I-TASSER results

I-TASSER results for job id Rv0356c

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

Input Sequence in FASTA format

>protein (214 residues)
MTDASVHPDELDPEYHHHGGFPEYGPASPGAGFGQFVATMRRLQDLAVAADPGDAVWDEA
AERAAALVELLSPFEADEGKAPAGRTPGLPGMGSLLLPPWTVTRYGTDGVEMRGSFSRFH
VGGNSAVHGGVLPLLFDHMFGMISHAAGRPISRTAFLHVDYRRITPIDVPLIVRGRVTNT
EGRKAFVCAELFDSDETLLAEGNGLMVRLLPGQP

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| MTDASVHPDELDPEYHHHGGFPEYGPASPGAGFGQFVATMRRLQDLAVAADPGDAVWDEAAERAAALVELLSPFEADEGKAPAGRTPGLPGMGSLLLPPWTVTRYGTDGVEMRGSFSRFHVGGNSAVHGGVLPLLFDHMFGMISHAAGRPISRTAFLHVDYRRITPIDVPLIVRGRVTNTEGRKAFVCAELFDSDETLLAEGNGLMVRLLPGQP
Prediction	CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEHCCEEEEEEEHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCEEEEEEEEEEHCCCCCCCEEEEEEEEEEHCCEEEEEEEEEEHCCCEEEEEEEEEEEEHCCCCC
Conf.Score	9888889877888778888888777888876567999999999999998489999999999999999999755678876677777788888887767988999986998999999786447999965479999999999999999879985799999989847789996899999999995969999999996997699999999999789999
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| MTDASVHPDELDPEYHHHGGFPEYGPASPGAGFGQFVATMRRLQDLAVAADPGDAVWDEAAERAAALVELLSPFEADEGKAPAGRTPGLPGMGSLLLPPWTVTRYGTDGVEMRGSFSRFHVGGNSAVHGGVLPLLFDHMFGMISHAAGRPISRTAFLHVDYRRITPIDVPLIVRGRVTNTEGRKAFVCAELFDSDETLLAEGNGLMVRLLPGQP
Prediction	7546535455355745543413525256444523400510340142034141436304402630550363056352653431322323022343010230203434642020203034412123021311000000110001001125443020130304023304364302020303645422010202032574301030401002143758
	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                 180                 200

                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEHCCEEEEEEEHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCEEEEEEEEEEHCCCCCCCEEEEEEEEEEHCCEEEEEEEEEEHCCCEEEEEEEEEEEEHCCCCC
MTDASVHPDELDPEYHHHGGFPEYGPASPGAGFGQFVATMRRLQDLAVAADPGDAVWDEAAERAAALVELLSPFEADEGKAPAGRTPGLPGMGSLLLPPWTVTRYGTDGVEMRGSFSRFHVGGNSAVHGGVLPLLFDHMFGMISHAAGRPISRTAFLHVDYRRITPIDVPLIVRGRVTNTEGRKAFVCAELFDSDETLLAEGNGLMVRLLPGQP

2ov9C

0.24

0.22

0.92

3.00

MUSTER

-----------HPTFENSPSGTVLTSPPDGSAVDRATDAARRVVDALLRTDRGNANLERVAEELNSIAGHLEEHAIDWNGEGVTRHDPVTGPENALAPPVVLEGLSDGSVRGTVTLTIPYQGPPGHVHGGVSALLLDHVLGVANAWGG--KAGTAQLSTRYHRPTPLFEPLTLTGKLS-VDGRKITTAGDIRTADGQVCVSVEGLFVDKT----

2ov9C

0.23

0.21

0.92

3.94

dPPAS

-----------HPTFENSPSGTVLTSPPDGSAVDRATDAARRVVDALLRTDRGNANLERVAEELNSIAGHLEEHAPAVAEEGVTRHDPVTGPENALAPPVVLEGLSDGSVRGTVTLTIPYQGPPGHVHGGVSALLLDHVLGVANAWGGKAG--TAQLSTRYHRPTPLFEPLTLTGKLSVD-GRKITTAGDIRTADGQVCVSVEGLFVDKT----

