I-TASSER results

I-TASSER results for job id Rv1088

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

Input Sequence in FASTA format

>protein (144 residues)
MSYMIATPAALTAAATDIDGIGSAVSVANAAAVAATTGVLAAGGDEVLAAIARLFNANAE
EYHALSAQVAAFQTLFVRTLTGGCGVFRRRRGRQCVTAAEHRAAGAGRRQRRRRSGDGQW
RLRQQRHFGCGGQPEFRQHSEHRR

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MSYMIATPAALTAAATDIDGIGSAVSVANAAAVAATTGVLAAGGDEVLAAIARLFNANAEEYHALSAQVAAFQTLFVRTLTGGCGVFRRRRGRQCVTAAEHRAAGAGRRQRRRRSGDGQWRLRQQRHFGCGGQPEFRQHSEHRR
Prediction	CCEEHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHCC
Conf.Score	976764579999999999998889999887777766545666676578999999999999999999999999999999999878888888887777777776654556666566788888888888999888988754555549
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MSYMIATPAALTAAATDIDGIGSAVSVANAAAVAATTGVLAAGGDEVLAAIARLFNANAEEYHALSAQVAAFQTLFVRTLTGGCGVFRRRRGRQCVTAAEHRAAGAGRRQRRRRSGDGQWRLRQQRHFGCGGQPEFRQHSEHRR
Prediction	643341324303300431441322143133301331231333344301320232023214302200330231042014103433322121123222433444444344454444344444536534341343433446436658
	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                 100                 120                 140

                   |                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCEEHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHCC
MSYMIATPAALTAAATDIDGIGSAVSVANAAAVAATTGVLAAGGDEVLAAIARLFNANAEEYHALSAQVAAFQTLFVRTLTGGCGVFRRRRGRQCVTAAEHRAAGAGRRQRRRRSGDGQWRLRQQRHFGCGGQPEFRQHSEHRR

2g38C

0.30

0.16

0.53

0.84

MUSTER

-------PEALTVAATEVRRIRDRAIQSDAQVAPMTTAVRPPAADLVSEKAATFLVEYARKYRQTIAAAAVVLEEFAHALTTG-------------------------------------------------------------

2g38C

0.30

0.16

0.53

0.91

dPPAS

-------PEALTVAATEVRRIRDRAIQSDAQVAPMTTAVRPPAADLVSEKAATFLVEYARKYRQTIAAAAVVLEEFAHALTTG-------------------------------------------------------------

2g38C

0.30

0.16

0.53

1.98

wdPPAS

-------PEALTVAATEVRRIRDRAIQSDAQVAPMTTAVRPPAADLVSEKAATFLVEYARKYRQTIAAAAVVLEEFAHALTTG-------------------------------------------------------------

2g38C

0.30

0.16

0.53

1.18

wMUSTER

-------PEALTVAATEVRRIRDRAIQSDAQVAPMTTAVRPPAADLVSEKAATFLVEYARKYRQTIAAAAVVLEEFAHALTTG-------------------------------------------------------------

2g38C

0.30

0.16

0.53

2.04

wPPAS

-------PEALTVAATEVRRIRDRAIQSDAQVAPMTTAVRPPAADLVSEKAATFLVEYARKYRQTIAAAAVVLEEFAHALTTG-------------------------------------------------------------

2g38C

0.30

0.16

0.53

1.77

dPPAS2

-------PEALTVAATEVRRIRDRAIQSDAQVAPMTTAVRPPAADLVSEKAATFLVEYARKYRQTIAAAAVVLEEFAHALTTG-------------------------------------------------------------

2g38C

0.30

0.16

0.53

1.20

PPAS

-------PEALTVAATEVRRIRDRAIQSDAQVAPMTTAVRPPAADLVSEKAATFLVEYARKYRQTIAAAAVVLEEFAHALTTG-------------------------------------------------------------

2g38C

0.30

0.16

0.53

1.12

Env-PPAS

-------PEALTVAATEVRRIRDRAIQSDAQVAPMTTAVRPPAADLVSEKAATFLVEYARKYRQTIAAAAVVLEEFAHALTTG-------------------------------------------------------------

5cwiA2

0.14

0.11

0.79

0.83

MUSTER

---------------ADIAKLCIKAASEAAEAASKAAELAQRHPDSQAARDAIKLASQAAEAVKLACELAQEHP---NADIAKKCIKAASEAAEEASKAAEEAQRHPDSQKARDEIKEASQKAEEV------------KERCER

