I-TASSER results

Input Sequence in FASTA format

>protein (60 residues)
MGRGRAKAKQTKVARELKYSSPQTDFQRLQRELSGTGTDRLDGDGPSDDDSWNDEDDWRR

Predicted Secondary Structure

Sequence	20 40 60 \| \| \| MGRGRAKAKQTKVARELKYSSPQTDFQRLQRELSGTGTDRLDGDGPSDDDSWNDEDDWRR
Prediction	CCHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCC
Conf.Score	975899999999999975679998899999999689999998888877788877655689
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 \| \| \| MGRGRAKAKQTKVARELKYSSPQTDFQRLQRELSGTGTDRLDGDGPSDDDSWNDEDDWRR
Prediction	875445435444304514243473425304641545568556655546446366456268
	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

CCHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCC
MGRGRAKAKQTKVARELKYSSPQTDFQRLQRELSGTGTDRLDGDGPSDDDSWNDEDDWRR

2m4gA

0.22

1.00

MUSTER

RGLTDEEYDEFKKRRESRYSIDDADREREEELLERDEEEAIFGDGFGLKATRRSRKAERA

2e5uA

0.25

0.17

0.67

1.09

dPPAS

IDVLRAKAAKERAERRLQSQQDDIDFKRAELALKRAMNRL--------------------

5fu7D

0.31

0.17

0.53

1.07

wdPPAS

----------TEIARSLKIFAQVTSMQDVMQEFATNGYASDD------------------

2m4gA

0.22

1.00

1.08

wMUSTER

RGLTDEEYDEFKKRRESRYSIDDADREREEELLERDEEEAIFGDGFGLKATRRSRKAERA

2kw3A

0.27

0.23

0.85

0.88

wPPAS

-GRGTSKAVQNKVEGILQF----SDNDKLYLYLQ---PSGPTTGDKSSEPSTLSNEEYM-

2kruA

0.17

0.12

0.70

1.76

dPPAS2

FVRKKVRKNTDNYAREIGEPTADV-FRKAKEHLGGLEHHHHHH-----------------

2e5uA

0.25

0.17

0.67

1.07

PPAS

IDVLRAKAAKERAERRLQSQQDDIDFKRAELALKRAMNRL--------------------

3v2hA1

0.15

1.00

1.05

Env-PPAS

TGSGIGLAIARTLAKALNGFGAPDEIRTVTDEVAGLSSGTVPADTKPSEIADAVADRFGG

3iz5D3

0.17

0.15

0.90

0.97

MUSTER

MA--RIKARKEKLDSKRTKLSP--EEAAKVKAAGKAWYKTMISDSDYAE--FDNFSKWLG

4wojA2

0.12

0.10

0.83

1.09

dPPAS

--AAAMQELLQQTSLLSKIDNRDEDREKILRELSKDSSKIPQQKTVQTLAYN--------

(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=-2.90

Estimated TM-score = 0.38±0.13

Estimated RMSD = 9.1±4.6Å

Download Model 2

C-score=-3.26

Download Model 3

C-score=-3.64

Download Model 4

C-score=-3.73

Download Model 5

C-score=-4.14

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	4or2A2	0.617	2.78	0.052	0.883
2	2q0jA	0.597	2.98	0.089	0.917
3	3e97A	0.594	2.95	0.057	0.833
4	3c17B	0.590	2.91	0.088	0.950
5	4gdtA	0.585	3.25	0.069	0.967
6	4kjsA	0.584	2.99	0.069	0.967
7	4q65A	0.584	3.01	0.051	0.983
8	5cvrA	0.581	3.42	0.086	0.950
9	1zt2B	0.579	3.07	0.070	0.917
10	4l9mA2	0.578	3.32	0.070	0.883

