I-TASSER results

I-TASSER results for job id Rv2478c

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

Input Sequence in FASTA format

>protein (161 residues)
MVGHIVNDLQRRKVGDQEVVKFRVASNSRRRTSDGGWEPGNSLFITVNCWGRLVTGVGAA
LGKGAPVIVVGHVYTSEYEDRDGIRRSSLEMRATSVGPDLSRVIVRIEKPAYTGPSAGDL
PAATGTGAAGAADAPASAADSVSDVVVDDAITGHNPLPISA

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MVGHIVNDLQRRKVGDQEVVKFRVASNSRRRTSDGGWEPGNSLFITVNCWGRLVTGVGAALGKGAPVIVVGHVYTSEYEDRDGIRRSSLEMRATSVGPDLSRVIVRIEKPAYTGPSAGDLPAATGTGAAGAADAPASAADSVSDVVVDDAITGHNPLPISA
Prediction	CCCCCCCCCEEEHCCCCEEEEEEEEHCCCEHCCCCCEEEHCCEEEEEEEHCHHHHHHHHHHCCCEEEEEEEEEEHCEEHCCCCCEEEEEEEEEEEHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Conf.Score	96766789855656995589999996697766998857765568999985666999999855896999999999556876899689999999966646655555666777888888888888888888888889988888888888888888888999999
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MVGHIVNDLQRRKVGDQEVVKFRVASNSRRRTSDGGWEPGNSLFITVNCWGRLVTGVGAALGKGAPVIVVGHVYTSEYEDRDGIRRSSLEMRATSVGPDLSRVIVRIEKPAYTGPSAGDLPAATGTGAAGAADAPASAADSVSDVVVDDAITGHNPLPISA
Prediction	74131153133332773320301000144143674544755132020100240043025205333300010203346152664452130202033124415434443544545455545444555545454554445465545544456644674513268
	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

CCCCCCCCCEEEHCCCCEEEEEEEEHCCCEHCCCCCEEEHCCEEEEEEEHCHHHHHHHHHHCCCEEEEEEEEEEHCEEHCCCCCEEEEEEEEEEEHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
MVGHIVNDLQRRKVGDQEVVKFRVASNSRRRTSDGGWEPGNSLFITVNCWGRLVTGVGAALGKGAPVIVVGHVYTSEYEDRDGIRRSSLEMRATSVGPDLSRVIVRIEKPAYTGPSAGDLPAATGTGAAGAADAPASAADSVSDVVVDDAITGHNPLPISA

1qvcA

0.18

0.15

0.82

3.47

MUSTER

LVGNLGQDPEVRYMPNGAVANITLATSESWRDKATGEMKEQTEWHRVVLFGKLAEVASEYLRKGSQVYIEGQLRTRKWTDQSGQDRYTTEVVVGTMQMLGGRQGGGAPAGGNIGGGQPQGGWGQPQQPQGGN-----------------------------

1qvcA

0.19

0.16

0.84

4.98

dPPAS

LVGNLGQDPEVRYMPGGAVANITLATSESWRDKATGEMKEQTEWHRVVLFGKLAEVASEYLRKGSQVYIEGQLRTRKWTDQSGQDRYTTEVVVNVGGTMQMLGGRQGGGAPAGGNIGGGQPQGGWGQPQQPQGGN--------------------------

1qvcA

0.18

0.15

0.82

6.07

wdPPAS

LVGNLGQDPEVRYMPGGAVANITLATSESWRDKATGEMKEQTEWHRVVLFGKLAEVASEYLRKGSQVYIEGQLRTRKWTDQSGQDRYTTEVVVGTMQMLGGRQGGGAPAGGNIGGGQPQGGWGQPQQPQGGN-----------------------------

1qvcA

0.18

0.15

0.82

4.30

wMUSTER

LVGNLGQDPEVRYMPNGAVANITLATSESWRDKATGEMKEQTEWHRVVLFGKLAEVASEYLRKGSQVYIEGQLRTRKWTDQSGQDRYTTEVVVGTMQMLGGRQGGGAPAGGNIGGGQPQGGWGQPQQPQGGN-----------------------------

1qvcA

0.18

0.15

0.82

4.73

wPPAS

LVGNLGQDPEVRYMPGGAVANITLATSESWRDKATGEMKEQTEWHRVVLFGKLAEVASEYLRKGSQVYIEGQLRTRKWTDQSGQDRYTTEVVVGTMQMLGGRQGGGAPAGGNIGGGQPQGGWGQPQQPQGGN-----------------------------

1x3eB

0.29

0.20

0.68

6.78

dPPAS2

VVGNLTADPELRFTPGAAVANFTVASTPRMFDRQSGEKDGEALFLRCNIWREAAENVAESLTRGSRVIVTGRLKQRSFETREGEKRTVVEVEVDEIGPSLRYATAKVNKA---------------------------------------------------

1qvcA

0.18

0.15

0.82

4.29

PPAS

LVGNLGQDPEVRYMPGGAVANITLATSESWRDKATGEMKEQTEWHRVVLFGKLAEVASEYLRKGSQVYIEGQLRTRKWTDQSGQDRYTTEVVVGTMQMLGGRQGGGAPAGGNIGGGQPQGGWGQPQQPQGGN-----------------------------

