I-TASSER results

I-TASSER results for job id Rv0724A

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

Input Sequence in FASTA format

>protein (111 residues)
SQDRLFDNSTELSVAGSTIATELVPGIVDFDAGRVREMADSFRKHGVDIDMASLVYSGER
SHVVDYLRAKGWDVEGTVRTDLFRRNGLPVPAPHDDDPLGEIIFISGRLNG

Predicted Secondary Structure

Sequence	20 40 60 80 100 \| \| \| \| \| SQDRLFDNSTELSVAGSTIATELVPGIVDFDAGRVREMADSFRKHGVDIDMASLVYSGERSHVVDYLRAKGWDVEGTVRTDLFRRNGLPVPAPHDDDPLGEIIFISGRLNG
Prediction	HHHHHHHHHHHCCCCCCEEEEHCCCCCCCCCHHHHHHHHHHHHHHCCCCCHHHCCCCCCCCCHHHHHHHHCCEEEEHCHHHHHHHHCCCCCCCCCCCCCCCCEEEEEEHCC
Conf.Score	688998876775887646887557887655589999999999998889988885667899868999987798899877899999989999999876666665899999889
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 \| \| \| \| \| SQDRLFDNSTELSVAGSTIATELVPGIVDFDAGRVREMADSFRKHGVDIDMASLVYSGERSHVVDYLRAKGWDVEGTVRTDLFRRNGLPVPAPHDDDPLGEIIFISGRLNG
Prediction	754322641450113301000022443654446414522541472437141440135363642452057241424434344003524142456566442341210103278
	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

                   |                   |                   |                   |                   |

Sec.Str
Seq

HHHHHHHHHHHCCCCCCEEEEHCCCCCCCCCHHHHHHHHHHHHHHCCCCCHHHCCCCCCCCCHHHHHHHHCCEEEEHCHHHHHHHHCCCCCCCCCCCCCCCCEEEEEEHCC
SQDRLFDNSTELSVAGSTIATELVPGIVDFDAGRVREMADSFRKHGVDIDMASLVYSGERSHVVDYLRAKGWDVEGTVRTDLFRRNGLPVPAPHDDDPLGEIIFISGRLNG

