I-TASSER results

Input Sequence in FASTA format

>protein (80 residues)
MTNVGDQGVDAVFGVIYPPQVALVSFGKPAQRVCAVDGAIHVMTTVLATLPADHGCSDDH
RGALFFLSINELTRCAAVTG

Predicted Secondary Structure

Sequence	20 40 60 80 \| \| \| \| MTNVGDQGVDAVFGVIYPPQVALVSFGKPAQRVCAVDGAIHVMTTVLATLPADHGCSDDHRGALFFLSINELTRCAAVTG
Prediction	CCCCHCCCCCCCCCCCCCCCEEEEHCCCEEEEEEEHCCEEEEEEEEEEEEHCCCCEHCHHHHHHHHHHHHHHHHCCCCCC
Conf.Score	98543467654677778875366645765665788799899998899999757745486999999999999997656789
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 \| \| \| \| MTNVGDQGVDAVFGVIYPPQVALVSFGKPAQRVCAVDGAIHVMTTVLATLPADHGCSDDHRGALFFLSINELTRCAAVTG
Prediction	73141133344220112331000011343463112466413324303000110010103340140043025105526468
	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

CCCCHCCCCCCCCCCCCCCCEEEEHCCCEEEEEEEHCCEEEEEEEEEEEEHCCCCEHCHHHHHHHHHHHHHHHHCCCCCC
MTNVGDQGVDAVFGVIYPPQVALVSFGKPAQRVCAVDGAIHVMTTVLATLPADHGCSDDHRGALFFLSINELTRCAAVTG