1qvcA

0.19

0.16

0.84

4.47

Env-PPAS

LVGNLGQDPEVRYMPGGAVANITLATSESWRDKATGEMKEQTEWHRVVLFGKLAEVASEYLRKGSQVYIEGQLRTRKWTDQSGQDRYTTEVVVNVGGTMQMLGGRQGGGAPAGGNIGGGQPQGGWGQPQQPQGGN--------------------------

1x3eB

0.30

0.20

0.68

3.43

MUSTER

VVGNLTADPELRFTPSGAVANFTVASTPRMFDRQSGWKDGEALFLRCNIWREAAENVAESLTRGSRVIVTGRLKQRSFETREGEKRTVVEVEVDEIGPSLRYATAKVNKA---------------------------------------------------

1x3eB

0.29

0.20

0.68

4.90

dPPAS

VVGNLTADPELRFTPGAAVANFTVASTPRMFDRQSGEKDGEALFLRCNIWREAAENVAESLTRGSRVIVTGRLKQRSFETREGEKRTVVEVEVDEIGPSLRYATAKVNKA---------------------------------------------------

(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=-1.07

Estimated TM-score = 0.58±0.14

Estimated RMSD = 7.2±4.2Å

Download Model 2

C-score=-1.57

Download Model 3

C-score=-2.03

Download Model 4

C-score=-2.73

Download Model 5

C-score=-1.95

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	1qvcA	0.712	2.01	0.153	0.814
2	2vw9A	0.556	2.01	0.208	0.627
3	1x3eB	0.552	2.45	0.294	0.646
4	3pgzA	0.536	1.69	0.189	0.590
5	3ulpA	0.529	2.15	0.155	0.603
6	3vdyA	0.526	1.76	0.204	0.578
7	3tqyA	0.526	2.28	0.214	0.609
8	5eanA1	0.524	4.02	0.046	0.739
9	2iheA	0.519	2.91	0.192	0.640
10	4dniA	0.516	2.54	0.157	0.633

(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	14	1eygA	NUC	Rep, Mult	4,6,7,12,14,21,23,27,28,29,30,40,41,42,43,44,46,50,63,74,75,76,78,87,88
2	0.06	4	2vw9A	NUC	Rep, Mult	4,5,6,12,14,25,44,48,50,52,56,60,63,64,72,76,78,88,96,97,98,99,100,101
3	0.05	3	3a5uB	NUC	Rep, Mult	4,6,8,9,10,11,12,13,14,15,16,17,18,19,21,23,25,27,29,44,46,50,51,55,58,59,63,64,75,76,78,87,88,89
4	0.05	3	3udgA	NUC	Rep, Mult	4,6,7,25,27,42,44,64
5	0.05	4	2vw9A	QNA	Rep, Mult	52,56,60,96,97,98,99,100,101
6	0.05	4	3udgA	NUC	Rep, Mult	12,17,19,48,50,51,72,74,76,92
7	0.04	3	1eqqA	5MU	Rep, Mult	75,76,77,87
8	0.04	3	1ltl2	III	Rep, Mult	21,49,50,51,56
9	0.03	2	3vdyA	NUC	Rep, Mult	12,21,50,76,78
10	0.03	3	1z9f0	III	Rep, Mult	1,2,3,4,25,26,27,28,42,43,44,45,66,73,74,75,77,89
11	0.03	2	3a5uA	NUC	Rep, Mult	6,7,12,13,27,44,46,51,72,75,76,78,79,87,89
12	0.01	1	3udgB	TMP	Rep, Mult	42,44,140,141,142
13	0.01	1	3udgA	TMP	Rep, Mult	44,108,109,112,114
14	0.01	1	1ue1B	ZN	Rep, Mult	52,55
15	0.01	1	3udgA	NUC	Rep, Mult	127,129,130
16	0.01	1	1eygA	QNA	Rep, Mult	28,29,30,41,43,75
17	0.01	1	3vdyB	NUC	Rep, Mult	53,56,60,96,97,98
18	0.01	1	1eqqB	NUC	Rep, Mult	23,44,46,87
19	0.01	1	3udgC	NUC	Rep, Mult	124
20	0.01	1	1v1qA	CYS	Rep, Mult	9,10,11,20,58,59