2ov9C

0.23

0.21

0.92

5.08

wdPPAS

-----------HPTFENSPSGTVLTSPPDGSAVDRATDAARRVVDALLRTDRGNANLERVAEELNSIAGHLEEHAPAVAERLVTRHDPVTGPENALAPPVVLEGLSDGSVRGTVTLTIPYQGPPGHVHGGVSALLLDHVLGVANAWGG--KAGTAQLSTRYHRPTPLFEPLTLTGKLSVD-GRKITTAGDIRTADGQVCVSVEGLFVDKT----

2ov9C

0.24

0.22

0.91

3.98

wMUSTER

------------PTFENSPSGTVLTSPPDGSAVDRATDAARRVVDALLRTDRGNANLERVAEELNSIAGHLEEHAIDWNGEGVTRHDPVTGPENALAPPVVLEGLSDGSVRGTVTLTIPYQGPPGHVHGGVSALLLDHVLGVANAWGG--KAGTAQLSTRYHRPTPLFEPLTLTGKLS-VDGRKITTAGDIRTADGQVCVSVEGLFVDKT----

2ov9C

0.23

0.21

0.92

4.92

wPPAS

-----------HPTFENSPSGTVLTSPPDGSAVDRATDAARRVVDALLRTDRGNANLERVAEELNSIAGHLEEHAPAVAERGVTRHDPVTGPENALAPPVVLEGLSDGSVRGTVTLTIPYQGPPGHVHGGVSALLLDHVLGVANAWGGK--AGTAQLSTRYHRPTPLFEPLTLTGKLSVD-GRKITTAGDIRTADGQVCVSVEGLFVDKT----

2ov9C

0.23

0.21

0.92

7.07

dPPAS2

-----------HPTFENSPSGTVLTSPPDGSAVDRATDAARRVVDALLRTDRGNANLERVAEELNSIAGHLEEHAPAVAEEGVTRHDPVTGPENALAPPVVLEGLSDGSVRGTVTLTIPYQGPPGHVHGGVSALLLDHVLGVANAWGG--KAGTAQLSTRYHRPTPLFEPLTLTGKLS-VDGRKITTAGDIRTADGQVCVSVEGLFVDKT----

2ov9C

0.23

0.21

0.92

4.20

PPAS

-----------HPTFENSPSGTVLTSPPDGSAVDRATDAARRVVDALLRTDRGNANLERVAEELNSIAGHLEEHAPAVAEEGVTRHDPVTGPENALAPPVVLEGLSDGSVRGTVTLTIPYQGPPGHVHGGVSALLLDHVLGVANAWGGK--AGTAQLSTRYHRPTPLFEPLTLTGKLSVD-GRKITTAGDIRTADGQVCVSVEGLFVDKT----

2ov9C

0.23

0.21

0.92

3.84

Env-PPAS

-----------HPTFENSPSGTVLTSPPDGSAVDRATDAARRVVDALLRTDRGNANLERVAEELNSIAGHLEEHAPAVAEEGVTRHDPVTGPENALAPPVVLEGLSDGSVRGTVTLTIPYQGPPGHVHGGVSALLLDHVLGVANAWGG--KAGTAQLSTRYHRPTPLFEPLTLTGKLSVD-GRKITTAGDIRTADGQVCVSVEGLFVDKT----

4ae8A

0.21

0.16

0.77

2.07

MUSTER

-----------------------------------------ILKDCSV---PNPSWNKDLRLLFDQFMKKCEDGSWKRLPSYKQAQLFTRSFDDGLGEYVMFYNDIEKRMVCLFQGGPYLEGPPGFIHGGAIATMIDATVGMCAMMAGG-IVMTANLNINYKRPIPLCSVVMINSQLDKVEGRKFFVSCNVQSVDETLYSEATSLFIKLN----

4ae8A

0.21

0.16

0.76

2.54

dPPAS

-----------------------------------------ILKDCSVPNPSWNKDLRLLFDQFMKKCE-----DGSWKRLPSYKQAQLFTRSFDDGLGVMFYNDIEKRMVCLFQGGPYLEGPPGFIHGGAIATMIDATVGMCAMMAGG-IVMTANLNINYKRPIPLCSVVMINSQLDKVEGRKFFVSCNVQSVDETLYSEATSLFIKLN----