5cwiA2

0.11

0.09

0.79

0.69

dPPAS

---------------ADIAKLCIKAASEAAEAASKAAELAQRHPDSQAARDAIKLASQAAEAVKLACELAQEHPNADIAKKCIKAASEAAEEASKAAEEAQRHPDSQKARDEIKEASQKAEEVKERCER---------------

(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=-2.13

Estimated TM-score = 0.46±0.15

Estimated RMSD = 9.3±4.6Å

Download Model 2

C-score=-3.40

Download Model 3

C-score=-3.49

Download Model 4

C-score=-4.10

Download Model 5

C-score=-3.79

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	3ripA	0.691	2.95	0.082	0.889
2	5cwiA2	0.680	1.96	0.140	0.792
3	3ay5A	0.647	3.46	0.056	0.896
4	5cwpA	0.642	2.31	0.082	0.764
5	5flzA	0.638	3.30	0.037	0.882
6	2yn7A	0.633	3.47	0.069	0.896
7	5cwoA	0.630	2.77	0.066	0.792
8	5flzB	0.627	3.64	0.029	0.889
9	3nz4A	0.623	3.38	0.050	0.833
10	1gkmA	0.622	3.59	0.063	0.847

(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	6	1brrC	ARC	Rep, Mult	32,55,59
2	0.08	3	5da5C	GOA	Rep, Mult	28,29,32,59
3	0.07	3	3s8gA	OLC	Rep, Mult	26,30,66,67,68
4	0.04	2	3riaB	IOD	Rep, Mult	6,8,9
5	0.04	2	5da5A	FE	Rep, Mult	29,59,62
6	0.02	1	3fyeA	DMU	Rep, Mult	19,21,65,66,69,70,73
7	0.02	1	3lw51	CLA	Rep, Mult	35,38,39
8	0.02	1	3u7qB	IMD	Rep, Mult	46,49
9	0.02	1	3c9iB	XE	Rep, Mult	18,21
10	0.02	1	1cc1L	SF4	Rep, Mult	93,124
11	0.02	1	2wsc4	CLA	Rep, Mult	72,76
12	0.02	1	2xqtE	CVM	Rep, Mult	62,65

