06	0.96	4nm9B	GO:0000166 GO:0003677 GO:0003700 GO:0003842 GO:0004029 GO:0004657 GO:0006351 GO:0006355 GO:0006560 GO:0006561 GO:0008152 GO:0010133 GO:0016491 GO:0016620 GO:0055114
16	0.07	0.563	3.35	0.05	0.98	4dalB	GO:0000166 GO:0008152 GO:0016491 GO:0016620 GO:0055114
17	0.07	0.623	3.01	0.07	0.96	3k9dA	GO:0004029 GO:0008152 GO:0016491 GO:0016620 GO:0055114
18	0.07	0.558	3.44	0.04	0.96	4v37A	GO:0004030 GO:0006081 GO:0008152 GO:0008802 GO:0009507 GO:0009536 GO:0016491 GO:0016620 GO:0019285 GO:0055114

Consensus prediction of GO terms

Molecular Function	GO:0016620
GO-Score	0.31
Biological Processes	GO:0055114
GO-Score	0.31
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 Rv2960c

[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]