	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	2ebsB	0.441	5.08	0.063	0.795	3.2.1.150	9
2	0.060	2fhbA	0.392	5.35	0.056	0.721	3.2.1.41	NA
3	0.060	1qs1A	0.395	5.31	0.078	0.689	2.4.2.30	90
4	0.060	1eqrA	0.426	2.56	0.080	0.491	6.1.1.12	NA
5	0.060	3f2bA	0.441	1.94	0.080	0.491	2.7.7.7	71,92,94
6	0.060	1e1tA	0.410	2.10	0.045	0.466	6.1.1.6	NA
7	0.060	3bjuA	0.418	2.16	0.059	0.472	6.1.1.6	NA
8	0.060	1b8aA	0.414	2.39	0.059	0.472	6.1.1.12	NA
9	0.060	1kyzE	0.388	4.87	0.060	0.652	2.1.1.68	155
10	0.060	2rgrA	0.393	5.39	0.007	0.683	5.99.1.3	NA
11	0.060	3k3wB	0.389	4.76	0.031	0.646	3.5.1.11	NA
12	0.060	1q8iA	0.401	3.79	0.098	0.528	2.7.7.7	18
13	0.060	1e3aB	0.394	4.93	0.045	0.665	3.5.1.11	NA
14	0.060	1kywC	0.342	5.21	0.058	0.596	2.1.1.68	NA
15	0.060	3f9vA	0.471	3.43	0.080	0.609	3.-.-.-	NA
16	0.060	2vkzG	0.386	5.14	0.058	0.702	2.3.1.38,3.1.2.14	45
17	0.060	2de6B	0.398	5.02	0.043	0.689	1.14.12.-	NA
18	0.060	3ebgA	0.401	4.84	0.022	0.646	3.4.11.-	NA
19	0.060	3i7fA	0.415	2.16	0.057	0.466	6.1.1.12	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	0.32	0.534	1.98	0.37	0.60	3eivB	GO:0003677 GO:0003697 GO:0006260
1	0.25	0.712	2.01	0.15	0.81	1qvcA	GO:0000725 GO:0003677 GO:0003697 GO:0005829 GO:0006260 GO:0006281 GO:0006298 GO:0006310 GO:0006974 GO:0008047 GO:0009432 GO:0042802 GO:0043085
2	0.24	0.480	2.42	0.29	0.55	4damC	GO:0003677 GO:0003697 GO:0006260
3	0.23	0.505	2.87	0.24	0.63	4damA	GO:0003677 GO:0003697 GO:0006260
4	0.23	0.537	2.54	0.28	0.63	1ue1B	GO:0003677 GO:0003697 GO:0005576 GO:0005886 GO:0006260 GO:0006974 GO:0046677
5	0.23	0.513	2.02	0.30	0.57	1ue6C	GO:0003677 GO:0003697 GO:0005576 GO:0005886 GO:0006260 GO:0006974 GO:0046677
6	0.22	0.526	1.76	0.20	0.58	3vdyA	GO:0003677 GO:0003697 GO:0005737 GO:0006260 GO:0006310 GO:0030420
7	0.22	0.540	2.15	0.15	0.61	3ulpC	GO:0003677 GO:0003697 GO:0006260 GO:0020011
8	0.20	0.491	1.41	0.22	0.53	1sruB	GO:0000725 GO:0003677 GO:0003697 GO:0005829 GO:0006260 GO:0006281 GO:0006298 GO:0006310 GO:0006974 GO:0008047 GO:0009432 GO:0042802 GO:0043085
9	0.19	0.547	2.48	0.27	0.64	3a5uA	GO:0003677 GO:0003697 GO:0006260
10	0.18	0.538	2.26	0.21	0.62	3tqyA	GO:0003677 GO:0003697 GO:0006260 GO:0006281 GO:0006310 GO:0006974
11	0.17	0.534	2.10	0.19	0.61	3pgzB	GO:0003677 GO:0003697 GO:0006260
12	0.16	0.482	1.34	0.19	0.52	3lgjB	GO:0003677 GO:0003697 GO:0006260
13	0.15	0.497	1.91	0.22	0.56	2cwaA	GO:0003677 GO:0003697 GO:0006260 GO:0006281 GO:0006310 GO:0006974
14	0.12	0.478	1.61	0.18	0.52	2dudB	GO:0003677 GO:0003682 GO:0003697 GO:0005634 GO:0005739 GO:0005759 GO:0006260 GO:0007005 GO:0042645 GO:0044822 GO:0051096 GO:0070062 GO:0070584
15	0.10	0.497	2.46	0.21	0.59	1s3oA	GO:0003677 GO:0003682 GO:0003697 GO:0005634 GO:0005739 GO:0005759 GO:0006260 GO:0007005 GO:0042645 GO:0044822 GO:0051096 GO:0070062 GO:0070584
16	0.10	0.556	2.01	0.21	0.63	2vw9A	GO:0003677 GO:0003697 GO:0006260 GO:0006281 GO:0006310 GO:0006974
17	0.09	0.523	2.75	0.16	0.63	3udgB	GO:0003677 GO:0003697 GO:0005737 GO:0006260 GO:0006281 GO:0006310 GO:0006974
18	0.07	0.469	1.27	0.28	0.50	1z9fA	GO:0003677 GO:0003697 GO:0006260

Consensus prediction of GO terms

Molecular Function	GO:0003697	GO:0005515	GO:0030234
GO-Score	0.77	0.51	0.51
Biological Processes	GO:0006260	GO:0031668	GO:0050790	GO:0006281	GO:0044093	GO:0042221
GO-Score	0.77	0.51	0.51	0.51	0.51	0.47
Cellular Component	GO:0044444	GO:0071944	GO:0016020
GO-Score	0.51	0.47	0.35

(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.