	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	0.094	2h8aA	0.547	3.11	0.095	0.722	2.5.1.18	NA
2	0.060	1fbvA	0.576	3.25	0.042	0.799	6.3.2.19	NA
3	0.060	2z8yD	0.603	2.91	0.049	0.743	1.2.7.4,1.2.99.2	66,70,74
4	0.060	3cf4A	0.616	3.79	0.070	0.840	1.2.99.2	124
5	0.060	1gu6A	0.554	3.26	0.071	0.722	1.7.2.2	NA
6	0.060	1b8fA	0.619	3.37	0.069	0.833	4.3.1.3	NA
7	0.060	3i39X	0.612	2.65	0.083	0.736	1.2.99.2	51
8	0.060	1j3uA	0.557	2.97	0.057	0.729	4.3.1.1	NA
9	0.060	2uxwA	0.562	3.40	0.053	0.757	1.3.99.-	NA
10	0.060	1yisA	0.551	3.09	0.028	0.708	4.3.2.2	NA
11	0.060	2z1qB	0.572	3.95	0.056	0.819	1.3.99.3	NA
12	0.060	2pfmA	0.577	2.86	0.057	0.715	4.3.2.2	NA
13	0.060	1q5nA	0.567	3.16	0.036	0.729	5.5.1.2	50
14	0.060	2ohyB	0.625	3.50	0.084	0.840	5.4.3.6	NA
15	0.060	3e04D	0.561	2.85	0.035	0.729	4.2.1.2	71
16	0.060	1fftA	0.593	3.82	0.068	0.861	1.10.3.-	NA
17	0.060	1qdbA	0.567	2.95	0.043	0.708	1.7.2.2	19,63
18	0.060	1rx0A	0.563	4.04	0.081	0.812	1.3.99.-	NA
19	0.060	3djlA	0.583	3.51	0.084	0.785	1.3.99.-	NA
20	0.060	1y2mB	0.562	4.04	0.050	0.840	4.3.1.24	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	0.10	0.647	3.46	0.06	0.90	3ay5A	GO:0005634 GO:0005654 GO:0005737 GO:0007049 GO:0051726
1	0.10	0.691	2.95	0.08	0.89	3ripA	GO:0000226 GO:0000922 GO:0000923 GO:0000930 GO:0005200 GO:0005737 GO:0005813 GO:0005815 GO:0005816 GO:0005829 GO:0005856 GO:0005874 GO:0006461 GO:0007020 GO:0007126 GO:0008274 GO:0015630 GO:0016020 GO:0031122 GO:0043015 GO:0044732 GO:0051011 GO:0051298 GO:0051415 GO:0055037 GO:0090307
2	0.07	0.638	3.30	0.04	0.88	5flzA	GO:0000226 GO:0000922 GO:0000923 GO:0000928 GO:0005200 GO:0005634 GO:0005737 GO:0005813 GO:0005815 GO:0005816 GO:0005822 GO:0005824 GO:0005856 GO:0005874 GO:0007020 GO:0007126 GO:0031122 GO:0043015 GO:0051011 GO:0051298 GO:0051415 GO:0090307
3	0.07	0.627	3.64	0.03	0.89	5flzB	GO:0000226 GO:0000922 GO:0000923 GO:0000928 GO:0005200 GO:0005634 GO:0005737 GO:0005813 GO:0005815 GO:0005816 GO:0005822 GO:0005824 GO:0005856 GO:0005874 GO:0007020 GO:0007126 GO:0030472 GO:0031122 GO:0043015 GO:0051011 GO:0051298 GO:0051415 GO:0090307
4	0.07	0.345	5.43	0.06	0.67	3ec7A	GO:0008152 GO:0016491 GO:0019310 GO:0050112 GO:0055114
5	0.06	0.331	4.69	0.04	0.54	2v57B	GO:0003677 GO:0006351 GO:0006355
6	0.06	0.355	5.12	0.01	0.63	3v7pA	GO:0009234 GO:0016787 GO:0016810 GO:0046872
7	0.06	0.356	5.22	0.05	0.63	2p5oB	GO:0000166 GO:0003676 GO:0003677 GO:0003887 GO:0004518 GO:0004527 GO:0006260 GO:0008408 GO:0016740 GO:0016779 GO:0016787 GO:0039693 GO:0071897 GO:0090305
8	0.06	0.345	4.41	0.02	0.56	5ekqD	GO:0009279 GO:0016020 GO:0043165 GO:0051205 GO:1990063
9	0.06	0.330	4.38	0.03	0.51	4q9oA	GO:0000287 GO:0004659 GO:0016740 GO:0016765 GO:0046872
10	0.06	0.351	3.59	0.03	0.47	3ctdB	GO:0003677 GO:0006260 GO:0006281 GO:0006310 GO:0009378 GO:0032508
11	0.06	0.319	4.81	0.04	0.53	2wgbB	GO:0003677 GO:0006351 GO:0006355
12	0.06	0.387	4.36	0.02	0.60	4ii3A	GO:0000166 GO:0000287 GO:0004839 GO:0004842 GO:0005524 GO:0005634 GO:0005737 GO:0005829 GO:0006464 GO:0008641 GO:0016567 GO:0016874 GO:0019941
13	0.06	0.279	5.00	0.06	0.49	2m83A	GO:0005975 GO:0005977 GO:0016020 GO:0016021
14	0.06	0.286	5.52	0.07	0.56	2rjzA	GO:0004576 GO:0016020 GO:0016021 GO:0043107 GO:0043683
15	0.06	0.243	3.69	0.04	0.33	2o5aA	GO:0005737 GO:0006417 GO:0017148 GO:0042256 GO:0090071
16	0.06	0.270	3.91	0.07	0.39	4dx8H	GO:0001525 GO:0001937 GO:0005546 GO:0005615 GO:0005737 GO:0005856 GO:0005874 GO:0005886 GO:0005911 GO:0007264 GO:0008017 GO:0010596 GO:0016020 GO:0016525 GO:0030054 GO:0030695 GO:0032092 GO:0032403 GO:0043234 GO:0045454 GO:0050790 GO:2000114 GO:2000352
17	0.06	0.322	3.88	0.11	0.47	2na4A	GO:0009279 GO:0022610 GO:0030288 GO:0042802 GO:0044010 GO:0071806
18	0.06	0.244	4.35	0.07	0.38	1b0nA	GO:0003677 GO:0006351 GO:0006355 GO:0010629 GO:0030435 GO:0043565 GO:0046983

Consensus prediction of GO terms

Molecular Function	GO:0005198	GO:0008017
GO-Score	0.43	0.43
Biological Processes	GO:0051225	GO:0051418	GO:1902850	GO:1903046	GO:0007098
GO-Score	0.43	0.43	0.43	0.43	0.43
Cellular Component	GO:0043231	GO:0032155	GO:0005815	GO:0000922	GO:0099513
GO-Score	0.43	0.43	0.43	0.43	0.43

(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.