(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	0.10	5	3wmoJ	BCL	Rep, Mult	10,13,17
2	0.10	5	3bk9C	TRP	Rep, Mult	5,8
3	0.08	4	3h45O	PO4	Rep, Mult	11,14
4	0.08	4	3v09A	UNK	Rep, Mult	14,26
5	0.04	2	4n67A	MG	Rep, Mult	2,4,5
6	0.02	1	1l5yA	BF2	Rep, Mult	9,12
7	0.02	1	3mnnG	MML	Rep, Mult	13,16,17
8	0.02	1	3rsyA	SO4	Rep, Mult	2,3,4,47,54
9	0.02	1	1mx1E	SIA	Rep, Mult	24,25
10	0.02	1	2ebaE	FAD	Rep, Mult	8,32,33

	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	2zalA	0.481	2.35	0.089	0.733	3.5.1.1	6
2	0.060	1vywA	0.520	3.27	0.077	0.867	2.7.11.22,2.7.1.37	18,23
3	0.060	1ampA	0.461	3.38	0.018	0.917	3.4.11.10	NA
4	0.060	3gb0A	0.563	2.74	0.021	0.800	3.4.11.-	NA
5	0.060	1f8iA	0.538	2.21	0.056	0.767	4.1.3.1	20
6	0.060	1siqA	0.555	3.23	0.140	0.883	1.3.99.7	32
7	0.060	1seoD	0.415	3.55	0.057	0.800	3.4.19.5	NA
8	0.060	2ewaA	0.527	3.52	0.056	0.883	2.7.11.24,2.7.1.37	18,20
9	0.060	1jn9D	0.423	2.95	0.020	0.750	3.4.19.5,3.5.1.1	NA
10	0.060	1ia8A	0.537	3.37	0.075	0.867	2.7.11.1	18
11	0.060	3lm0A	0.540	3.48	0.056	0.900	2.7.11.1	NA
12	0.060	1cb7B	0.535	2.70	0.061	0.817	5.4.99.1	NA
13	0.060	1e1tA	0.418	3.87	0.069	0.967	6.1.1.6	NA
14	0.060	2r8qA	0.561	2.58	0.057	0.883	3.1.4.17	29
15	0.060	3eolA	0.524	1.97	0.038	0.717	4.1.3.1	NA
16	0.060	3ii9C	0.552	3.38	0.105	0.900	1.3.99.7	NA
17	0.060	1ua2A	0.533	3.55	0.093	0.900	2.7.11.22,2.7.11.23	18
18	0.060	2g9xC	0.520	3.34	0.077	0.867	2.7.11.22,2.7.1.37	18,23
19	0.060	2biyA	0.535	3.45	0.111	0.900	2.7.11.1	18