2ckdA

0.28

0.99

0.86

MUSTER

AQDGLFTEIGGLSAVGSRIAVETSPLHGDEWREQMQLRFRRVSDALQAVDVQELIYHDERAVVADWLNRHGWRATAQSAPDEMRRVGRWGDGPMADDKDAFAEFVTAHRL-

2ckdA

0.28

0.99

1.82

dPPAS

AQDGLFTEIGGLSAVGSRIAVETSPLHGDEWREQMQLRFRRVSDALQAVDVQELIYHDERAVVADWLNRHGWRATAQSAPDEMRRVGRWGDGPMADDKDAFAEFVTAHRL-

2ckdA

0.28

0.98

1.50

wdPPAS

AQDGLFTEIGGLSAVGSRIAVETSPLHGDEWREQMQLRFRRVSDA-QAVDVQELIYHDERAVVADWLNRHGWRATAQSAPDEMRRVGRWGDGPMADDKDAFAEFVTAHRL-

2ckdA

0.28

0.99

0.97

wMUSTER

AQDGLFTEIGGLSAVGSRIAVETSPLHGDEWREQMQLRFRRVSDALQAVDVQELIYHDERAVVADWLNRHGWRATAQSAPDEMRRVGRWGDGPMADDKDAFAEFVTAHRL-

2ckdA

0.28

0.99

1.17

wPPAS

AQDGLFTEIGGLSAVGSRIAVETSPLHGDEWREQMQLRFRRVSDALQAVDVQELIYHDERAVVADWLNRHGWRATAQSAPDEMRRVGRWGDGPMADDKDAFAEFVTAHRL-

2ckdA

0.28

0.99

6.58

dPPAS2

AQDGLFTEIGGLSAVGSRIAVETSPLHGDEWREQMQLRFRRVSDALQAVDVQELIYHDERAVVADWLNRHGWRATAQSAPDEMRRVGRWGDGPMADDKDAFAEFVTAHRL-

2ckdA

0.28

0.99

1.20

PPAS

AQDGLFTEIGGLSAVGSRIAVETSPLHGDEWREQMQLRFRRVSDALQAVDVQELIYHDERAVVADWLNRHGWRATAQSAPDEMRRVGRWGDGPMADDKDAFAEFVTAHRL-

2ckdA

0.28

0.99

1.14

Env-PPAS

AQDGLFTEIGGLSAVGSRIAVETSPLHGDEWREQMQLRFRRVSDALQAVDVQELIYHDERAVVADWLNRHGWRATAQSAPDEMRRVGRWGDGPMADDKDAFAEFVTAHRL-

3p7eA2

0.12

0.11

0.86

0.84

MUSTER

NKLALFKEIHRVLRDGGELYFSDVYADRRLS-EAAQQDPILYGEC--------LGGALYLEDFRRLVAEAGFDVRLVSVGPV------DVSDPQLRKLVPDVQFYSCTFRC

3cggA1

0.19

0.14

0.70

1.16

dPPAS

---------------------DNNPAHSENYAQRWRNLAAAGNDIYGEARLIDAAPRGAKGRIGGYLSKQGHDVLGTDLDPILIDY--------AKQDFPEARWVVG----

(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=0.39

Estimated TM-score = 0.77±0.10

Estimated RMSD = 3.4±2.4Å

Download Model 2

C-score=-4.06

Download Model 3

C-score=-3.54

Download Model 4

C-score=-4.49

Download Model 5

C-score=-3.98

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	2ckdA	0.915	1.36	0.282	0.991
2	4ckbA	0.633	3.63	0.102	0.928
3	2vdwA	0.633	3.79	0.096	0.919
4	3g5lA	0.617	3.00	0.086	0.838
5	3bgvC	0.610	3.39	0.057	0.847
6	5jdyA	0.607	3.28	0.069	0.865
7	3d2lC	0.605	3.14	0.146	0.820
8	1ri4A	0.602	3.46	0.101	0.865
9	1rjeC2	0.594	3.57	0.062	0.865
10	3bkwA	0.592	3.02	0.108	0.793

(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	0.06	3	3hiyB	MG	Rep, Mult	48,50
2	0.04	2	4ku8A	GLY	Rep, Mult	28,32
3	0.04	2	5i50A	NUC	Rep, Mult	40,43
4	0.04	2	1tkoB	FE	Rep, Mult	37,40
5	0.02	1	1kpgB	CO3	Rep, Mult	20,21,22,104
6	0.02	1	1uvqA	GLY	Rep, Mult	22,79,104
7	0.02	1	2uyqA	SAM	Rep, Mult	64,67,72,73,74,75
8	0.02	1	1cvjA	A	Rep, Mult	20,106
9	0.02	1	2bfnA	CA	Rep, Mult	2,3
10	0.02	1	3pzqA	MAL	Rep, Mult	3,62,66
11	0.02	1	1d2hA	SAH	Rep, Mult	3,4,8,9,66,70
12	0.02	1	3thrB	C2F	Rep, Mult	74,76,104,106
13	0.02	1	3sm3A	CA	Rep, Mult	48,59
14	0.02	1	1tfyA	MG	Rep, Mult	17,50
15	0.02	1	4jhuA	CU	Rep, Mult	18,108
16	0.02	1	1lr5A	BMA	Rep, Mult	10,111
17	0.02	1	1l1eB	CO3	Rep, Mult	17,72,73
18	0.02	1	1cruA	HDN	Rep, Mult	66,72
19	0.02	1	3n3uA	ZN	Rep, Mult	22,37
20	0.02	1	3ojcA	CA	Rep, Mult	73,87

