I-TASSER results

I-TASSER results for job id Rv3836

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

Input Sequence in FASTA format

>protein (137 residues)
MTVRMDPQRFDELVSDALDLIPPELADAMDNVVVLVANRHPQHENLLGQYEGVALTERGS
DYAGSLPDAITIYREALLDACDSEDEVVDQVAITVIHEVAHHFGIDDERLDQLGWRDEPA
PGRGNPDLSAPDAMNGP

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MTVRMDPQRFDELVSDALDLIPPELADAMDNVVVLVANRHPQHENLLGQYEGVALTERGSDYAGSLPDAITIYREALLDACDSEDEVVDQVAITVIHEVAHHFGIDDERLDQLGWRDEPAPGRGNPDLSAPDAMNGP
Prediction	CCCCCCHHHHHHHHHHHHHHCCHHHHHHHCCCEEEHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEHCHHHHHHHCCHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCC
Conf.Score	99889999999999999998779999986796899858999998766655577777678888888898899873688999889778999999999999888759997788886565567888887666665566789
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MTVRMDPQRFDELVSDALDLIPPELADAMDNVVVLVANRHPQHENLLGQYEGVALTERGSDYAGSLPDAITIYREALLDACDSEDEVVDQVAITVIHEVAHHFGIDDERLDQLGWRDEPAPGRGNPDLSAPDAMNGP
Prediction	67442447303500440164036404730560201014315764412011423311432464434313101001400142056653025102300010112334244630462426457366534553546754658
	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

                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCCCCHHHHHHHHHHHHHHCCHHHHHHHCCCEEEHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEHCHHHHHHHCCHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCC
MTVRMDPQRFDELVSDALDLIPPELADAMDNVVVLVANRHPQHENLLGQYEGVALTERGSDYAGSLPDAITIYREALLDACDSEDEVVDQVAITVIHEVAHHFGIDDERLDQLGWRDEPAPGRGNPDLSAPDAMNGP

3e11A

0.54

0.45

0.82

3.50

MUSTER

-GVYVDPDRFDELVAEALDGIPEEFAR-ARNVAVFVEDEPDDP-ELLGLYVGIPLTERTTAYGGVLPDRIIIYRNTICALCETESEVIDEVRKTVVHEIAHHFGIDDERLHELGY----------------------

3e11A

0.54

0.45

0.82

7.73

dPPAS

-GVYVDPDRFDELVAEALDGIPEEFA-RARNVAVFVEDEPDDP-ELLGLYVGIPLTERTTAYGGVLPDRIIIYRNTICALCETESEVIDEVRKTVVHEIAHHFGIDDERLHELGY----------------------

3e11A

0.54

0.45

0.82

7.10

wdPPAS

-GVYVDPDRFDELVAEALDGIPEEFAR-ARNVAVFVEDEPDDP-ELLGLYVGIPLTERTTAYGGVLPDRIIIYRNTICALCETESEVIDEVRKTVVHEIAHHFGIDDERLHELGY----------------------

3e11A

0.54

0.44

0.81

4.00

wMUSTER

V--YVDPDRFDELVAEALDGIPEEFAR-ARNVAVFVEDEPDDP-ELLGLYVGIPLTERTTAYGGVLPDRIIIYRNTICALCETESEVIDEVRKTVVHEIAHHFGIDDERLHELGY----------------------

3e11A

0.54

0.45

0.82

4.71

wPPAS

-GVYVDPDRFDELVAEALDGIPEEFAR-ARNVAVFVEDEPDDP-ELLGLYVGIPLTERTTAYGGVLPDRIIIYRNTICALCETESEVIDEVRKTVVHEIAHHFGIDDERLHELGY----------------------

3e11A

0.54

0.45

0.82

10.66

dPPAS2

-GVYVDPDRFDELVAEALDGIPEEFA-RARNVAVFVEDEPDDP-ELLGLYVGIPLTERTTAYGGVLPDRIIIYRNTICALCETESEVIDEVRKTVVHEIAHHFGIDDERLHELGY----------------------

3e11A

0.54

0.45

0.82

4.34

PPAS

-GVYVDPDRFDELVAEALDGIPEEFAR-ARNVAVFVEDEPDDP-ELLGLYVGIPLTERTTAYGGVLPDRIIIYRNTICALCETESEVIDEVRKTVVHEIAHHFGIDDERLHELGY----------------------

3e11A

0.54

0.45

0.82

4.74

Env-PPAS

-GVYVDPDRFDELVAEALDGIPEEFAR-ARNVAVFVEDEPDDP-ELLGLYVGIPLTERTTAYGGVLPDRIIIYRNTICALCETESEVIDEVRKTVVHEIAHHFGIDDERLHELGY----------------------

