I-TASSER results

Input Sequence in FASTA format

>protein (58 residues)
MTIDPDQIRAEIDALLASLPDPADAENGPSLAELEGIARRLSEAHEVLLAALESAEKG

Predicted Secondary Structure

Sequence	20 40 \| \| MTIDPDQIRAEIDALLASLPDPADAENGPSLAELEGIARRLSEAHEVLLAALESAEKG
Prediction	CCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHC
Conf.Score	9999899999999999969998888888875569999999999999999999998769
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 \| \| MTIDPDQIRAEIDALLASLPDPADAENGPSLAELEGIARRLSEAHEVLLAALESAEKG
Prediction	8755375035404511451453465775344440551154255124101412542678
	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

CCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHC
MTIDPDQIRAEIDALLASLPDPADAENGPSLAELEGIARRLSEAHEVLLAALESAEKG

2cfxA1

0.27

0.22

0.84

1.12

Env-PPAS

MKLD--QIDLNIIEELKK-------DSRLSMRELGRKIKLSPPSVTERVRQLESFGKQ

3f8mA1

0.20

0.19

0.97

1.10

Env-PPAS

--LKHQVVRAELDRMLDGMRIGDPFPAEREIAEQFEVRETVRQALRELLIDVERRGRT

4xwpA

0.17

1.00

0.62

MUSTER

VTVDQQEILNRANEVEAPMADPPTDVPITPCEAAKNAAQQLVLSADNMREYLAAGAKE

4pkiG3

0.11

0.10

0.98

0.65

dPPAS

-QPLGNKVEMEIVSMLEKNATLLKFGYHFTQQGPRLRASNAMMNNNDLVRKRRLADLT

1hh0A

0.20

0.16

0.79

0.69

wdPPAS

MDFNPSEVASQVTNYIQAI--------AAAGVGVLALAIGLSAAWKYAKRFL----KG

3zxqA1

0.21

0.19

0.91

0.85

wMUSTER

-----TGLRHRLDKVIDQLAIPALHTTVQYTGPLSVVTVLANHAEAVLREAVSNAVRN

1hh0A

0.20

0.16

0.79

0.84

wPPAS

MDFNPSEVASQVTNYIQAIAA--------AGVGVLALAIGLSAAWKYAKRFL----KG

2w83C

0.19

0.98

0.72

dPPAS2

-AMDPEFMGREVENLILENTQLLETKNALNKNDLIAKVDELTCEKDVLQGELEAVKQA

2w83C

0.20

0.19

0.97

0.84

PPAS

-AMDPEFMGREVENLILENTQLLETKNALN-NDLIAKVDELTCEKDVLQGELEAVKQA

3zxqA1

0.21

0.19

0.91

1.02

Env-PPAS

-----TGLRHRLDKVIDQLAIPALHTTVQYTGPLSVVTVLANHAEAVLREAVSNAVRH

(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=-2.24

Estimated TM-score = 0.45±0.15

Estimated RMSD = 7.5±4.3Å

Download Model 2

C-score=-2.72

Download Model 3

C-score=-3.71

Download Model 4

C-score=-4.87

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	4amsA1	0.749	2.09	0.086	1.000
2	1dofA	0.737	2.16	0.103	1.000
3	3t6gB	0.734	1.78	0.053	0.983
4	4amqA	0.725	2.06	0.069	1.000
5	3c8tA1	0.712	2.21	0.138	1.000
6	4l3iA	0.695	2.55	0.088	0.948
7	3c18A2	0.691	2.26	0.155	1.000
8	4oe8C	0.691	2.06	0.179	0.966
9	2yyjA	0.689	2.44	0.155	1.000
10	4iggA3	0.688	2.08	0.073	0.948

(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	0.11	82	3wmmW	CRT	Rep, Mult	38,41,44,45,48,51,52
2	0.11	81	4ub6X	CLA	Rep, Mult	37,39,40,41,43,44,46
3	0.08	51	4pj0h	CLA	Rep, Mult	44,47,48,51,52
4	0.07	49	3d5d2	MG	Rep, Mult	52,53,54,55,56,57
5	0.07	48	2fkwM	BCL	Rep, Mult	46,49,50,53,54,57
6	0.07	48	7insF	UNK	Rep, Mult	42,43,46,47
7	0.05	43	4n3eX	2AN	Rep, Mult	45,46,49
8	0.03	24	4i7zF	OZ2	Rep, Mult	37,38,41,42
9	0.01	11	2e75E	OPC	Rep, Mult	36,37,40,41
10	0.01	7	3gs2A	III	Rep, Mult	55,56,57,58
11	0.00	1	2wdrC	PCI	Rep, Mult	10,13,14,17
12	0.00	1	3op0A	NA	Rep, Mult	13,16,17,46

