I-TASSER results

I-TASSER results for job id Rv2468A

[Click on result.tar.bz2 to download the tarball file including all modelling results listed on this page]

Input Sequence in FASTA format

>protein (77 residues)
MEIHLFFVGIPLLLVVVLSVLIWSRKGPHPATYKLSEPWTHPPILWAATDEVVGSAHGGH
GHDASEFTVGGGASGTW

Predicted Secondary Structure

Sequence	20 40 60 \| \| \| MEIHLFFVGIPLLLVVVLSVLIWSRKGPHPATYKLSEPWTHPPILWAATDEVVGSAHGGHGHDASEFTVGGGASGTW
Prediction	CEEEEEEEHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCEEEHCCCCCCCCCCCCCCCCCCCCCCCCCEEHCC
Conf.Score	95899874778999999999864788999887799998888876787588887777777778888777788566569
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 \| \| \| MEIHLFFVGIPLLLVVVLSVLIWSRKGPHPATYKLSEPWTHPPILWAATDEVVGSAHGGHGHDASEFTVGGGASGTW
Prediction	54221132333333233112213346474355153756162411001234653544444445454544334234378
	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

CEEEEEEEHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCEEEHCCCCCCCCCCCCCCCCCCCCCCCCCEEHCC
MEIHLFFVGIPLLLVVVLSVLIWSRKGPHPATYKLSEPWTHPPILWAATDEVVGSAHGGHGHDASEFTVGGGASGTW

5kowA1

0.19

0.18

0.95

0.97

MUSTER

-ETLLADVRIVETLTAVVAEVRKTQLRFGAVPA--GDGF-FRLIVPAQGLSADRAAPTLDEKRCLHATAGGVHSPRW

2rmsB

0.18

0.14

0.79

1.34

dPPAS

----SSTWLSEAEMIALAGLLQMSQGEQTPNCVASSLPSTSCP-----DPVSVSEDPGPSGDQSCSGTDT-------

2l6wA

0.12

0.05

0.44

1.09

wdPPAS

FKVVVISAILALVVLTIISLIILIMLWQKKPRYE-------------------------------------------

2rmsB

0.19

0.14

0.74

0.97

wMUSTER

LS--------EAEMIALAGLLQMSQGEQTPNCVASSLPSTSCP-----DPVSVSEDPGPSGDQSCSGTDT-------

2n7qA

0.19

0.10

0.55

0.87

wPPAS

LELITLTVGFGILIFSLIVTYCINAK---------------ADVLFIAPREPGAVSY--------------------

2l6wA

0.12

0.05

0.44

1.66

dPPAS2

FKVVVISAILALVVLTIISLIILIMLWQKKPRYE-------------------------------------------

2rmsB

0.20

0.16

0.78

1.19

PPAS

SSTWL-----EAEMIALAGLLQMSQGEQTPNCVASSLPSTSCP-----DPVSVSEDPGPSGDQSCSGTDT-------

3fwzA1

0.13

0.10

0.81

0.82

Env-PPAS

ICNHALLVGYGRVGSLLGEKLLASDIPTSRTRVDELRERGV-RAVLGAANEEI--------------QLAHLECAKW

2rmsB

0.19

0.14

0.74

0.90

MUSTER

LS--------EAEMIALAGLLQMSQGEQTPNCVASSLPSTSCP-----DPVSVSEDPGPSGDQSCSGTDT-------

1s5li

0.21

0.10

0.49

1.00

dPPAS

METLKITVYIVVTFFVLLFVFGFLSGDPARNPKRKDLE---------------------------------------

(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=-3.20

Estimated TM-score = 0.36±0.12

Estimated RMSD = 10.4±4.6Å

Download Model 2

C-score=-3.48

Download Model 3

C-score=-3.91

Download Model 4

C-score=-3.67

Download Model 5

C-score=-4.17

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	2vpyC	0.510	4.08	0.105	0.857
2	4rd8A	0.503	4.24	0.055	0.948
3	1e6vB2	0.484	3.76	0.042	0.883
4	3wwxA	0.481	3.40	0.071	0.766
5	3l6wA	0.481	3.49	0.031	0.766
6	1z6tB	0.480	3.80	0.066	0.857
7	2zm9A	0.480	3.73	0.070	0.805
8	1e6yE	0.480	4.44	0.039	0.922
9	5djfA	0.479	3.81	0.134	0.818
10	3wrtA	0.479	3.68	0.057	0.805

(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	0.11	6	5d56E	78M	Rep, Mult	15,18,22
2	0.05	3	2nwxB	NA	Rep, Mult	43,74,75,76
3	0.05	3	1smyF	MG	Rep, Mult	13,14,77
4	0.05	3	1txgA	UUU	Rep, Mult	46,47,49,69,70
5	0.04	2	1e7cA	HLT	Rep, Mult	18,33,36
6	0.04	2	2vjoA	OXL	Rep, Mult	58,60,61,62
7	0.04	2	3tf1A	XE	Rep, Mult	14,17,18,21,44,45
8	0.02	1	2anuA	ZN	Rep, Mult	51,60
9	0.02	1	4pe1A	DCD	Rep, Mult	17,20
10	0.02	1	3rj8A	ZN	Rep, Mult	50,51
11	0.02	1	2vpyG	PCI	Rep, Mult	1,4,21,24
12	0.02	1	1aczA	GLC	Rep, Mult	39,77
13	0.02	1	2o011	CLA	Rep, Mult	36,39
14	0.02	1	1e6vB	UUU	Rep, Mult	43,44,45