2ejqB

0.27

0.21

0.80

1.53

MUSTER

-----TYEAFVELVERLWEEVPEDFKRGLQGVHVFPEAKP--EPGLEGVWR---LGEYLDPGG----RHIALYYGSFLEVAGEGFDWEAEVWETMLHELRHHL-RDDLVQEDLRRLD--AFRRG-----------GP

2ejqB

0.22

0.18

0.79

2.39

dPPAS

-----TYEAFVELVERLWEEVPEDFKRGLQGVHVFPEAKP--EPGLEGVWR---LGEYLDPGG----RHIALYYGSFLEVAGEGFDWEAEVWETMLHELRHHLELVQEDLRRLDAFRRGGPS---------------

(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=0.47

Estimated TM-score = 0.78±0.10

Estimated RMSD = 3.6±2.5Å

Download Model 2

C-score=-0.73

Download Model 3

C-score=-2.49

Download Model 4

C-score=-3.72

Download Model 5

C-score=-3.38

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	3e11A	0.776	1.09	0.545	0.818
2	3cmnA	0.628	3.54	0.097	0.883
3	3o0yA	0.596	3.69	0.157	0.876
4	1xm5A	0.589	3.19	0.151	0.781
5	1r1hA	0.569	3.92	0.117	0.839
6	3dwbA	0.560	4.16	0.089	0.861
7	1oz9A	0.552	3.63	0.085	0.766
8	3vuoA1	0.548	3.97	0.096	0.788
9	3v0aB1	0.547	4.01	0.112	0.796
10	3c37A	0.546	3.34	0.115	0.752

(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	0.26	15	2qlaA	ZN	Rep, Mult	97,101
2	0.06	4	3msaA	B3R	Rep, Mult	18,34,95,99
3	0.02	1	3a8mB	TAN	Rep, Mult	73,74
4	0.02	1	3a0hI	CLA	Rep, Mult	96,103
5	0.02	1	2nr9A	PA6	Rep, Mult	95,99
6	0.02	1	2x2vH	DPV	Rep, Mult	87,95
7	0.02	1	1q3aA	ZN	Rep, Mult	97,101,116
8	0.02	1	1fjqA	ACN	Rep, Mult	24,29,32,99,103
9	0.02	1	1i19B	MN	Rep, Mult	106,107
10	0.02	1	2k9cA	CO	Rep, Mult	57,97,98,101
11	0.02	1	4flfA	XXH	Rep, Mult	83,85
12	0.02	1	2ejqB	MG	Rep, Mult	78,79,81
13	0.02	1	1zzhB	ZN	Rep, Mult	107,111
14	0.02	1	4owaB	IOD	Rep, Mult	10,20,91