(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	0.411	2.17	0.05	0.60	4or2B	GO:0000186 GO:0000187 GO:0004871 GO:0004930 GO:0005506 GO:0005634 GO:0005886 GO:0005887 GO:0007165 GO:0007186 GO:0007205 GO:0007216 GO:0007268 GO:0007626 GO:0008066 GO:0009055 GO:0014069 GO:0016020 GO:0016021 GO:0019233 GO:0020037 GO:0022900 GO:0030425 GO:0038037 GO:0038038 GO:0038042 GO:0042597 GO:0043005 GO:0043408 GO:0046872 GO:0051482 GO:0051930 GO:0051966 GO:0055114 GO:0071257
1	0.07	0.606	2.98	0.05	0.87	3e97A	GO:0003677 GO:0006351 GO:0006355
2	0.07	0.552	3.48	0.05	0.88	2oz6A	GO:0000166 GO:0003677 GO:0003700 GO:0005622 GO:0006351 GO:0006355 GO:0009405 GO:0030552 GO:0043902
3	0.07	0.522	3.16	0.07	0.88	3iwzD	GO:0003677 GO:0003700 GO:0003824 GO:0005622 GO:0005737 GO:0006351 GO:0006355 GO:0008152 GO:0009405 GO:0035438 GO:0046983
4	0.07	0.455	2.90	0.03	0.70	5cgcA	GO:0003796 GO:0003824 GO:0004871 GO:0004930 GO:0005737 GO:0005886 GO:0005887 GO:0007165 GO:0007186 GO:0007205 GO:0007206 GO:0007216 GO:0007268 GO:0007612 GO:0007626 GO:0008066 GO:0008152 GO:0009253 GO:0014069 GO:0016020 GO:0016021 GO:0016787 GO:0016798 GO:0016998 GO:0019076 GO:0019835 GO:0030430 GO:0042742 GO:0043005 GO:0048169 GO:0050890 GO:0051966 GO:0070062
5	0.07	0.462	4.05	0.02	0.88	2q42A	GO:0004416 GO:0005506 GO:0005739 GO:0008270 GO:0016787 GO:0019243 GO:0046872
6	0.07	0.597	2.98	0.09	0.92	2q0jA	GO:0044550
7	0.07	0.458	4.25	0.05	0.88	1adoA	GO:0003824 GO:0004332 GO:0005737 GO:0006096 GO:0016829 GO:0031430 GO:0031674 GO:0051289
8	0.07	0.367	3.81	0.08	0.80	3adrA	GO:0008270 GO:0046872
9	0.07	0.458	3.42	0.04	0.87	3gh4A	GO:0004553 GO:0004563 GO:0005975
10	0.07	0.415	3.90	0.00	0.85	2zo4A	GO:0046872
11	0.07	0.399	4.62	0.05	0.83	4d02A	GO:0005506 GO:0005737 GO:0009055 GO:0010181 GO:0016491 GO:0016661 GO:0016966 GO:0042802 GO:0046210 GO:0046872 GO:0051289 GO:0055114 GO:0071731
12	0.07	0.386	4.07	0.07	0.85	3a4yA	GO:0003723 GO:0004518 GO:0004519 GO:0005737 GO:0006364 GO:0016787 GO:0046872 GO:0090305
13	0.07	0.411	4.08	0.06	0.72	4ev0D	GO:0000166 GO:0003677 GO:0003700 GO:0006351 GO:0006355 GO:0010628 GO:0030552 GO:0042803 GO:0043565 GO:0044212 GO:0045893
14	0.07	0.452	3.31	0.04	0.82	1xfbA	GO:0003824 GO:0004332 GO:0005739 GO:0005829 GO:0005856 GO:0006000 GO:0006094 GO:0006096 GO:0008092 GO:0016829 GO:0030388 GO:0030855 GO:0061621 GO:0070062
15	0.07	0.460	4.25	0.05	0.88	1fbaA	GO:0003824 GO:0004332 GO:0005829 GO:0006096 GO:0007095 GO:0007498 GO:0016829 GO:0030018 GO:0031430
16	0.07	0.404	3.40	0.00	0.65	2qj3B	GO:0003824 GO:0004314 GO:0005835 GO:0006629 GO:0006631 GO:0006633 GO:0008152 GO:0016740 GO:0016746
17	0.07	0.395	2.67	0.04	0.53	1l0oA	GO:0000166 GO:0004672 GO:0004674 GO:0005524 GO:0006468 GO:0010468 GO:0016301 GO:0016310 GO:0016740 GO:0016989 GO:0030435 GO:0030436 GO:0045892
18	0.07	0.442	3.92	0.05	0.85	2q0aA	GO:0000166 GO:0005216 GO:0005222 GO:0005244 GO:0005248 GO:0005249 GO:0005267 GO:0005272 GO:0005886 GO:0005887 GO:0006810 GO:0006811 GO:0006813 GO:0006814 GO:0016020 GO:0016021 GO:0030552 GO:0034765 GO:0035725 GO:0042391 GO:0042802 GO:0055085 GO:0060078 GO:0071320 GO:0071321 GO:0071805

Consensus prediction of GO terms

Molecular Function	GO:0003676
GO-Score	0.37
Biological Processes	GO:0010468	GO:2000112	GO:0006351	GO:1903506
GO-Score	0.37	0.37	0.37	0.37
Cellular Component	GO:0014069	GO:0005737	GO:0030425	GO:0042597	GO:0038038	GO:0005634	GO:0070062	GO:0030430
GO-Score	0.14	0.13	0.07	0.07	0.07	0.07	0.07	0.07

(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 Rv0810c

[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]