I-TASSER results

Input Sequence in FASTA format

>protein (60 residues)
MWRHLWLMQPQRRYPRGSGTTRTARRDAGVAPLYGVSRVTVLASTTATTAPPVKSFPDLL

Predicted Secondary Structure

Sequence	20 40 60 \| \| \| MWRHLWLMQPQRRYPRGSGTTRTARRDAGVAPLYGVSRVTVLASTTATTAPPVKSFPDLL
Prediction	CHHHHHHCCCCCCCCCCCCCCEEHCCCCCCCCCCCCEEEEEEEHCCCCCCCCCCCCCCCC
Conf.Score	845566548665689999863444444787765576678998755567899877786559
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 \| \| \| MWRHLWLMQPQRRYPRGSGTTRTARRDAGVAPLYGVSRVTVLASTTATTAPPVKSFPDLL
Prediction	734321323355524645444443445332231343431332243444434425524747
	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

CHHHHHHCCCCCCCCCCCCCCEEHCCCCCCCCCCCCEEEEEEEHCCCCCCCCCCCCCCCC
MWRHLWLMQPQRRYPRGSGTTRTARRDAGVAPLYGVSRVTVLASTTATTAPPVKSFPDLL

1kanA

0.30

0.27

0.90

0.88

MUSTER

KWRNIRVQGPTTFLP--SLTVQVAM--AG-AMLIGLHH-RICYTTSASVLTEAVKQSDLP

1kvpA1

0.27

0.25

0.92

0.85

dPPAS

-----PVTTKFRDVPNLSGTPLIFRDNKGRTIKTGVDAGFLVAQNTAQAANGERAIPSNL

5a4gA1

0.25

0.18

0.73

0.82

wdPPAS

YWRD---MVPGQRFDK-----------PGKSPYMDMPLIPVYEEENADGAA-VRIDGRV-

5a4gA1

0.25

0.18

0.73

0.77

wMUSTER

YWRD---MVPGQRFDK-----------PGKSPYMDMPLIPVYEEENADGAA-VRIDGRV-

4p6cA2

0.45

0.37

0.82

0.68

wPPAS

LADRLALMVVNNNSA--NQTAFTVSIEAGVT---GVSRVTIAANPQAK--PPV--FP--L

1tn9A

0.25

0.20

0.80

0.78

dPPAS2

---------EKRRDNRGRKTGESQRKD-GIDSF-G-EPQFVYSWKLVATDRVPAGKRDAI

5a4gA1

0.26

0.18

0.72

0.84

PPAS

YWRD---MVPGQRFDK-----------PGKSPYMDMPLIPVYEEENADGA--VRIDGRV-

1gjsA

0.24

0.23

0.97

0.89

Env-PPAS

M-KAIFVLNAQHDEAVDANSLAEAKVLA-NRELYGVSDYYKNLINNAKTVEGVKALIDEI

3j6vJ

0.21

0.20

0.97

0.86

MUSTER

LGRRLW--QGSKNFSVSSSRSNIAKNDGFLLSMKWVQFSNLHVDVPKDLTKPTITIPDTL

1pftA

0.17

0.13

0.80

0.82

dPPAS

------MVNKQKVCPACESAELIYDPERGVCAKCGY----VIEENIIDMGPEWRAFDA--

(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=-2.61

Estimated TM-score = 0.41±0.14

Estimated RMSD = 8.4±4.5Å

Download Model 2

C-score=-3.43

Download Model 3

C-score=-3.65

Download Model 4

C-score=-4.41

Download Model 5

C-score=-3.16

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	5a1sA	0.473	3.56	0.069	0.950
2	2yikA	0.460	3.78	0.085	0.917
3	3bjuA2	0.460	3.57	0.132	0.817
4	5elnA	0.451	3.77	0.058	0.817
5	4acqA2	0.451	3.70	0.083	0.883
6	3v39A2	0.451	3.88	0.094	0.817
7	3x17B	0.450	3.86	0.036	0.883
8	2bcfA	0.448	3.54	0.054	0.883
9	3n4fA	0.445	3.15	0.055	0.850
10	3jroA	0.443	3.80	0.019	0.833