3l60A

0.26

1.00

2.10

MUSTER

VSNFGALGVDDGVPVINHPEAAILGLGAIKPRPVVVGGEVVARPTMTLTCVFDHRVVDGAQVAQFMCELRDLIESPETLD

3l60A

0.26

1.00

5.03

dPPAS

VSNFGALGVDDGVPVINHPEAAILGLGAIKPRPVVVGGEVVARPTMTLTCVFDHRVVDGAQVAQFMCELRDLIESPETAL

3l60A

0.26

1.00

4.28

wdPPAS

VSNFGALGVDDGVPVINHPEAAILGLGAIKPRPVVVGGEVVARPTMTLTCVFDHRVVDGAQVAQFMCELRDLIESPELLD

3l60A

0.26

1.00

2.27

wMUSTER

VSNFGALGVDDGVPVINHPEAAILGLGAIKPRPVVVGGEVVARPTMTLTCVFDHRVVDGAQVAQFMCELRDLIESPETLD

3l60A

0.26

1.00

1.95

wPPAS

VSNFGALGVDDGVPVINHPEAAILGLGAIKPRPVVVGGEVVARPTMTLTCVFDHRVVDGAQVAQFMCELRDLIESPELLD

3l60A

0.26

1.00

6.09

dPPAS2

VSNFGALGVDDGVPVINHPEAAILGLGAIKPRPVVVGGEVVARPTMTLTCVFDHRVVDGAQVAQFMCELRDLIESPELLD

3l60A

0.26

1.00

2.19

PPAS

VSNFGALGVDDGVPVINHPEAAILGLGAIKPRPVVVGGEVVARPTMTLTCVFDHRVVDGAQVAQFMCELRDLIESPELLD

3l60A

0.26

1.00

2.01

Env-PPAS

VSNFGALGVDDGVPVINHPEAAILGLGAIKPRPVVVGGEVVARPTMTLTCVFDHRVVDGAQVAQFMCELRDLIESPELLD

1sczA

0.26

1.00

1.98

MUSTER

ITNGGVFGSLMSTPIINPPQSAILGMHAIKDRPMAVNGQVEILPMMYLALSYDHRLIDGRESVGFLVTIKELLEDPTRLL

1sczA

0.26

1.00

4.80

dPPAS

ITNGGVFGSLMSTPIINPPQSAILGMHAIKDRPMAVNGQVEILPMMYLALSYDHRLIDGRESVGFLVTIKELLEDPTRLL

(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=1.04

Estimated TM-score = 0.86±0.07

Estimated RMSD = 1.6±1.4Å

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	3l60A	0.956	0.72	0.262	1.000
2	1sczA	0.927	1.19	0.262	1.000
3	3maeA	0.922	1.21	0.237	1.000
4	4n72A	0.903	1.12	0.200	1.000
5	1dpbA	0.897	1.22	0.162	1.000
6	1b5sA	0.895	1.20	0.250	1.000
7	2ihwA	0.881	1.32	0.213	1.000
8	3rqcA	0.819	1.08	0.208	0.900
9	1q23B	0.677	2.31	0.087	0.863
10	3b8kA	0.671	2.54	0.230	0.925

(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	0.30	19	2ii5A	CO6	Rep, Mult	3,5,6,27,28,29
2	0.21	20	1q23K	FUA	Rep, Mult	2,12,14,16,18,23
3	0.08	7	3u9fK	CLM	Rep, Mult	54
4	0.07	4	2xr7A	MLC	Rep, Mult	51,58,59,60,61
5	0.01	1	1xl8B	MPD	Rep, Mult	48,50,66,69,70
6	0.01	1	3kziT	CLA	Rep, Mult	65,69

