I-TASSER results

Input Sequence in FASTA format

>protein (75 residues)
MIAGVDQALAATGQASQRAAGASGGVTVGVGVGTEQRNLSVVAPSQFTFSSRSPDFVDET
AGQSWCAILGLNQFH

Predicted Secondary Structure

Sequence	20 40 60 \| \| \| MIAGVDQALAATGQASQRAAGASGGVTVGVGVGTEQRNLSVVAPSQFTFSSRSPDFVDETAGQSWCAILGLNQFH
Prediction	CCCCHHHHHHHHHHHHHHHHCCCCCCEEEEHCCCCCEEEEEHCCCEEEHCCCCCCCCCCCCCCHHHHHHCCCCCC
Conf.Score	988677888877777777656778858997566654556776565577757898866556884545666786569
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 \| \| \| MIAGVDQALAATGQASQRAAGASGGVTVGVGVGTEQRNLSVVAPSQFTFSSRSPDFVDETAGQSWCAILGLNQFH
Prediction	743424522333353454344353323212223354441322234414145543522464344310001434638
	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

CCCCHHHHHHHHHHHHHHHHCCCCCCEEEEHCCCCCEEEEEHCCCEEEHCCCCCCCCCCCCCCHHHHHHCCCCCC
MIAGVDQALAATGQASQRAAGASGGVTVGVGVGTEQRNLSVVAPSQFTFSSRSPDFVDETAGQSWCAILGLNQFH

3dqqA1

0.24

0.23

0.93

0.78

MUSTER

MLKGVDDFTGATDIASFLVEN---GMPTVQINDVPTGTQPEGCDAVISLKTRSP--AQEAIKQVWLKKQGCQQVY

4py5A1

0.07

0.92

0.73

dPPAS

MKLSSSEKEKLLKKLKALGAKEKPPEHAQYRLRLNDAILTVYKSGSVVYGGKGREKLKELVAETVLSDT------

1jdiA1

0.21

0.19

0.89

0.67

wdPPAS

MLEDLKRQVLEANLALPKHTLTWGNVSAVD-----ERGVFVIKPSGVDYSIMTADVVSIETGE---VVEGAKKTH

3dqqA1

0.25

0.23

0.92

0.73

wMUSTER

MLKGVDDFTGATDIASFLVEN---GMPTVQINDVPTGTQPEGCD-VISLKTRSP--AQEAIKQVWLKKQGCQQVY

1kslA1

0.36

0.21

0.59

0.60

wPPAS

---GLDKFIAQQLGVSRAIAGRGNRVTV----G------EIV---------RNAAFLLPEHGN-------LAQ--

3dqqA1

0.23

0.21

0.93

0.81

dPPAS2

LKIGVDDFTGATDIASFLVE---NGMPTVQINDVPTGTQPEGCDAVISLKTRSP--AQEAIKQVWLKKQGCQQVY

3dqqA1

0.23

0.21

0.92

0.80

PPAS

LKIGVDDFTGATDIASFLVEN---GMPTVQINDVPTGTQPEGCD-VISLKTRSP--AQEAIKQVWLKKQGCQQVY

1vioA1

0.13

0.09

0.71

1.00

Env-PPAS

LR--LDKFIAENVGLTRSQATRQSAVKIGEIVKSGSV---QISQEEIYFEDELLTWIE-----------------

4rslA1

0.20

0.16

0.79

0.64

MUSTER

MISSSKEGIENLRRKYQTLLDA--------GIGLEKTNVWLESEDEIL--AKAPNFTEQVKG--WKGLFCT----

3dqqA1

0.21

0.20

0.95

0.71

dPPAS

LKIGVDDFTGATDIASFLVE---NGMPTVQINDVPTGTQPEGCDAVISLKTRSCP-AQEAIKQVWLKKQGCQQVY

(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=-3.00

Estimated TM-score = 0.38±0.13

Estimated RMSD = 9.9±4.6Å

Download Model 2

C-score=-3.61

Download Model 3

C-score=-3.57

Download Model 4

C-score=-3.56

Download Model 5

C-score=-4.19

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	1e6yA	0.516	3.12	0.068	0.773
2	1ysdB	0.515	3.81	0.044	0.880
3	1tjfB	0.510	3.79	0.083	0.813
4	4jkvA	0.505	3.42	0.061	0.813
5	2p02A	0.501	3.89	0.060	0.880
6	3dh1A	0.501	3.73	0.083	0.853
7	3nd0A	0.498	3.21	0.095	0.800
8	4qr8A	0.497	3.58	0.101	0.813
9	2nx8A	0.497	3.61	0.097	0.853
10	4av3A	0.497	3.17	0.080	0.787