(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=0.88

Estimated TM-score = 0.83±0.08

Estimated RMSD = 3.7±2.5Å

Download Model 2

C-score=-1.04

Download Model 3

C-score=-1.07

Download Model 4

C-score=-3.78

Download Model 5

C-score=-1.98

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	2ov9C	0.894	0.92	0.235	0.916
2	4ae7A	0.585	2.78	0.131	0.668
3	4ae8A	0.567	2.34	0.205	0.626
4	1vi8B	0.551	2.57	0.123	0.635
5	3f5oA	0.548	2.15	0.146	0.608
6	4kc5A	0.543	4.23	0.063	0.724
7	2b6eD	0.543	2.30	0.089	0.617
8	1vh9A	0.542	2.48	0.119	0.622
9	3e1eC	0.540	2.47	0.126	0.612
10	2fs2B	0.534	2.59	0.143	0.608

(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	0.34	24	1vpmB	COA	Rep, Mult	127,129,160,161,163,164,199
2	0.12	7	4gahA	0ET	Rep, Mult	137,153,154,155,183,184,205,207
3	0.09	7	3f5oA	UOC	Rep, Mult	86,138,141,142,145,152,153,154,206
4	0.06	5	3ed0A	EMO	Rep, Mult	161,162,163,164
5	0.02	2	3f5oA	UUU	Rep, Mult	179,181,182,183,184,186
6	0.01	1	2f410	III	Rep, Mult	128,130,133,134,154,155,156,157,158,159,160,161
7	0.01	1	1mkaA	DAC	Rep, Mult	140,155,157
8	0.01	1	3nwzB	COA	Rep, Mult	153,154,209,211
9	0.01	1	1vh50	III	Rep, Mult	93,94,96,97,118,119,121,123,128,129,130,131,133,134,137,138,154,155,156,157,158,159,160,161
10	0.01	1	3doyB	2BE	Rep, Mult	172,174,194

