I-TASSER results

I-TASSER results for job id Rv2438A

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

Input Sequence in FASTA format

>protein (92 residues)
MARTGHVQYRRGVGRRVTDGGVVSAGGNAHEPVLVGGVKVHRPFIVAQRRQNARITRRVS
TLDTVESPALLADGGIDRRGDATDWAAADPGP

Predicted Secondary Structure

Sequence	20 40 60 80 \| \| \| \| MARTGHVQYRRGVGRRVTDGGVVSAGGNAHEPVLVGGVKVHRPFIVAQRRQNARITRRVSTLDTVESPALLADGGIDRRGDATDWAAADPGP
Prediction	CCCCCCEEEEHCCCCEHCCCCEEHCCCCCCCCEEEHCEEEHCCEHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Conf.Score	98767668875676555588578668887887677556765454456677777888754566777885333457877677654444578999
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 \| \| \| \| MARTGHVQYRRGVGRRVTDGGVVSAGGNAHEPVLVGGVKVHRPFIVAQRRQNARITRRVSTLDTVESPALLADGGIDRRGDATDWAAADPGP
Prediction	74544434244424442454232334453333211232434322121444662513541542542643232353315544534514455668
	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                  80

                   |                   |                   |                   |

Sec.Str
Seq

CCCCCCEEEEHCCCCEHCCCCEEHCCCCCCCCEEEHCEEEHCCEHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
MARTGHVQYRRGVGRRVTDGGVVSAGGNAHEPVLVGGVKVHRPFIVAQRRQNARITRRVSTLDTVESPALLADGGIDRRGDATDWAAADPGP