	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	1eakD	0.495	4.04	0.088	0.752	3.4.24.24	41,46,101
2	0.060	2pffB	0.520	3.40	0.078	0.730	2.3.1.86	NA
3	0.060	2dqmA	0.521	4.23	0.034	0.796	3.4.11.2	NA
4	0.060	3lmdA	0.517	3.45	0.069	0.715	2.5.1.30	47,50,53
5	0.060	1dgpA	0.512	3.37	0.029	0.715	4.2.3.9,4.1.99.7	NA
6	0.060	3ciaA	0.520	3.86	0.069	0.774	3.4.11.-	NA
7	0.060	1j7mA	0.182	3.57	0.018	0.263	3.4.24.24	50
8	0.060	1gw6A	0.518	4.01	0.079	0.766	3.3.2.6	NA
9	0.060	1wmwA	0.509	3.49	0.080	0.730	2.5.1.-	NA
10	0.060	1e1hD	0.235	4.84	0.029	0.380	3.4.24.69	NA
11	0.060	3dwbA	0.560	4.16	0.089	0.861	3.4.24.71	16
12	0.060	2vuaA	0.339	5.34	0.018	0.671	3.4.24.69	84,86
13	0.060	1gxdA	0.506	4.29	0.103	0.781	3.4.24.24	NA
14	0.060	1t3cA	0.532	3.63	0.127	0.745	3.4.24.69	NA
15	0.060	1fj3A	0.535	4.33	0.079	0.810	3.4.24.27	NA
16	0.060	1khoA	0.376	5.17	0.059	0.708	3.1.4.3	NA
17	0.060	3ebgA	0.509	4.29	0.068	0.788	3.4.11.-	NA
18	0.060	1eakA	0.481	3.84	0.098	0.708	3.4.24.24	41,46,68
19	0.060	1ca1A	0.331	5.25	0.051	0.584	3.1.4.3	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	0.29	0.589	3.19	0.15	0.78	1xm5A	GO:0000478 GO:0004222 GO:0004518 GO:0004519 GO:0004521 GO:0005737 GO:0006364 GO:0006412 GO:0006508 GO:0008270 GO:0009408 GO:0016151 GO:0016787 GO:0016892 GO:0030490 GO:0031564 GO:0042254 GO:0042274 GO:0046872
1	0.07	0.529	4.36	0.06	0.82	4iuwA	GO:0004222 GO:0006508 GO:0008237
2	0.07	0.552	3.63	0.09	0.77	1oz9A	GO:0004222 GO:0004518 GO:0004519 GO:0004521 GO:0005737 GO:0006364 GO:0006508 GO:0008270 GO:0016787 GO:0042254 GO:0046872 GO:0090305 GO:0090502
3	0.07	0.596	3.69	0.16	0.88	3o0yA
4	0.07	0.560	4.16	0.09	0.86	3dwbA	GO:0001666 GO:0001921 GO:0003100 GO:0004175 GO:0004222 GO:0005765 GO:0005768 GO:0005769 GO:0005886 GO:0006508 GO:0006915 GO:0007507 GO:0008217 GO:0008233 GO:0008237 GO:0009897 GO:0010613 GO:0010814 GO:0010815 GO:0010816 GO:0016020 GO:0016021 GO:0016485 GO:0016486 GO:0016787 GO:0017046 GO:0019229 GO:0030141 GO:0030819 GO:0031302 GO:0031410 GO:0031982 GO:0033093 GO:0034959 GO:0035994 GO:0042312 GO:0042447 GO:0042493 GO:0042733 GO:0042803 GO:0043583 GO:0045745 GO:0046686 GO:0046872 GO:0048471 GO:0060037 GO:0070062 GO:0070372
5	0.07	0.496	3.83	0.07	0.73	1tviA	GO:0004222 GO:0004518 GO:0004519 GO:0004521 GO:0005737 GO:0006364 GO:0006508 GO:0008270 GO:0016787 GO:0042254 GO:0046872 GO:0090305 GO:0090502
6	0.07	0.532	4.28	0.08	0.87	3u24A	GO:0046872
7	0.07	0.457	4.44	0.07	0.72	1xaxA	GO:0004222 GO:0004518 GO:0004519 GO:0004521 GO:0005737 GO:0006364 GO:0006508 GO:0008270 GO:0016787 GO:0042254 GO:0046872 GO:0090305 GO:0090502
8	0.06	0.396	5.33	0.04	0.76	3ramA	GO:0008152 GO:0016787
9	0.06	0.415	4.24	0.06	0.63	4fb5A	GO:0008152 GO:0016491 GO:0055114
10	0.06	0.399	4.68	0.03	0.69	4girB	GO:0000287 GO:0003824 GO:0008152 GO:0009063 GO:0046872
11	0.06	0.340	4.79	0.05	0.58	1wowA	GO:0004392 GO:0006788 GO:0015979 GO:0016491 GO:0046872 GO:0055114
12	0.06	0.350	3.69	0.07	0.50	1rlkA	GO:0004045 GO:0005737 GO:0006412 GO:0016787
13	0.06	0.365	4.54	0.13	0.62	3jz3B	GO:0000155 GO:0000160 GO:0000166 GO:0004673 GO:0005524 GO:0005622 GO:0005886 GO:0007165 GO:0016020 GO:0016021 GO:0016301 GO:0016310 GO:0016740 GO:0016772 GO:0018106 GO:0023014
14	0.06	0.405	4.50	0.03	0.65	4yzrA	GO:0004497 GO:0005506 GO:0005886 GO:0016020 GO:0016021 GO:0016491 GO:0016705 GO:0017000 GO:0020037 GO:0046872 GO:0055114
15	0.06	0.349	5.48	0.05	0.69	2f2fB	GO:0009405 GO:0044072
16	0.06	0.350	4.76	0.07	0.61	2az1A	GO:0000166 GO:0004550 GO:0005524 GO:0005622 GO:0005737 GO:0006163 GO:0006165 GO:0006183 GO:0006220 GO:0006228 GO:0006241 GO:0009117 GO:0009142 GO:0016301 GO:0016310 GO:0016740 GO:0046872
17	0.06	0.324	4.90	0.01	0.55	4jroA	GO:0000166 GO:0004316 GO:0006633 GO:0016491 GO:0051287 GO:0055114
18	0.06	0.343	4.52	0.06	0.57	3gfvA	GO:0005576 GO:0006810

Consensus prediction of GO terms

Molecular Function	GO:0016894	GO:0004222	GO:0004521	GO:0008270
GO-Score	0.58	0.42	0.34	0.34
Biological Processes	GO:0009266	GO:0031555	GO:0006950	GO:0044267	GO:0090502	GO:0043043	GO:0000469	GO:0042274	GO:0006508
GO-Score	0.58	0.58	0.58	0.58	0.58	0.58	0.58	0.58	0.42
Cellular Component	GO:0005737
GO-Score	0.34

(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.