(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	0.15	5	3pfdD	FDA	Rep, Mult	15,28,44
2	0.06	2	1qhoA	MAL	Rep, Mult	14,15,16,19,50,51
3	0.06	2	2vl1D	III	Rep, Mult	54,55,58
4	0.06	2	3sqgA	M43	Rep, Mult	60,63,66,73
5	0.06	2	1rz9A	QNA	Rep, Mult	9,10,13,14,17,65,66
6	0.06	2	3q79A	3CX	Rep, Mult	19,48
7	0.03	1	4bntD	36E	Rep, Mult	5,9
8	0.03	1	3sqgD	M43	Rep, Mult	2,3,8,63,66

	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	1ox7B	0.512	3.82	0.059	0.880	3.5.4.1	40
2	0.060	1e6yA	0.516	3.12	0.068	0.773	2.8.4.1	41
3	0.060	1cdgA	0.479	4.02	0.041	0.880	2.4.1.19	NA
4	0.060	1d7fA	0.475	4.06	0.027	0.880	2.4.1.19	NA
5	0.060	1ea0A	0.472	4.11	0.082	0.920	1.4.1.13	NA
6	0.060	1a76A	0.471	3.89	0.045	0.827	3.1.-.-	NA
7	0.060	3nxkA	0.471	4.22	0.099	0.867	3.5.1.1	42
8	0.060	1cgtA	0.471	4.05	0.027	0.880	2.4.1.19	NA
9	0.060	1smkA	0.442	3.97	0.042	0.867	1.1.1.37	39
10	0.060	1ffuB	0.473	3.41	0.018	0.733	1.2.99.2	NA
11	0.060	1yfeA	0.473	4.20	0.097	0.880	4.2.1.2	NA
12	0.060	1hlpA	0.414	4.05	0.076	0.853	1.1.1.37	NA
13	0.060	2ewdA	0.444	4.08	0.014	0.880	1.1.1.27	NA
14	0.060	2hj2B	0.501	3.90	0.060	0.880	2.5.1.6	25,58
15	0.060	1agxA	0.478	4.42	0.082	0.880	3.5.1.38	NA
16	0.060	1ciuA	0.455	4.05	0.014	0.893	2.4.1.19	NA
17	0.060	2vdcA	0.472	4.11	0.082	0.920	1.4.1.13	NA
18	0.060	2vdcF	0.465	4.29	0.082	0.933	1.4.1.13	NA
19	0.060	1civA	0.473	3.97	0.132	0.907	1.1.1.82	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	0.486	3.53	0.12	0.81	2a8nB	GO:0002100 GO:0003824 GO:0008033 GO:0008251 GO:0008270 GO:0016787 GO:0046872 GO:0052717
1	0.07	0.412	4.41	0.04	0.80	1n9wA	GO:0000166 GO:0003676 GO:0004812 GO:0004815 GO:0005524 GO:0005737 GO:0006412 GO:0006418 GO:0006422 GO:0016874 GO:0050560
2	0.07	0.512	3.82	0.06	0.88	1ox7B	GO:0003824 GO:0004131 GO:0008270 GO:0008655 GO:0009451 GO:0016787 GO:0019858 GO:0044206 GO:0046087 GO:0046872
3	0.07	0.490	3.72	0.09	0.85	2b3jC	GO:0002100 GO:0003824 GO:0008033 GO:0008251 GO:0008270 GO:0016787 GO:0046872 GO:0052717
4	0.07	0.476	3.39	0.07	0.79	3sqgA	GO:0015948 GO:0016740 GO:0046872 GO:0050524
5	0.07	0.379	4.46	0.05	0.76	4n6hA	GO:0000060 GO:0004871 GO:0004930 GO:0004985 GO:0005506 GO:0005737 GO:0005886 GO:0005887 GO:0006955 GO:0007165 GO:0007186 GO:0007187 GO:0007193 GO:0007200 GO:0007218 GO:0007268 GO:0008344 GO:0009055 GO:0010629 GO:0016020 GO:0016021 GO:0019233 GO:0020037 GO:0022900 GO:0031226 GO:0031982 GO:0032460 GO:0032590 GO:0032793 GO:0033138 GO:0038003 GO:0038046 GO:0042597 GO:0042755 GO:0042923 GO:0043005 GO:0043679 GO:0045121 GO:0045211 GO:0046872 GO:0051881 GO:0051924 GO:0051930 GO:0055114 GO:0071363 GO:0071456 GO:0097237
6	0.07	0.458	4.33	0.07	0.85	2g84A	GO:0003824 GO:0008270 GO:0016787 GO:0046872
7	0.07	0.433	4.51	0.07	0.85	4g3mA	GO:0003824 GO:0005829 GO:0008152 GO:0008270 GO:0008703 GO:0008835 GO:0009231 GO:0009451 GO:0016491 GO:0016787 GO:0046872 GO:0050661 GO:0055114