3i4lA1

0.28

0.25

0.89

1.34

MUSTER

LARAGRVVTLGSDYRSVSVIGAVSPGGDFSEPVVQNTLRVVKVFWLDADLARRRHFPAINWLTSY---SLYVD-------AVKDWWHKNIDP

3i4lA

0.28

0.25

0.89

1.34

MUSTER

LARAGRVVTLGSDYRSVSVIGAVSPGGDFSEPVVQNTLRVVKVFWLDADLARRRHFPAINWLTSY---SLYVD-------AVKDWWHKNIDP

3a5cA

0.23

0.99

1.16

MUSTER

LARAGKVITLGGEEGAVTIVGAVSPGGDMSEPVTQSTLRIVGAFWLDASLAFRRHFPAINWNGSYSLFTSALDPWYRENVA-EDYPEQLVGP

3hxjA2

0.21

0.18

0.87

0.70

dPPAS

INTDGTEKWRFKTKKAIYATPIVSEDGT----IYVGSLYAINP--------DGTEKWRFKTNDAITSAASIGKDGTIYFGSDKVYAINPDGT

2zmzB

0.35

0.28

0.80

0.68

wdPPAS

-AAPESEVYK---GRRI--GRPAHEHGGGYE-VFVDGVQLH----VMRNADGSWIS--VSHYDPVPTPRAAARAAVDEQG-----APLLPFP

2zmzB

0.31

0.26

0.84

0.72

wMUSTER

APESFDEVYK---GRRIQ-GRPAHEHGGGYE-VFVDGVQLH---VM--RNADGSWISVVSHYDPVPTPRAAARAAVDEQG-----APLLPFP

2zmzB

0.39

0.28

0.72

0.59

wPPAS

----A-EVYK---GRRI--GRPAHEHGGGYE-VFVDGVQLH---VM----RNA-IS--VSHYDPVPTPRAAARAAVDEQG-----APLLPFP

3hxjA2

0.24

0.20

0.80

0.72

dPPAS2

INTDGTEKWRFKTKKAIYATPIVSEDGT----IYVGNLYAINP--------DGTEKWRFKTNDAITSAASIGKDGINPDGYAGYWT------

2zmzB

0.33

0.27

0.83

0.71

PPAS

APESFDEVYK---GRRI-QGRPAHEHGGGYE-VFVDGVQLH----VMRNADGSWIS--VSHYDPVPTPRAAARAAVDEQG-----APLLPFP

2zmzB

0.32

0.27

0.84

0.75

Env-PPAS

APESFDEVYK---GRRIQ-GRPAHEHGGGYE-VFVDGVQLH----VMRNADGSWIS-VVSHYDPVPTPRAAARAAVDEQG-----APLLPFP

(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=-2.36

Estimated TM-score = 0.44±0.14

Estimated RMSD = 8.8±4.6Å

Download Model 2

C-score=-4.16

Download Model 3

C-score=-3.99

Download Model 4

C-score=-4.73

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	1t1eA	0.512	3.99	0.059	0.870
2	4kg7A	0.507	3.77	0.092	0.859
3	1wmfA	0.506	3.72	0.057	0.859
4	1r64A	0.505	3.34	0.095	0.804
5	4j94A	0.500	3.79	0.057	0.859
6	1p8jA1	0.497	3.71	0.092	0.837
7	4tr2A1	0.495	3.48	0.060	0.804
8	3gt3A	0.490	4.05	0.078	0.870
9	3edyA	0.490	3.61	0.034	0.826
10	2p4eA1	0.490	4.01	0.080	0.848

(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	0.22	7	3fu1A	ZN	Rep, Mult	73,77
2	0.09	3	3edyA	CA	Rep, Mult	76,80,81,82,84
3	0.09	3	1hn4B	MJI	Rep, Mult	67,70
4	0.03	1	2pkcA	NA	Rep, Mult	31,32,33,34,38
5	0.03	1	4xniA	78M	Rep, Mult	69,76
6	0.03	1	2f2hA	XTG	Rep, Mult	62,63