	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	2boaA	0.463	3.34	0.030	0.779	3.4.17.-	NA
2	0.060	1e5mA	0.461	4.65	0.132	0.948	2.3.1.179	NA
3	0.060	1afwB	0.461	4.54	0.120	0.922	2.3.1.16	72
4	0.060	2wzxA	0.458	4.00	0.043	0.818	3.5.2.6	37,42
5	0.060	2qz6A	0.463	3.86	0.041	0.805	3.5.2.6	NA
6	0.060	1yj8A	0.469	3.75	0.083	0.766	1.1.1.8	NA
7	0.060	1txgA	0.477	3.67	0.057	0.766	1.1.1.94	76
8	0.060	1zg7A	0.462	3.42	0.045	0.792	3.4.17.2	NA
9	0.060	1pcaA	0.460	3.20	0.015	0.766	3.4.17.1	NA
10	0.060	2qflA	0.458	4.14	0.071	0.844	3.1.3.25	NA
11	0.060	1pytA	0.326	4.03	0.030	0.623	3.4.17.1	66
12	0.060	1ub7A	0.463	4.67	0.082	0.922	2.3.1.41	NA
13	0.060	1dd8A	0.455	4.74	0.078	0.948	2.3.1.41	NA
14	0.060	1wdkD	0.468	4.44	0.068	0.909	2.3.1.16	NA
15	0.060	2wefA	0.450	3.83	0.108	0.805	3.1.3.7	NA
16	0.060	3c20B	0.471	3.40	0.040	0.818	2.7.2.4	26
17	0.060	2dd4H	0.460	3.09	0.056	0.688	3.5.5.8	NA
18	0.060	3il5A	0.465	4.48	0.083	0.883	2.3.1.180	NA
19	0.060	2hs4A	0.474	3.82	0.054	0.792	6.3.5.3	19

(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	0.461	3.78	0.07	0.88	3sqgB	GO:0015948 GO:0016740 GO:0050524
1	0.07	0.384	4.08	0.03	0.73	1hzoA	GO:0008800 GO:0016787 GO:0030655 GO:0046677
2	0.07	0.334	4.60	0.03	0.73	5e2gA	GO:0008800 GO:0016787 GO:0017001 GO:0030288 GO:0046677
3	0.07	0.461	3.76	0.03	0.79	4gb7A	GO:0016054 GO:0016787 GO:0019875
4	0.07	0.480	4.44	0.04	0.92	1e6yE	GO:0015948 GO:0016740 GO:0050524
5	0.07	0.447	4.05	0.03	0.82	2zc7A	GO:0008800 GO:0016787 GO:0017001 GO:0030288 GO:0046677
6	0.07	0.471	3.58	0.03	0.78	1cefA	GO:0004180 GO:0005576 GO:0006508 GO:0008233 GO:0008360 GO:0009002 GO:0009252 GO:0016787 GO:0071555
7	0.07	0.476	3.73	0.07	0.81	5e2hA	GO:0008800 GO:0016787 GO:0017001 GO:0030288 GO:0046677
8	0.07	0.443	4.06	0.06	0.83	3s4xA	GO:0008800 GO:0016787 GO:0017001 GO:0030288 GO:0042597 GO:0046677
9	0.06	0.457	3.62	0.16	0.78	1ci8A	GO:0005737 GO:0016787
10	0.06	0.472	3.47	0.06	0.77	4y7pA	GO:0004180 GO:0006508
11	0.06	0.483	3.59	0.06	0.81	3ws1A	GO:0008800 GO:0016787 GO:0017001 GO:0030288 GO:0046677 GO:0046872
12	0.06	0.463	3.86	0.04	0.81	2qz6A	GO:0008800 GO:0016787 GO:0017001 GO:0030288 GO:0042597 GO:0046677
13	0.06	0.379	4.10	0.04	0.74	3o3vA	GO:0008800 GO:0016020 GO:0016021 GO:0016787 GO:0017001 GO:0030288 GO:0046677
14	0.06	0.369	4.26	0.03	0.70	1zkjA	GO:0008800 GO:0016787 GO:0017001 GO:0030288 GO:0046677
15	0.06	0.385	4.05	0.02	0.68	5evlA	GO:0008800 GO:0016787 GO:0017001 GO:0030288 GO:0046677
16	0.06	0.456	3.81	0.09	0.81	3hlfA	GO:0016740 GO:0016746 GO:0016787 GO:0017000 GO:0030639 GO:0050832
17	0.06	0.360	4.42	0.04	0.73	4gdnA	GO:0005886 GO:0016020 GO:0016021
18	0.06	0.451	3.82	0.07	0.81	5cgwA	GO:0008800 GO:0016787 GO:0017001 GO:0030288 GO:0046677

Consensus prediction of GO terms

Molecular Function	GO:0008800	GO:0050524	GO:0019875
GO-Score	0.13	0.13	0.07
Biological Processes	GO:0015948	GO:0046677	GO:0030655	GO:0016054
GO-Score	0.13	0.13	0.07	0.07
Cellular Component	GO:0030288
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.