I-TASSER results

I-TASSER results for job id Rv2598

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

Input Sequence in FASTA format

>protein (164 residues)
MPLHQLAIAPVDVSGALLGLVLNAPAPRPLATHRLAHTDGSALQLGVLGASHVVTVEGRF
CEEVSCVARSRGGDLPESTHAPGYHLQSHTETHDEAAFRRLARHLRERCTRATGWLGGVF
PGDDAALTALAAEPDGTGWRWRTWHLYPSASGGTVVHTTSRWRP

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MPLHQLAIAPVDVSGALLGLVLNAPAPRPLATHRLAHTDGSALQLGVLGASHVVTVEGRFCEEVSCVARSRGGDLPESTHAPGYHLQSHTETHDEAAFRRLARHLRERCTRATGWLGGVFPGDDAALTALAAEPDGTGWRWRTWHLYPSASGGTVVHTTSRWRP
Prediction	CCEEEEHCCCCCCCHHHCCEHCCCCCCCCCEEEEEHCCCCEEEEEEEHCCCEEEEHCCCEEEEEEHCCCCCCCCCCCCCCCCCEEEEEEEEHCCHHHHHHHHHHHHHHHHCCCCCEEEHCCCCCCEEEEEEEEHCCCEEEEEEEEHCCCCCCEEEEEEEEHCCC
Conf.Score	98578866777789778345449999887567887668985999999866479998686689998578988899997556897899999998698899999999999996799958998799986579999887599589998887689998699999766589
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MPLHQLAIAPVDVSGALLGLVLNAPAPRPLATHRLAHTDGSALQLGVLGASHVVTVEGRFCEEVSCVARSRGGDLPESTHAPGYHLQSHTETHDEAAFRRLARHLRERCTRATGWLGGVFPGDDAALTALAAEPDGTGWRWRTWHLYPSASGGTVVHTTSRWRP
Prediction	45334161333233052010216473132003231643541402010010111020445031100022654645135536544130313254245740451054036305744410002023453100001012577403020100115656131122324358
	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                 160

                   |                   |                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCEEEEHCCCCCCCHHHCCEHCCCCCCCCCEEEEEHCCCCEEEEEEEHCCCEEEEHCCCEEEEEEHCCCCCCCCCCCCCCCCCEEEEEEEEHCCHHHHHHHHHHHHHHHHCCCCCEEEHCCCCCCEEEEEEEEHCCCEEEEEEEEHCCCCCCEEEEEEEEHCCC
MPLHQLAIAPVDVSGALLGLVLNAPAPRPLATHRLAHTDGSALQLGVLGASHVVTVEGRFCEEVSCVARSRGGDLPESTHAPGYHLQSHTETHDEAAFRRLARHLRERCTRATGWLGGVFPGDDAALTALAAEPDGTGWRWRTWHLYPSASGGTVVHTTSRWRP

5b68A1

0.11

0.04

0.40

1.73

dPPAS2

---------------------------------------------------------------------------------------------NDDAIQRQIALFHDREFTRPPPSVVAVEGDELVFPVHVHDGSPADVHIEL-----EDGTQRDVSQVENWTA

2a4xA

0.16

0.11

0.68

1.44

dPPAS2

ISLFAVVVE--DMAYRKLGVEIPAEADSA-PHTEAVLDGGIRLAWDTVET----------------VRSYDPEWQAPTGGHRF---AIAFEFPDTASVDKKYAELVDAWNAVWGQRYAIVPGN---VVDLFAPLPLE---------------------------

2a4xA

0.17

0.13

0.74

0.72

MUSTER

ISLFAVVVE--DMAYRKLGVEIPAEADSA-PHTEAVLDGGIRLAWDTV-------------ETVR----SYDPEWQAPTGGHRFAIAFEFP--DTASVDKKYAELVDAGYEGHLKPWNAVWG---QRYAIVKDPDGNVVDLFAP---PLE--------------

2a4xA

0.15

0.12

0.76

0.81

dPPAS

ISLFAVVVEDMAKSYRKLGVEIPAEADSAP-HTEAVLDGGIRLAWDTVET----------------VRSYDPEWQAPTGGHRF---AIAFEFPDTASVDKKYAELVDAGYEGHLKPWNAVWG---QRYAIVKDPDGNVVDLFAPL--PLE--------------

2a4xA

0.19

0.13

0.69

0.70

wdPPAS

ISLFAVVVE--DMAYRKLGVEIPAEADSA-PHTEAVLDGGIRLAWDT--------------ETVR----SYDPEWQAPTGGHRFAIAFEFP--DTASVDKKYAELVDA-------GHLK-PG---QRYAIVKDPDGNVVDLFAP---PLE--------------

2a4xA

0.17

0.13

0.74

0.78

wMUSTER

ISLFAVVVE--DMAYRKLGVEIPAEADSA-PHTEAVLDGGIRLAWDTV-------------ETVR----SYDPEWQAPTGGHRFAIAFEFP--DTASVDKKYAELVDAGYEGHLKPWNAVWG---QRYAIVKDPDGNVVDLFAP---PLE--------------