	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	1crkA	0.605	2.80	0.130	0.897	2.7.3.2	NA
2	0.060	2irpA	0.618	3.25	0.070	0.948	4.2.1.109	NA
3	0.060	2pnrF	0.588	2.78	0.035	0.966	2.7.11.2	NA
4	0.060	2i2xA	0.608	2.95	0.071	0.948	2.1.1.90	10
5	0.060	1dofA	0.737	2.16	0.103	1.000	4.3.2.2	NA
6	0.060	2ix6E	0.633	2.14	0.019	0.931	1.3.3.6	NA
7	0.060	2idxC	0.604	2.65	0.070	0.845	2.5.1.17	NA
8	0.060	2hvgA	0.430	3.09	0.111	0.862	4.3.2.2	33,35
9	0.060	1xmeA	0.606	3.00	0.105	0.983	1.9.3.1	40
10	0.060	2pg0A	0.615	2.42	0.077	0.897	1.3.99.3	25
11	0.060	1y8pA	0.608	2.59	0.036	0.966	2.7.11.2	46
12	0.060	2htnG	0.485	3.06	0.140	0.759	1.16.3.1	NA
13	0.060	1bucA	0.617	2.37	0.057	0.897	1.3.99.2	NA
14	0.060	1udyA	0.622	2.65	0.056	0.931	1.3.99.3	26
15	0.060	2fenD	0.654	2.37	0.155	1.000	5.5.1.2	NA
16	0.060	2jifA	0.606	2.50	0.057	0.914	1.3.99.-	NA
17	0.060	2ix6A	0.633	2.14	0.019	0.931	1.3.3.6	NA
18	0.060	1bucB	0.621	2.72	0.086	1.000	1.3.99.2	37,46,49
19	0.060	3ju5C	0.611	2.98	0.132	0.914	2.7.3.3	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	0.14	0.737	2.16	0.10	1.00	1dofA	GO:0003824 GO:0004018 GO:0006163 GO:0009152 GO:0016829 GO:0051262 GO:0070626
1	0.14	0.632	2.62	0.09	1.00	1yisA	GO:0003824 GO:0004018 GO:0006163 GO:0006164 GO:0006189 GO:0016829 GO:0044208 GO:0051262 GO:0070626
2	0.13	0.473	2.45	0.03	0.64	3rd8A	GO:0003824 GO:0004333 GO:0005737 GO:0006099 GO:0006106 GO:0016829 GO:0045239
3	0.13	0.390	3.03	0.12	0.74	1yfeA	GO:0003824 GO:0004333 GO:0005737 GO:0005829 GO:0006099 GO:0006106 GO:0006108 GO:0006979 GO:0008152 GO:0016829 GO:0045239 GO:0051262
4	0.13	0.428	3.27	0.08	0.76	4apbD	GO:0003824 GO:0004333 GO:0005576 GO:0005618 GO:0005737 GO:0005829 GO:0005886 GO:0006099 GO:0006106 GO:0006108 GO:0016829 GO:0040007 GO:0045239 GO:0051262
5	0.13	0.672	2.29	0.10	1.00	1re5D	GO:0003824 GO:0016853 GO:0019619 GO:0047472
6	0.12	0.558	3.14	0.10	0.97	2pfmA	GO:0003824 GO:0004018 GO:0006164 GO:0006189 GO:0009152 GO:0016829 GO:0044208 GO:0070626
7	0.12	0.446	3.04	0.06	0.76	2x75A	GO:0003824 GO:0004018 GO:0006164 GO:0006189 GO:0009152 GO:0016829 GO:0044208 GO:0070626
8	0.11	0.424	3.30	0.07	0.84	3gzhA	GO:0003824 GO:0004018 GO:0006164 GO:0006188 GO:0006189 GO:0009152 GO:0016829 GO:0044208 GO:0070626
9	0.11	0.492	2.35	0.10	0.67	1vdkA	GO:0003824 GO:0004333 GO:0005737 GO:0006099 GO:0006106 GO:0016829 GO:0045239
10	0.11	0.474	2.52	0.03	0.66	1yfmA	GO:0003824 GO:0004333 GO:0005737 GO:0005739 GO:0005759 GO:0005829 GO:0006099 GO:0006106 GO:0006108 GO:0016829 GO:0045239 GO:0051262
11	0.11	0.500	3.23	0.07	0.90	4efcA	GO:0000166 GO:0003824 GO:0004018 GO:0006163 GO:0006164 GO:0006188 GO:0006189 GO:0009152 GO:0016829 GO:0044208 GO:0046872 GO:0051262 GO:0070626
12	0.11	0.423	2.84	0.10	0.74	1jswB	GO:0003824 GO:0005829 GO:0006099 GO:0006106 GO:0006108 GO:0006531 GO:0008652 GO:0008797 GO:0016020 GO:0016829 GO:0051262
13	0.11	0.654	2.37	0.15	1.00	2fenD	GO:0003824 GO:0016853 GO:0019619 GO:0047472
14	0.10	0.405	2.90	0.06	0.71	3e04D	GO:0003824 GO:0004333 GO:0005737 GO:0005739 GO:0005759 GO:0005829 GO:0006099 GO:0006106 GO:0006108 GO:0016829 GO:0045239 GO:0048873 GO:0051262 GO:0070062
15	0.10	0.465	2.97	0.07	0.67	4flcB	GO:0003824 GO:0004018 GO:0005829 GO:0006164 GO:0006167 GO:0006189 GO:0009152 GO:0009168 GO:0016829 GO:0044208 GO:0051262 GO:0070626
16	0.10	0.712	2.21	0.14	1.00	3c8tA	GO:0003824 GO:0016853 GO:0047472
17	0.10	0.725	2.06	0.07	1.00	4amqA	GO:0019012
18	0.10	0.441	3.66	0.07	0.67	1tj7A	GO:0003824 GO:0004056 GO:0005737 GO:0005829 GO:0006526 GO:0008652 GO:0016829 GO:0042450 GO:0051262

Consensus prediction of GO terms

Molecular Function	GO:0016842	GO:0004333
GO-Score	0.52	0.35
Biological Processes	GO:0009117	GO:0072521	GO:0051262	GO:0006106	GO:0006099
GO-Score	0.52	0.52	0.44	0.35	0.35
Cellular Component	GO:0045239
GO-Score	0.35

(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 Rv1693

[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]