	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	1xl7A	0.523	2.67	0.100	0.750	2.3.1.137	49,62
2	0.060	2ii4A	0.888	1.26	0.213	1.000	2.3.1.168	15,18
3	0.060	11asA	0.516	3.71	0.042	0.900	6.3.1.1	NA
4	0.060	3errA	0.532	3.79	0.104	0.938	6.1.1.11	58
5	0.060	1b5sA	0.895	1.20	0.250	1.000	2.3.1.12	2
6	0.060	1b5sE	0.895	1.20	0.250	1.000	2.3.1.12	2,16,22,50
7	0.060	2debA	0.529	2.48	0.083	0.750	2.3.1.21	NA
8	0.060	2eabA	0.538	3.48	0.063	0.850	3.2.1.63	NA
9	0.060	1xl7B	0.553	2.70	0.079	0.762	2.3.1.137	NA
10	0.060	2zr3B	0.533	3.46	0.080	0.900	6.1.1.11	24,52
11	0.060	3g98A	0.564	2.63	0.046	0.762	6.1.1.7	52
12	0.060	1serB	0.526	3.58	0.076	0.912	6.1.1.11	58
13	0.060	1ciaA	0.668	2.28	0.116	0.863	2.3.1.28	NA
14	0.060	1sczA	0.927	1.19	0.262	1.000	2.3.1.61	2
15	0.060	1q6xA	0.521	2.66	0.082	0.738	2.3.1.6	NA
16	0.060	1q23B	0.677	2.31	0.087	0.863	2.3.1.28	NA
17	0.060	1ua4A	0.532	2.31	0.102	0.725	2.7.1.147	NA
18	0.060	1b76A	0.518	3.44	0.055	0.863	6.1.1.14	NA
19	0.060	2ddmB	0.517	3.59	0.060	0.825	2.7.1.35	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	0.26	0.956	0.72	0.26	1.00	3l60A	GO:0004739 GO:0005618 GO:0005886 GO:0008152 GO:0016740 GO:0016746 GO:0043754
1	0.24	0.924	1.18	0.24	1.00	3maeB	GO:0008152 GO:0016740 GO:0016746
2	0.22	0.896	1.08	0.20	0.99	4n72C	GO:0004742 GO:0006090 GO:0006096 GO:0008152 GO:0016740 GO:0016746 GO:0045254
3	0.22	0.895	1.20	0.25	1.00	1b5sA	GO:0004742 GO:0006096 GO:0008152 GO:0016740 GO:0016746
4	0.21	0.927	1.19	0.26	1.00	1sczA	GO:0004149 GO:0005829 GO:0006099 GO:0008152 GO:0016740 GO:0016746 GO:0031405 GO:0033512 GO:0045252
5	0.21	0.881	1.32	0.21	1.00	2ihwA	GO:0005739 GO:0005759 GO:0008152 GO:0016740 GO:0016746 GO:0031625 GO:0042645 GO:0043754
6	0.21	0.897	1.22	0.16	1.00	1dpbA	GO:0004742 GO:0006096 GO:0008152 GO:0016740 GO:0016746 GO:0045254
7	0.16	0.801	1.23	0.21	0.90	3rqcC	GO:0008152 GO:0016740 GO:0016746 GO:0042802
8	0.08	0.671	2.54	0.23	0.93	3b8kA	GO:0004742 GO:0005739 GO:0005759 GO:0005967 GO:0005975 GO:0006006 GO:0006086 GO:0006090 GO:0006099 GO:0008152 GO:0010510 GO:0016740 GO:0016746 GO:0030431 GO:0034604 GO:0043209 GO:0045254 GO:0046487
9	0.08	0.652	1.64	0.16	0.76	2xt6A	GO:0003824 GO:0004149 GO:0004591 GO:0006099 GO:0008152 GO:0008683 GO:0016491 GO:0016624 GO:0016740 GO:0016746 GO:0016829 GO:0016831 GO:0030976 GO:0046872 GO:0050439 GO:0055114
10	0.06	0.383	3.62	0.09	0.64	2z0sA	GO:0000178 GO:0003676 GO:0003723 GO:0005737 GO:0006401 GO:0008143
11	0.06	0.371	3.86	0.05	0.68	5dmnA	GO:0006974 GO:0008168 GO:0008652 GO:0008898 GO:0009086 GO:0016740 GO:0032259 GO:0033477 GO:0046872
12	0.06	0.370	4.26	0.13	0.78	4knsA	GO:0005507 GO:0006807 GO:0046872 GO:0050421 GO:0055114
13	0.06	0.387	4.05	0.04	0.64	3sdsB	GO:0004585 GO:0005737 GO:0005739 GO:0005759 GO:0005829 GO:0006520 GO:0006526 GO:0006591 GO:0008652 GO:0016597 GO:0016740 GO:0016743 GO:0042450
14	0.06	0.381	4.37	0.07	0.74	4ayiD	GO:0016021
15	0.06	0.352	3.97	0.00	0.64	1yz4A	GO:0004721 GO:0004725 GO:0005737 GO:0005886 GO:0006470 GO:0007179 GO:0008138 GO:0016020 GO:0016311 GO:0016787 GO:0016791 GO:0035335 GO:0042127 GO:0046330
16	0.06	0.394	3.78	0.07	0.72	2f6kA	GO:0016787 GO:0046872
17	0.06	0.371	4.30	0.09	0.61	5ahwB	GO:0000166 GO:0006950
18	0.06	0.348	4.50	0.03	0.60	1p32A	GO:0000122 GO:0001849 GO:0002250 GO:0002376 GO:0003714 GO:0003729 GO:0005080 GO:0005540 GO:0005576 GO:0005615 GO:0005634 GO:0005730 GO:0005737 GO:0005739 GO:0005759 GO:0005829 GO:0005886 GO:0006351 GO:0006355 GO:0006397 GO:0006915 GO:0006955 GO:0006958 GO:0007597 GO:0008134 GO:0008380 GO:0009986 GO:0014065 GO:0016020 GO:0016032 GO:0030449 GO:0030984 GO:0031690 GO:0032689 GO:0032695 GO:0039534 GO:0039536 GO:0042254 GO:0042256 GO:0043065 GO:0045087 GO:0045785 GO:0048025 GO:0050687 GO:0051897 GO:0070131 GO:0090023 GO:0097177 GO:1900026 GO:1901165 GO:2000510

Consensus prediction of GO terms

Molecular Function	GO:0016624	GO:0004738	GO:0016751	GO:0005504	GO:0050662	GO:0004742
GO-Score	0.52	0.52	0.42	0.42	0.42	0.39
Biological Processes	GO:0009060	GO:0019474	GO:0006096
GO-Score	0.42	0.42	0.39
Cellular Component	GO:0030312	GO:1990234	GO:0045240	GO:0016020
GO-Score	0.52	0.42	0.42	0.39

(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 Rv1734c

[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]