(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	9	1t85A	UUU	Rep, Mult	19,20,30,40,41,44,45,46,49,50
2	0.06	6	2z97A	7HE	Rep, Mult	15,21,22,23,25,27
3	0.05	5	2qbnA	HEM	Rep, Mult	16,22,30,39,54,55
4	0.04	4	3q2wA	MAN	Rep, Mult	30,40
5	0.04	4	1nx0B	III	Rep, Mult	1,5
6	0.03	3	1dz4B	HEM	Rep, Mult	20,21,24,28,39,51
7	0.03	3	2zawA	6HE	Rep, Mult	15,16,23,32,33,34,39
8	0.02	2	1usyF	HIS	Rep, Mult	5,9
9	0.02	2	1iwjA	HEM	Rep, Mult	4,5,16,17,20,29,30,39,41
10	0.02	2	2gcpA	MG	Rep, Mult	3,14
11	0.01	1	1mpwA	TMH	Rep, Mult	25,29,40
12	0.01	1	1le9A	NUC	Rep, Mult	12,13,16,17
13	0.01	1	3p6oA	ETG	Rep, Mult	14,15,41,46
14	0.01	1	3fxrA	SO4	Rep, Mult	1,2,3,54,56
15	0.01	1	1w77A	CU	Rep, Mult	48,58
16	0.01	1	1vkxA	NUC	Rep, Mult	12,13
17	0.01	1	1akdA	CAM	Rep, Mult	9,36,39
18	0.01	1	2nxfA	ZN	Rep, Mult	4,8

