I-TASSER results

Input Sequence in FASTA format

>protein (75 residues)
MLGADQARAGGPARIWREHSMAAMKPRTGDGPLEATKEGRGIVMRVPLEGGGRLVVELTP
DEAAALGDELKGVTS

Predicted Secondary Structure

Sequence	20 40 60 \| \| \| MLGADQARAGGPARIWREHSMAAMKPRTGDGPLEATKEGRGIVMRVPLEGGGRLVVELTPDEAAALGDELKGVTS
Prediction	CCCCCCCCCCCCCCHHHHHHHHHCCCCCCCCCEEEEEHCCEEEEEEHCCCCCEEEEHCCHHHHHHHHHHHHHHHC
Conf.Score	998655556777543445554444788899976899859968999976899889999699999999999999869
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 \| \| \| MLGADQARAGGPARIWREHSMAAMKPRTGDGPLEATKEGRGIVMRVPLEGGGRLVVELTPDEAAALGDELKGVTS
Prediction	744154325444343246431331445447242422554431013023633130103035720540251045138
	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

                   |                   |                   |

Sec.Str
Seq

CCCCCCCCCCCCCCHHHHHHHHHCCCCCCCCCEEEEEHCCEEEEEEHCCCCCEEEEHCCHHHHHHHHHHHHHHHC
MLGADQARAGGPARIWREHSMAAMKPRTGDGPLEATKEGRGIVMRVPLEGGGRLVVELTPDEAAALGDELKGVTS

2qa1A

0.26

0.24

0.91

0.78

MUSTER

AAGFD--FPGTAAMEM----LADIKGVELQPRMIGETLPGGMVMVGPLPGG-RIIVCERGTPWHEVADAWKRLTG

2fblB1

0.16

0.12

0.75

0.74

dPPAS

-------------------RQGYLTTPTDSIELRLRQQGTEYFMTLKSEGGQEYEIQIDVTQFEMLWPATEGRRV

3prbA1

0.30

0.17

0.59

0.79

wdPPAS

---------RDPSKILSEFTKRGIKPIKG---LTITIDGPGKIVSIN---SGRVLVDFN----------------

2f7lA3

0.23

0.21

0.92

0.77

wMUSTER

DLKPGLMVEEIYKKILEVYSTSSVKAITIDG-VKIIGKDFWFLVRKPI----RIMAE-DENVANNLVNELKKIVE

3prbA1

0.30

0.17

0.57

0.75

wPPAS

----------RPSKILSEFTKRGIKPIKG---LTITIDGPGKIVSIN---SGRVLVDFN----------------

3prbA1

0.30

0.17

0.59

0.91

dPPAS2

---------RDPSKILSEFTKRGIKPIKG---LTITIDGPGKIVSIN---SGRVLVDFN----------------

3prbA1

0.30

0.17

0.59

0.84

PPAS

---------RDPSKILSEFTKRGIKPIKG---LTITIDGPGKIVSIN---SGRVLVDFN----------------

3prbA1

0.30

0.17

0.59

0.94

Env-PPAS

---------RDPSKILSEFTKRGIKPIKG---LTITIDGPGKIVSIN---SGRVLVDFN----------------

4k2xA

0.21

0.20

0.95

0.74

MUSTER

LLGID--FPGQDPHFAV--IAARFREELPHGPYGVMRDLRAWFAAFPLEPDVRATVAFFDAPEEDVRAALTEVAG

3ihsA

0.12

0.11

0.92

0.74

dPPAS

QVSLKNGLQARPAALFVQEANRF------HADIFIEKDGKTVNGISLAIGTGSITITTEGSDAEEALEALAAYVQ

(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=-2.52

Estimated TM-score = 0.42±0.14

Estimated RMSD = 8.7±4.6Å

Download Model 2

C-score=-2.58

Download Model 3

C-score=-3.56

Download Model 4

C-score=-3.24

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	2rkkA	0.543	2.29	0.014	0.707
2	2zkr6	0.521	3.23	0.031	0.840
3	2aleA	0.520	3.39	0.044	0.853
4	1ho8A1	0.517	3.40	0.056	0.840
5	2xzmU	0.516	3.17	0.048	0.813
6	3o85A	0.511	3.72	0.061	0.880
7	5ewrA	0.511	3.59	0.103	0.893
8	3iz5H	0.507	3.52	0.059	0.840
9	4hd1A	0.506	3.08	0.088	0.760
10	2aifA	0.498	3.23	0.063	0.827