2a4xA

0.16

0.12

0.71

0.72

wPPAS

ISLFAVVVE--DMAYRKLGVEIPAEA-DSAPHTEAVLDGGIRLAWDTV-------------ETVR---SYDPEWQAPT-GGHRFAIAFEFP--DTASVDKKYAELVDA------------------YEGHLKPWNAV---WGQRYAIPD---GNVVDLFAPL-P

1k2yX3

0.15

0.09

0.55

1.35

dPPAS2

ISTPEINITVTEDSKFAIALQRDAQWGEG----NITTLDGVRVDYP----KGWGLVRAS-----------NTTP----------VLVLRFEADTEEELERIKTVFRNQLKAVDSSLPVPF--------------------------------------------

3el6A1

0.20

0.15

0.72

0.74

PPAS

-----------DVSALGV-----RGAEHPLAAVDVPGHGGAVFTGRLSTDEQPWLAEHVVGG-RTLVP--------------------------GSVLVDLALAAGEDVGLPQRPLV---AGAGALLRMSVGAPDESGRRTIDVHAAEDVADLASQHATGTLAQ

2a4xA

0.17

0.13

0.76

0.72

Env-PPAS

ISLFAVVVEDMAKSYRKLGVEIPAEA-DSAPHTEAVLDGGIRLAWDTV-------------ETVR----SYDPEWQAPTGGHRFAIAFEFP--DTASVDKKYAELVDAGYEGHLKPWNAVWG---QRYAIVKDPDGNVVDLFAPL--PLE--------------

(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=-2.37

Estimated TM-score = 0.44±0.14

Estimated RMSD = 10.2±4.6Å

Download Model 2

C-score=-2.83

Download Model 3

C-score=-3.51

Download Model 4

C-score=-5.00

Download Model 5

C-score=-2.70

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	2a4xA	0.673	1.90	0.128	0.762
2	2ehzA	0.598	3.40	0.110	0.768
3	2rbbA	0.595	2.68	0.083	0.726
4	1mpyA	0.589	3.61	0.122	0.756
5	3hpvA	0.587	3.56	0.090	0.756
6	3ecjA	0.586	3.56	0.115	0.768
7	2zi8A	0.585	3.80	0.133	0.780
8	1eiqA	0.584	3.31	0.079	0.744
9	3zi1A	0.584	3.10	0.118	0.744
10	1kmyA	0.584	3.64	0.084	0.762

(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	0.20	10	1froA	ZN	Rep, Mult	85,140
2	0.08	4	1f9z0	III	Rep, Mult	2,3,4,5,6,7,41,44,77,84,85,86,87,88,89,137,140,142,144
3	0.04	2	1w8qA	CO	Rep, Mult	48,51,52
4	0.02	1	1lkdA	BP6	Rep, Mult	80,84,135,136,138
5	0.02	1	2ehzA	MCT	Rep, Mult	6,7,8,32,45,46,48
6	0.02	1	3rpeA	FAD	Rep, Mult	128,147
7	0.02	1	3dfmA	ZN	Rep, Mult	80,94
8	0.02	1	3rykA	TYD	Rep, Mult	60,62
9	0.02	1	2ehzA	MCT	Rep, Mult	7,52,54,55,83
10	0.02	1	2vrsA	ZN	Rep, Mult	145,147
11	0.02	1	3fd3A	CA	Rep, Mult	98,116
12	0.02	1	1kllA	MC	Rep, Mult	3,32,46,71