	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	2a4kB	0.399	3.81	0.091	0.867	1.1.1.100	NA
2	0.060	1w6jA	0.429	3.45	0.133	0.900	5.4.99.7	NA
3	0.060	1px8A	0.378	4.32	0.035	0.917	3.2.1.37	NA
4	0.060	1zd1A	0.426	3.76	0.036	0.750	2.8.2.-	NA
5	0.060	2a4kA	0.431	3.69	0.127	0.850	1.1.1.100	NA
6	0.060	3eolA	0.397	3.75	0.019	0.850	4.1.3.1	NA
7	0.060	1e5eA	0.434	3.69	0.073	0.850	4.4.1.11	NA
8	0.060	2cb1A	0.433	4.00	0.089	0.883	4.2.99.10	NA
9	0.060	1bsgA	0.428	3.97	0.073	0.900	3.5.2.6	NA
10	0.060	1e6vA	0.426	3.92	0.018	0.900	2.8.4.1	NA
11	0.060	1f89A	0.432	3.61	0.058	0.833	3.5.-.-	NA
12	0.060	1xkyA	0.418	3.92	0.037	0.867	4.2.1.52	NA
13	0.060	3cogD	0.437	3.67	0.036	0.850	4.4.1.1	NA
14	0.060	3eolB	0.386	3.87	0.018	0.883	4.1.3.1	NA
15	0.060	1ut9A	0.430	3.81	0.036	0.900	3.2.1.4	NA
16	0.060	4matA	0.426	3.40	0.093	0.783	3.4.11.18	NA
17	0.060	1cb7B	0.431	3.81	0.019	0.850	5.4.99.1	NA
18	0.060	1fo2A	0.425	3.95	0.033	0.867	3.2.1.113	NA
19	0.060	1y4iA	0.434	3.89	0.073	0.867	4.4.1.11	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	0.07	0.446	3.55	0.17	0.78	4up8A	GO:0000049 GO:0000166 GO:0003676 GO:0004812 GO:0004824 GO:0005524 GO:0005737 GO:0006418 GO:0006430
1	0.06	0.342	3.88	0.05	0.75	4dpgB	GO:0000049 GO:0000166 GO:0003676 GO:0004812 GO:0004824 GO:0005524 GO:0005576 GO:0005634 GO:0005737 GO:0005739 GO:0005759 GO:0005829 GO:0005886 GO:0006412 GO:0006418 GO:0006430 GO:0008033 GO:0015630 GO:0015966 GO:0016020 GO:0016032 GO:0016597 GO:0016874 GO:0017101 GO:0046872
2	0.06	0.375	3.81	0.04	0.78	4up7A	GO:0000049 GO:0000166 GO:0003676 GO:0004812 GO:0004824 GO:0005524 GO:0005737 GO:0006418 GO:0006430
3	0.06	0.402	3.69	0.06	0.75	1asyA	GO:0000166 GO:0003676 GO:0003723 GO:0004812 GO:0004815 GO:0005524 GO:0005634 GO:0005737 GO:0006412 GO:0006418 GO:0006422 GO:0016874
4	0.06	0.460	3.78	0.09	0.92	2yikA	GO:0000272 GO:0003824 GO:0004553 GO:0005975 GO:0016787 GO:0046872
5	0.06	0.378	3.42	0.02	0.75	3kfuC	GO:0000166 GO:0003676 GO:0004812 GO:0004815 GO:0005524 GO:0005737 GO:0006412 GO:0006418 GO:0006422 GO:0016874 GO:0050560
6	0.06	0.332	4.20	0.04	0.77	4pe5C	GO:0004872 GO:0004970 GO:0004972 GO:0005102 GO:0005216 GO:0005234 GO:0005886 GO:0006810 GO:0006811 GO:0007611 GO:0010942 GO:0014069 GO:0014070 GO:0014075 GO:0016020 GO:0016021 GO:0016594 GO:0016595 GO:0017146 GO:0019899 GO:0022843 GO:0030054 GO:0032590 GO:0034220 GO:0034765 GO:0035235 GO:0035254 GO:0042165 GO:0043025 GO:0043083 GO:0043195 GO:0043197 GO:0044307 GO:0045202 GO:0045211 GO:0046982 GO:0046983 GO:0048511 GO:0051262 GO:0051592 GO:0060076 GO:0060992 GO:0071287 GO:2000463
7	0.06	0.391	3.75	0.09	0.82	3a5yA	GO:0000166 GO:0004812 GO:0004824 GO:0005524 GO:0005737 GO:0005829 GO:0006418 GO:0006430 GO:0016874 GO:0016880 GO:0043687 GO:0052868 GO:0071915 GO:0072581
8	0.06	0.382	3.74	0.05	0.80	1b8aA	GO:0000166 GO:0003676 GO:0004812 GO:0004815 GO:0005524 GO:0005737 GO:0006412 GO:0006418 GO:0006422 GO:0016874 GO:0046872
9	0.06	0.342	4.25	0.03	0.80	1ia7A	GO:0000272 GO:0003824 GO:0004553 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0046872
10	0.06	0.373	3.80	0.07	0.82	3i7fA	GO:0000166 GO:0004812 GO:0004815 GO:0005524 GO:0005737 GO:0006418 GO:0006422
11	0.06	0.372	3.72	0.13	0.78	5a9zAI	GO:0003723 GO:0005622 GO:0005840 GO:0006412 GO:0019843 GO:0030529 GO:0042254 GO:0070180
12	0.06	0.362	3.81	0.05	0.72	2cxfA	GO:0005737 GO:0007015 GO:0007275 GO:0007399 GO:0012505 GO:0016020 GO:0030027 GO:0030054 GO:0030154 GO:0030175 GO:0030335 GO:0030424 GO:0030425 GO:0030426 GO:0042995 GO:0043025 GO:0043204 GO:0045773 GO:0050770 GO:0050771 GO:0050772 GO:0071437 GO:0090316 GO:2000114
13	0.06	0.382	4.49	0.10	0.87	4dodA	GO:0000272 GO:0003824 GO:0004553 GO:0005975 GO:0008152 GO:0008810 GO:0016787 GO:0016798 GO:0030245 GO:0030246 GO:0030248 GO:0046872
14	0.06	0.366	3.36	0.04	0.75	1n9wA	GO:0000166 GO:0003676 GO:0004812 GO:0004815 GO:0005524 GO:0005737 GO:0006412 GO:0006418 GO:0006422 GO:0016874 GO:0050560
15	0.06	0.360	3.83	0.06	0.77	3m4qB	GO:0000166 GO:0003676 GO:0004812 GO:0004816 GO:0005524 GO:0005737 GO:0006418 GO:0006421
16	0.06	0.351	3.39	0.05	0.65	4piaA	GO:0004040 GO:0016020 GO:0016021
17	0.06	0.334	4.52	0.04	0.85	5fxkA	GO:0004872 GO:0004970 GO:0004972 GO:0005102 GO:0005216 GO:0005234 GO:0005886 GO:0006810 GO:0006811 GO:0007611 GO:0010942 GO:0014069 GO:0014070 GO:0014075 GO:0016020 GO:0016021 GO:0016594 GO:0016595 GO:0017146 GO:0019899 GO:0022843 GO:0030054 GO:0032590 GO:0034220 GO:0034765 GO:0035235 GO:0035254 GO:0042165 GO:0043025 GO:0043083 GO:0043195 GO:0043197 GO:0044307 GO:0045202 GO:0045211 GO:0046982 GO:0046983 GO:0048511 GO:0051262 GO:0051592 GO:0060076 GO:0060992 GO:0071287 GO:2000463
18	0.06	0.366	4.32	0.07	0.83	4cj1A	GO:0000272 GO:0003824 GO:0004553 GO:0005975 GO:0008152 GO:0008810 GO:0016787 GO:0016798 GO:0030245

Consensus prediction of GO terms

Molecular Function	GO:0032559	GO:0035639	GO:0032550	GO:0016876	GO:0003723
GO-Score	0.47	0.47	0.47	0.47	0.36
Biological Processes	GO:0043039	GO:0006412
GO-Score	0.47	0.47
Cellular Component	GO:0044424
GO-Score	0.47

(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 Rv2307D

[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]