8	0.07	0.473	4.17	0.10	0.85	1wwrC	GO:0002100 GO:0003824 GO:0008033 GO:0008251 GO:0008270 GO:0016787 GO:0019239 GO:0046872 GO:0052717
9	0.07	0.462	3.98	0.11	0.84	2g6vB	GO:0000166 GO:0003824 GO:0008270 GO:0008703 GO:0008835 GO:0009231 GO:0016491 GO:0016787 GO:0046872 GO:0050661 GO:0055114
10	0.07	0.497	3.61	0.10	0.85	2nx8A	GO:0002100 GO:0003824 GO:0008033 GO:0008251 GO:0008270 GO:0016787 GO:0046872 GO:0052717
11	0.07	0.340	2.72	0.05	0.51	4ntjA	GO:0001609 GO:0001621 GO:0001973 GO:0004871 GO:0004930 GO:0005085 GO:0005506 GO:0005622 GO:0005739 GO:0005886 GO:0005887 GO:0005901 GO:0006930 GO:0007165 GO:0007186 GO:0007188 GO:0007193 GO:0007596 GO:0007599 GO:0008347 GO:0009055 GO:0009897 GO:0009925 GO:0009986 GO:0010700 GO:0016020 GO:0016021 GO:0020037 GO:0022900 GO:0030030 GO:0030168 GO:0031224 GO:0035589 GO:0042597 GO:0043270 GO:0043491 GO:0043547 GO:0045028 GO:0045596 GO:0046872 GO:0051924 GO:0055114 GO:0070527 GO:0070588 GO:0071318 GO:0071407 GO:0071805 GO:1904139
12	0.07	0.458	4.40	0.09	0.84	1wkqA	GO:0003824 GO:0006144 GO:0006147 GO:0008270 GO:0008892 GO:0009451 GO:0016787 GO:0019239 GO:0046872
13	0.07	0.460	3.89	0.09	0.84	3zpcA	GO:0003824 GO:0008270 GO:0008703 GO:0008835 GO:0009231 GO:0016491 GO:0016787 GO:0046872 GO:0050661 GO:0055114
14	0.07	0.486	3.62	0.11	0.84	1z3aA	GO:0002100 GO:0003824 GO:0008033 GO:0008251 GO:0008270 GO:0016787 GO:0046872 GO:0052717
15	0.07	0.482	3.20	0.10	0.77	1e6vA	GO:0015948 GO:0016740 GO:0046872 GO:0050524
16	0.07	0.416	4.07	0.03	0.72	4z34A	GO:0000187 GO:0001965 GO:0004871 GO:0004930 GO:0005506 GO:0005543 GO:0005737 GO:0005768 GO:0005886 GO:0005887 GO:0007165 GO:0007186 GO:0007193 GO:0007202 GO:0007204 GO:0007420 GO:0008289 GO:0008360 GO:0009055 GO:0009986 GO:0010942 GO:0010977 GO:0014003 GO:0016020 GO:0016021 GO:0020037 GO:0021549 GO:0021554 GO:0022008 GO:0022038 GO:0022900 GO:0030139 GO:0030165 GO:0030818 GO:0032060 GO:0035025 GO:0035727 GO:0042552 GO:0042597 GO:0043005 GO:0043025 GO:0043065 GO:0043123 GO:0043197 GO:0043198 GO:0043410 GO:0046872 GO:0051482 GO:0051496 GO:0055114 GO:0060326 GO:0060999 GO:0070915 GO:0071453 GO:0071673 GO:1904566
17	0.07	0.442	4.38	0.12	0.83	1vq2A	GO:0003824 GO:0004132 GO:0006220 GO:0008152 GO:0008270 GO:0009165 GO:0016787 GO:0046872
18	0.07	0.454	3.94	0.11	0.85	2hxvA	GO:0000166 GO:0003824 GO:0008270 GO:0008703 GO:0008835 GO:0009231 GO:0009451 GO:0016491 GO:0016787 GO:0019239 GO:0046872 GO:0055114

Consensus prediction of GO terms

Molecular Function	GO:0046914
GO-Score	0.37
Biological Processes	GO:0002100	GO:0019858	GO:0046087	GO:0044206	GO:0006422	GO:0015948
GO-Score	0.13	0.07	0.07	0.07	0.07	0.07
Cellular Component	GO:0005737
GO-Score	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 Rv2660c

[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]