	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	0.195	1fa7B	0.541	3.01	0.140	0.683	4.4.1.5	6,18,134,136
2	0.132	1npbA	0.526	3.30	0.140	0.683	2.5.1.18	7,17,19,134
3	0.067	1f9zA	0.553	3.01	0.140	0.683	4.4.1.5	NA
4	0.066	2c21A	0.533	3.46	0.118	0.689	4.1.1.-	NA
5	0.060	1lqoB	0.532	3.02	0.171	0.677	2.5.1.18	3,7,16,134,136
6	0.060	3c66A	0.426	4.51	0.092	0.616	2.7.7.19	NA
7	0.060	1a5lC	0.331	5.53	0.038	0.622	3.5.1.5	NA
8	0.060	1a5kC	0.416	5.00	0.085	0.695	3.5.1.5	NA
9	0.060	3kzuA	0.420	5.40	0.065	0.774	2.3.1.41	NA
10	0.060	1vj7A	0.413	4.20	0.056	0.604	2.7.6.5,3.1.7.2	106
11	0.060	2d3aA	0.428	5.54	0.066	0.738	6.3.1.2	NA
12	0.060	1mpyA	0.589	3.61	0.122	0.756	1.13.11.2	NA
13	0.060	2fiqC	0.430	5.29	0.094	0.762	2.7.1.144	108
14	0.060	1q78A	0.415	4.05	0.047	0.585	2.7.7.19	NA
15	0.060	1lqkA	0.533	3.04	0.171	0.677	2.5.1.18	NA
16	0.060	1k3iA	0.421	5.36	0.033	0.787	1.1.3.9	NA
17	0.060	1kraC	0.418	5.13	0.070	0.707	3.5.1.5	NA
18	0.060	1zg7A	0.366	5.19	0.067	0.652	3.4.17.2	NA
19	0.060	1cjxA	0.534	4.19	0.097	0.787	1.13.11.27	NA
20	0.060	1r3nA	0.420	4.88	0.049	0.701	3.5.1.6	NA
21	0.060	1f1uA	0.583	3.52	0.121	0.768	1.13.11.15	NA
22	0.060	3lm4D	0.579	3.57	0.078	0.750	1.13.11.2	43,45
23	0.060	1ie7C	0.420	5.06	0.063	0.701	3.5.1.5	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	0.23	0.553	3.01	0.14	0.68	1f9zA	GO:0004462 GO:0005829 GO:0016151 GO:0016829 GO:0019243 GO:0046872
1	0.21	0.569	2.81	0.16	0.70	3kolA	GO:0004462 GO:0046872 GO:0051213 GO:0055114
2	0.20	0.527	2.64	0.13	0.64	3g12B	GO:0016829
3	0.17	0.598	3.40	0.11	0.77	2ehzA	GO:0003824 GO:0006725 GO:0008198 GO:0016491 GO:0016702 GO:0019439 GO:0046872 GO:0051213 GO:0055114 GO:1901170
4	0.15	0.551	2.95	0.12	0.70	3ct8A	GO:0046872
5	0.14	0.520	3.31	0.11	0.68	3ey7A	GO:0003824 GO:0051213 GO:0055114
6	0.11	0.599	2.67	0.07	0.73	2rbbA	GO:0051213 GO:0055114
7	0.10	0.510	3.26	0.10	0.67	3hnqA	GO:0009405
8	0.10	0.521	3.20	0.11	0.68	4hc5D	GO:0051213 GO:0055114
9	0.07	0.566	2.72	0.10	0.70	4qb5D	GO:0051213 GO:0055114
10	0.07	0.595	3.47	0.12	0.77	2wl9A	GO:0003824 GO:0005506 GO:0006725 GO:0008198 GO:0016491 GO:0019439 GO:0042178 GO:0046872 GO:0051213 GO:0055114
11	0.07	0.587	3.56	0.09	0.76	3hpvA	GO:0003824 GO:0006725 GO:0008198 GO:0016491 GO:0018577 GO:0019439 GO:0046872 GO:0051213 GO:0055114
12	0.07	0.585	3.80	0.13	0.78	2zi8A	GO:0003824 GO:0005506 GO:0006629 GO:0006707 GO:0006725 GO:0008198 GO:0008202 GO:0008203 GO:0009405 GO:0016042 GO:0016491 GO:0019439 GO:0046872 GO:0047071 GO:0051213 GO:0055114 GO:0070723
13	0.07	0.589	3.61	0.12	0.76	1mpyA	GO:0003824 GO:0006725 GO:0008198 GO:0016491 GO:0018577 GO:0019439 GO:0042203 GO:0046872 GO:0051213 GO:0055114
14	0.07	0.558	2.88	0.10	0.69	4z04A	GO:0046872 GO:0051213 GO:0055114
15	0.07	0.589	3.47	0.12	0.76	4ghcC	GO:0046872 GO:0051213 GO:0055114
16	0.07	0.585	3.31	0.08	0.74	1eilA	GO:0003824 GO:0005506 GO:0006725 GO:0008198 GO:0016491 GO:0018583 GO:0019439 GO:0042178 GO:0046872 GO:0051213 GO:0055114
17	0.07	0.583	3.52	0.12	0.77	1f1uA	GO:0046872 GO:0051213 GO:0055114
18	0.07	0.584	3.64	0.08	0.76	1kmyA	GO:0003824 GO:0005506 GO:0006725 GO:0008198 GO:0016491 GO:0018583 GO:0019439 GO:0042178 GO:0046872 GO:0051213 GO:0055114
19	0.07	0.553	3.38	0.07	0.73	2rk0A	GO:0051213 GO:0055114
20	0.07	0.578	3.37	0.07	0.75	3vb0A	GO:0003824 GO:0006725 GO:0008198 GO:0016491 GO:0019439 GO:0046872 GO:0051213 GO:0055114
21	0.07	0.590	3.48	0.09	0.76	3lm4D	GO:0016491 GO:0018577 GO:0046872 GO:0051213 GO:0055114
22	0.07	0.583	3.40	0.09	0.76	3b59A	GO:0046872 GO:0051213 GO:0055114

Consensus prediction of GO terms

Molecular Function	GO:0004462	GO:0051213	GO:0005506	GO:0016701
GO-Score	0.39	0.34	0.33	0.33
Biological Processes	GO:0061727	GO:0055114	GO:1901361	GO:0019439	GO:0018931
GO-Score	0.46	0.34	0.33	0.33	0.33
Cellular Component	GO:0044444
GO-Score	0.46

(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.