	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	1hkgA	0.454	4.43	0.057	0.870	2.7.1.1	2
2	0.060	3cqyA	0.462	4.20	0.066	0.848	2.7.1.-	16,80
3	0.060	1thmA	0.452	4.42	0.044	0.870	3.4.21.66	67
4	0.060	1maaD	0.415	4.44	0.068	0.793	3.1.1.7	NA
5	0.060	1b41A	0.408	4.39	0.082	0.783	3.1.1.7	NA
6	0.060	153lA	0.468	3.51	0.042	0.761	3.2.1.17	44
7	0.060	1r64A	0.505	3.34	0.095	0.804	3.4.21.61	NA
8	0.060	1ah2A	0.462	4.34	0.066	0.880	3.4.21.-	NA
9	0.060	1x15A	0.472	3.98	0.044	0.826	1.6.1.2	NA
10	0.060	1jjfA	0.467	4.02	0.122	0.815	3.2.1.8	NA
11	0.060	2p4eA	0.483	4.34	0.088	0.902	3.4.21.-	NA
12	0.060	3f7mA	0.474	4.33	0.080	0.859	3.4.21.-	NA
13	0.060	3f7oA	0.477	3.92	0.044	0.859	3.4.21.-	NA
14	0.060	1qj4A	0.451	4.44	0.046	0.848	4.1.2.37	NA
15	0.060	1qgeE	0.288	4.66	0.033	0.576	3.1.1.3	60
16	0.060	1s2nA	0.487	4.22	0.057	0.870	3.4.21.-	NA
17	0.060	3edyA	0.490	3.61	0.034	0.826	3.4.14.9	NA
18	0.060	1wmdA	0.459	4.33	0.069	0.837	3.4.21.-	NA
19	0.060	1u6zB	0.466	4.08	0.026	0.826	3.6.1.11	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	0.15	0.477	3.92	0.04	0.86	3f7oA	GO:0004252 GO:0006508 GO:0008233 GO:0008236 GO:0016787 GO:0046872
1	0.12	0.395	4.34	0.04	0.75	2b6nA	GO:0004252 GO:0006508 GO:0008233 GO:0008236 GO:0016787 GO:0046872
2	0.07	0.383	4.88	0.07	0.78	1v6cB	GO:0004252 GO:0006508 GO:0008233 GO:0046872
3	0.07	0.459	4.33	0.07	0.84	1wmdA	GO:0004252 GO:0006508 GO:0008233 GO:0046872
4	0.07	0.467	3.96	0.05	0.83	1tecE	GO:0004252 GO:0005576 GO:0006508 GO:0008233 GO:0008236 GO:0016787 GO:0046872
5	0.07	0.481	4.27	0.05	0.90	3zxyA	GO:0004252 GO:0006508
6	0.07	0.434	4.42	0.04	0.82	3wivC	GO:0004252 GO:0005576 GO:0006508 GO:0008233 GO:0008236 GO:0016787 GO:0042802
7	0.07	0.399	4.29	0.05	0.77	2gkoA	GO:0004252 GO:0006508 GO:0008233 GO:0008236 GO:0016787 GO:0046872
8	0.07	0.397	4.52	0.02	0.78	4tr2B	GO:0004252 GO:0006508 GO:0008233 GO:0008236 GO:0016787 GO:0046872
9	0.07	0.472	4.18	0.02	0.85	4mzdA	GO:0004252 GO:0005576 GO:0005618 GO:0006508 GO:0008233 GO:0008236 GO:0016787
10	0.07	0.401	4.42	0.10	0.78	4kb5A	GO:0004252 GO:0006508 GO:0016020 GO:0016021
11	0.07	0.482	4.13	0.09	0.90	4hvlA	GO:0004252 GO:0006508 GO:0016020 GO:0016021 GO:0046872
12	0.07	0.394	4.83	0.07	0.84	3bpsA	GO:0001822 GO:0001889 GO:0001920 GO:0002092 GO:0004252 GO:0005576 GO:0005615 GO:0005737 GO:0005764 GO:0005768 GO:0005769 GO:0005770 GO:0005783 GO:0005791 GO:0005794 GO:0005886 GO:0006508 GO:0006629 GO:0006641 GO:0006644 GO:0006915 GO:0007041 GO:0008202 GO:0008203 GO:0008233 GO:0008236 GO:0009267 GO:0009986 GO:0010469 GO:0010989 GO:0016485 GO:0016540 GO:0016787 GO:0019871 GO:0022008 GO:0030134 GO:0030169 GO:0030182 GO:0030547 GO:0031232 GO:0032799 GO:0032802 GO:0032803 GO:0032805 GO:0032869 GO:0034185 GO:0034189 GO:0034190 GO:0042157 GO:0042632 GO:0043523 GO:0043525 GO:0043621 GO:0044822 GO:0048471 GO:0050750 GO:0070326 GO:1990666 GO:1990667 GO:2000272 GO:2000650
13	0.07	0.396	4.44	0.09	0.76	2x8jD	GO:0004252 GO:0006508 GO:0008233 GO:0008236 GO:0016787 GO:0046872
14	0.07	0.512	3.99	0.06	0.87	1t1eA	GO:0004252 GO:0006508 GO:0008236 GO:0046872
15	0.07	0.308	5.07	0.06	0.66	3eifA	GO:0004252 GO:0005618 GO:0006508 GO:0008233 GO:0008236 GO:0016020 GO:0016787
16	0.06	0.447	4.34	0.03	0.84	3d43B	GO:0004252 GO:0006508 GO:0008233 GO:0008236 GO:0016787 GO:0046872
17	0.06	0.383	4.77	0.08	0.79	1lw6E	GO:0004252 GO:0005576 GO:0006508 GO:0008233 GO:0008236 GO:0016787 GO:0030435 GO:0042730 GO:0046872
18	0.06	0.380	5.19	0.06	0.84	2o6lB	GO:0001972 GO:0005783 GO:0005789 GO:0006629 GO:0008152 GO:0008202 GO:0008209 GO:0009813 GO:0015020 GO:0016020 GO:0016021 GO:0016740 GO:0016757 GO:0016758 GO:0031090 GO:0043231 GO:0052695 GO:0052696 GO:0070062

Consensus prediction of GO terms

Molecular Function	GO:0004252	GO:0046872
GO-Score	0.39	0.39
Biological Processes	GO:0006508
GO-Score	0.39
Cellular Component	GO:0005576
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.