(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	0.09	4	2byqB	EPJ	Rep, Mult	46,56
2	0.04	2	3c46A	2HP	Rep, Mult	20,24,25,26
3	0.04	2	2wtfB	CA	Rep, Mult	31,34,49
4	0.04	2	3wmoP	BCL	Rep, Mult	21,22
5	0.04	2	2xquB	CVM	Rep, Mult	9,13
6	0.04	2	2ql2B	NUC	Rep, Mult	62,65
7	0.02	1	2h10A	MA4	Rep, Mult	40,42,70
8	0.02	1	3klzD	FMT	Rep, Mult	21,23,25
9	0.02	1	3kxdA	CD	Rep, Mult	8,29,62
10	0.02	1	4rkuL	CLA	Rep, Mult	66,70
11	0.02	1	1z6kA	MG	Rep, Mult	38,61
12	0.02	1	1kmhB	TTX	Rep, Mult	23,28,30
13	0.02	1	4p0sF	NUC	Rep, Mult	8,65,69
14	0.02	1	1pieA	PO4	Rep, Mult	32,33,45,71
15	0.02	1	2zkrf	QNA	Rep, Mult	16,56,57,58

	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	2hj9D	0.448	4.04	0.042	0.827	2.7.13.3	NA
2	0.060	1e6yA	0.460	3.77	0.033	0.813	2.8.4.1	57,73
3	0.060	1rr8C	0.406	3.48	0.056	0.707	5.99.1.2	NA
4	0.060	3fwlA	0.465	4.15	0.070	0.907	2.4.1.129	NA
5	0.060	1fo4A	0.443	3.63	0.036	0.733	1.17.1.4	NA
6	0.060	1ohdA	0.342	4.52	0.076	0.720	3.1.3.16,3.1.3.48	33,42
7	0.060	2uv8G	0.495	3.28	0.052	0.773	2.3.1.86	NA
8	0.060	1sc7A	0.469	3.31	0.013	0.760	5.99.1.2	NA
9	0.060	3ig5A	0.458	3.71	0.031	0.787	6.3.2.2	34
10	0.060	1uwkA	0.457	3.44	0.135	0.800	4.2.1.49	NA
11	0.060	2gaiA	0.459	3.82	0.028	0.787	5.99.1.2	NA
12	0.060	8tlnE	0.466	3.31	0.089	0.747	3.4.24.27	NA
13	0.060	1pfuA	0.456	3.72	0.056	0.773	6.1.1.10	11
14	0.060	1a31A	0.327	5.14	0.041	0.747	5.99.1.2	NA
15	0.060	3b9jJ	0.439	3.62	0.036	0.733	1.17.1.4,1.17.3.2	31
16	0.060	2z02B	0.476	3.80	0.096	0.827	6.3.2.6	NA
17	0.060	2a2dA	0.498	2.93	0.083	0.773	2.7.1.157,2.7.1.-	NA
18	0.060	3fwmA	0.488	3.80	0.055	0.880	2.4.1.129,	NA
19	0.060	2gajB	0.460	3.81	0.028	0.787	5.99.1.2	27