	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	1nw7A	0.499	3.54	0.076	0.712	2.1.1.72	16,71
2	0.060	3cklB	0.472	3.93	0.081	0.748	2.8.2.-	17
3	0.060	3d35A	0.507	3.63	0.105	0.775	2.3.1.48	NA
4	0.060	3e05D	0.492	2.49	0.132	0.613	2.1.1.132	67
5	0.060	2ad1A	0.452	4.17	0.095	0.730	2.8.2.-	NA
6	0.060	3e05B	0.492	2.28	0.134	0.604	2.1.1.132	10
7	0.060	1kpiA	0.547	3.66	0.074	0.820	2.1.1.79	NA
8	0.060	1booA	0.488	3.51	0.049	0.694	2.1.1.113	NA
9	0.060	3c3yA	0.470	3.15	0.114	0.631	2.1.1.104	NA
10	0.060	1cjmA	0.445	4.03	0.075	0.703	2.8.2.1	NA
11	0.060	2p35A	0.484	3.17	0.068	0.685	2.1.1.144	NA
12	0.060	1wznA	0.529	3.41	0.138	0.739	2.1.1.-	NA
13	0.060	1kphC	0.557	3.60	0.095	0.829	2.1.1.79	NA
14	0.060	3nwoA	0.484	4.15	0.084	0.793	3.4.11.5	NA
15	0.060	2aovA	0.473	4.03	0.023	0.784	2.1.1.8	NA
16	0.060	1xxlA	0.541	3.36	0.091	0.775	2.1.1.-	NA
17	0.060	1o54A	0.477	2.97	0.155	0.640	2.1.1.-	NA
18	0.060	2h8kA	0.475	3.98	0.059	0.766	2.8.2.2	NA
19	0.060	3cf4A	0.470	4.32	0.046	0.739	1.2.99.2	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	0.22	0.915	1.36	0.28	0.99	2ckdA	GO:0008168 GO:0016740 GO:0032259
1	0.21	0.861	1.33	0.28	0.93	2uyoA	GO:0008168 GO:0016740 GO:0032259
2	0.07	0.617	3.00	0.09	0.84	3g5lA
3	0.07	0.604	3.50	0.06	0.88	5je1A	GO:0008168 GO:0016740 GO:0032259
4	0.07	0.613	3.43	0.06	0.86	3bgvB	GO:0003723 GO:0004482 GO:0005634 GO:0005654 GO:0005730 GO:0005845 GO:0006366 GO:0006370 GO:0006397 GO:0008168 GO:0016740 GO:0032259 GO:0036265 GO:0043235
5	0.07	0.608	3.11	0.15	0.82	3d2lC	GO:0008168 GO:0016740 GO:0032259
6	0.07	0.579	3.06	0.13	0.80	3uj7A	GO:0008168 GO:0016740 GO:0032259 GO:0046872 GO:0051536 GO:0051539
7	0.07	0.367	4.23	0.01	0.59	4mwzB	GO:0008168 GO:0016740 GO:0032259 GO:0046872 GO:0051536 GO:0051539
8	0.07	0.566	3.47	0.11	0.84	4ineA	GO:0000773 GO:0005737 GO:0006656 GO:0008152 GO:0008168 GO:0016740 GO:0032259 GO:0080101
9	0.07	0.568	3.50	0.13	0.85	4krhA	GO:0008152 GO:0008168 GO:0032259 GO:0046872 GO:0051536 GO:0051539
10	0.07	0.599	3.02	0.11	0.80	3bkwA	GO:0008152 GO:0008168 GO:0032259
11	0.07	0.554	3.59	0.09	0.79	4gekG	GO:0002098 GO:0008168 GO:0016300 GO:0016740 GO:0016743 GO:0030488 GO:0032259 GO:1904047
12	0.07	0.533	3.22	0.08	0.73	3e7pA	GO:0046872 GO:0051536 GO:0051539
13	0.07	0.336	4.19	0.03	0.59	4iv8A	GO:0000234 GO:0008152 GO:0008168 GO:0016740 GO:0032259 GO:0046872 GO:0051536 GO:0051539
14	0.07	0.545	3.45	0.09	0.78	2gluA	GO:0005737 GO:0008152 GO:0008168 GO:0008757 GO:0016740 GO:0032259
15	0.07	0.541	3.28	0.10	0.76	1vl5A	GO:0008152 GO:0008168 GO:0016740 GO:0032259
16	0.07	0.544	3.94	0.09	0.82	2avnA	GO:0008152 GO:0008168 GO:0016740 GO:0032259
17	0.07	0.526	3.12	0.10	0.73	3f4kA	GO:0005737 GO:0008168 GO:0008757 GO:0016740 GO:0032259 GO:0046872 GO:0051536 GO:0051539
18	0.07	0.560	3.62	0.12	0.81	1kpgA	GO:0005737 GO:0005886 GO:0006629 GO:0008168 GO:0008610 GO:0008825 GO:0016740 GO:0032259 GO:0046500 GO:0071768

Consensus prediction of GO terms

Molecular Function	GO:0008168
GO-Score	0.47
Biological Processes	GO:0032259
GO-Score	0.47
Cellular Component	GO:0043235	GO:0005654	GO:0005845	GO:0005730
GO-Score	0.07	0.07	0.07	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.