(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	0.488	3.63	0.01	0.85	1pxwA	GO:0001682 GO:0003723 GO:0003735 GO:0004526 GO:0005622 GO:0005737 GO:0005840 GO:0006412 GO:0008033 GO:0019843 GO:0030529 GO:0042254 GO:0090501 GO:0090502
1	0.07	0.520	3.39	0.04	0.85	2aleA	GO:0000398 GO:0000451 GO:0000462 GO:0000470 GO:0003723 GO:0005634 GO:0005654 GO:0005681 GO:0005730 GO:0006364 GO:0006397 GO:0006412 GO:0008380 GO:0022625 GO:0030529 GO:0030621 GO:0031167 GO:0031428 GO:0032040 GO:0034511 GO:0042254 GO:0046540 GO:0071011
2	0.07	0.494	3.53	0.03	0.84	4adxF	GO:0001682 GO:0003723 GO:0003735 GO:0004526 GO:0005622 GO:0005737 GO:0005840 GO:0006412 GO:0008033 GO:0019843 GO:0030529 GO:0042254 GO:0090501 GO:0090502
3	0.07	0.511	3.59	0.10	0.89	5ewrA	GO:0003723 GO:0005730 GO:0030529 GO:0042254
4	0.07	0.508	3.28	0.05	0.81	4btsAU	GO:0003735 GO:0005622 GO:0005840 GO:0006412
5	0.07	0.488	3.85	0.06	0.89	2jnbA	GO:0000398 GO:0000470 GO:0001651 GO:0003723 GO:0005634 GO:0005654 GO:0005681 GO:0005730 GO:0006364 GO:0006397 GO:0006412 GO:0008380 GO:0022625 GO:0030490 GO:0030515 GO:0030529 GO:0030621 GO:0030622 GO:0031428 GO:0032040 GO:0034511 GO:0034512 GO:0042254 GO:0043234 GO:0044822 GO:0046540 GO:0051117 GO:0071011
6	0.07	0.498	3.23	0.06	0.83	2aifA	GO:0003723 GO:0005730 GO:0005840
7	0.07	0.444	3.82	0.09	0.84	4v8pBF	GO:0005840 GO:0030529 GO:0042254
8	0.07	0.478	3.64	0.04	0.84	3plaC	GO:0001682 GO:0003723 GO:0003735 GO:0004526 GO:0005622 GO:0005737 GO:0005840 GO:0006412 GO:0008033 GO:0019843 GO:0030529 GO:0042254 GO:0090501 GO:0090502
9	0.07	0.353	4.48	0.04	0.80	5dc3L8	GO:0000470 GO:0002181 GO:0003723 GO:0003735 GO:0005737 GO:0005840 GO:0006412 GO:0022625 GO:0030529 GO:0042254
10	0.07	0.511	3.45	0.11	0.87	5it7GG	GO:0030529 GO:0042254
11	0.07	0.513	3.50	0.06	0.87	3o85B	GO:0000398 GO:0000470 GO:0003723 GO:0005730 GO:0005840 GO:0006412 GO:0022625 GO:0030490 GO:0030529 GO:0031428 GO:0032040 GO:0042254 GO:0046540 GO:0071011
12	0.07	0.479	3.68	0.03	0.85	2fc3A	GO:0001682 GO:0003723 GO:0003735 GO:0004526 GO:0005622 GO:0005737 GO:0005840 GO:0006412 GO:0008033 GO:0019843 GO:0030529 GO:0042254 GO:0090501 GO:0090502
13	0.07	0.446	3.95	0.09	0.88	4v8mBx	GO:0000470 GO:0003723 GO:0003735 GO:0005840 GO:0006412 GO:0022625
14	0.07	0.476	3.82	0.11	0.84	2lbwA	GO:0000469 GO:0000470 GO:0003723 GO:0005634 GO:0005730 GO:0005732 GO:0006364 GO:0006412 GO:0022625 GO:0030515 GO:0030529 GO:0031118 GO:0031120 GO:0031429 GO:0034513 GO:0042254
15	0.07	0.439	4.10	0.08	0.84	5it9M	GO:0003735 GO:0005622 GO:0005840 GO:0006412 GO:0022627 GO:0030529
16	0.07	0.463	4.07	0.08	0.88	1xbiA	GO:0000470 GO:0001682 GO:0003723 GO:0003735 GO:0004526 GO:0005622 GO:0005737 GO:0005840 GO:0006412 GO:0008033 GO:0019843 GO:0022625 GO:0030529 GO:0042254 GO:0090501 GO:0090502
17	0.07	0.462	3.63	0.08	0.80	4kzxM	GO:0003735 GO:0005622 GO:0005840 GO:0006412 GO:0030529
18	0.07	0.466	3.70	0.09	0.84	5fj4C	GO:0001682 GO:0003723 GO:0003735 GO:0004526 GO:0005622 GO:0005737 GO:0005840 GO:0006412 GO:0008033 GO:0019843 GO:0030529 GO:0042254 GO:0090501 GO:0090502

Consensus prediction of GO terms

Molecular Function	GO:0003676	GO:0005198
GO-Score	0.48	0.37
Biological Processes	GO:0043043	GO:0034645	GO:0044267	GO:0022613	GO:0010467
GO-Score	0.48	0.48	0.48	0.48	0.48
Cellular Component	GO:1990904	GO:0044444	GO:0043232
GO-Score	0.48	0.37	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 Rv1211

[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]