	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	0.068	1u1zB	0.504	2.88	0.053	0.608	4.2.1.-	NA
2	0.067	1z6bA	0.497	3.08	0.069	0.612	4.2.1.-	NA
3	0.060	3b7kC	0.460	2.03	0.120	0.505	3.1.2.1	129
4	0.060	1lo8A	0.437	2.50	0.065	0.495	3.1.2.23	NA
5	0.060	2q8nB	0.419	5.86	0.021	0.743	5.3.1.9	NA
6	0.060	1tbuB	0.421	1.79	0.092	0.458	3.1.2.2	129,157,198
7	0.060	2qq2C	0.472	2.30	0.148	0.523	3.1.2.2	129,131,141,154
8	0.060	2q8nC	0.420	5.86	0.026	0.743	5.3.1.9	NA
9	0.060	2cvpA	0.408	5.97	0.042	0.715	5.3.1.9	NA
10	0.060	2ckjA	0.413	5.78	0.063	0.715	1.17.1.4,1.17.3.2	NA
11	0.060	2e1qA	0.419	5.87	0.076	0.738	1.17.3.2,1.17.1.4	NA
12	0.060	3b9jC	0.398	6.11	0.067	0.729	1.17.3.2,1.17.1.4	NA
13	0.060	1t3tA	0.447	4.77	0.044	0.668	6.3.5.3	NA
14	0.060	2uv8G	0.446	3.89	0.057	0.575	2.3.1.86	NA
15	0.060	2v1oE	0.436	2.09	0.155	0.477	3.1.2.2	130,143,178
16	0.060	1iriA	0.411	5.64	0.043	0.701	5.3.1.9	NA
17	0.060	3ljkA	0.418	5.72	0.047	0.720	5.3.1.9	130
18	0.060	3b9jI	0.235	5.88	0.052	0.430	1.17.1.4,1.17.3.2	192
19	0.060	1fo4A	0.414	5.81	0.083	0.724	1.17.1.4	NA
20	0.060	1mkaA	0.514	3.42	0.083	0.659	4.2.1.60	129
21	0.060	2gllA	0.510	3.07	0.089	0.626	4.2.1.-	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	0.33	0.587	2.70	0.20	0.66	4gahB	GO:0005737 GO:0005739 GO:0005743 GO:0005758 GO:0005759 GO:0005829 GO:0005886 GO:0006629 GO:0006631 GO:0006915 GO:0016020 GO:0016290 GO:0016787 GO:0032587 GO:0035338 GO:0042995 GO:0043491 GO:0047617 GO:1902108
1	0.31	0.500	1.75	0.23	0.54	1wluA	GO:0016790
2	0.28	0.548	2.65	0.13	0.63	2fs2B	GO:0010124 GO:0016289 GO:0016787 GO:0016790
3	0.25	0.585	2.78	0.13	0.67	4ae7A	GO:0005739 GO:0005759 GO:0006629 GO:0006631 GO:0016290 GO:0016787 GO:0035336 GO:0035338 GO:0035965 GO:0047617
4	0.24	0.530	2.97	0.11	0.62	1q4sA	GO:0016787 GO:0018739
5	0.20	0.567	2.34	0.20	0.63	4ae8A	GO:0005737 GO:0005739 GO:0005743 GO:0005758 GO:0005759 GO:0005829 GO:0005886 GO:0006629 GO:0006631 GO:0006915 GO:0016020 GO:0016290 GO:0016787 GO:0032587 GO:0035338 GO:0042995 GO:0043491 GO:0047617 GO:1902108
6	0.15	0.548	2.15	0.15	0.61	3f5oA	GO:0005634 GO:0005737 GO:0005739 GO:0005819 GO:0005829 GO:0005856 GO:0016787 GO:0035338 GO:0047617 GO:0051289 GO:0070062
7	0.12	0.553	2.62	0.09	0.64	2b6eD	GO:0016787
8	0.10	0.511	2.08	0.17	0.57	3s4kA	GO:0016787
9	0.07	0.472	2.72	0.09	0.54	4zv3B	GO:0000062 GO:0005654 GO:0005737 GO:0005829 GO:0009062 GO:0015937 GO:0016290 GO:0016787 GO:0036042 GO:0036114 GO:0036116 GO:0042803 GO:0043005 GO:0044297 GO:0051792 GO:0052689 GO:0070062 GO:1900535
10	0.06	0.431	2.56	0.09	0.49	1njkA	GO:0006635 GO:0016787 GO:0047617
11	0.06	0.427	2.54	0.11	0.49	3hm0A	GO:0016787 GO:0016790
12	0.06	0.273	5.23	0.05	0.44	5dwnA	GO:0008080 GO:0016740 GO:0016746
13	0.06	0.257	5.79	0.06	0.44	1vyvB	GO:0005245 GO:0005886 GO:0005891 GO:0006816 GO:0006874 GO:0007214 GO:0007268 GO:0007528 GO:0007628 GO:0008331 GO:0014051 GO:0019227 GO:0019901 GO:0035249 GO:0042391 GO:0045202 GO:0046058 GO:0048536 GO:0048538 GO:0048541 GO:0048747 GO:0050852 GO:0050877 GO:0050908 GO:0070588 GO:1901385
14	0.06	0.259	5.19	0.05	0.39	5cqrA	GO:0000123 GO:0000993 GO:0002098 GO:0004871 GO:0005634 GO:0005730 GO:0005737 GO:0006351 GO:0006355 GO:0006357 GO:0006368 GO:0006461 GO:0006468 GO:0006955 GO:0007165 GO:0008023 GO:0008607 GO:0030335 GO:0033588 GO:0045859
15	0.06	0.276	5.39	0.04	0.43	3p6bA	GO:0000272 GO:0003824 GO:0004553 GO:0005576 GO:0005615 GO:0005975 GO:0008152 GO:0008810 GO:0016162 GO:0016787 GO:0016798
16	0.06	0.287	5.67	0.05	0.50	2n5fA	GO:0004364 GO:0005737 GO:0006749
17	0.06	0.295	4.87	0.03	0.43	4c9iA	GO:0006952 GO:0009607
18	0.06	0.214	3.94	0.10	0.29	3kkbB	GO:0000155 GO:0000160 GO:0000166 GO:0004673 GO:0004871 GO:0005524 GO:0005622 GO:0005886 GO:0007165 GO:0016020 GO:0016021 GO:0016301 GO:0016310 GO:0016740 GO:0016772 GO:0018106 GO:0023014 GO:0042121 GO:0050896
19	0.06	0.513	3.18	0.16	0.60	3nwzA
20	0.06	0.500	1.95	0.22	0.55	1zkiA
21	0.06	0.540	2.47	0.13	0.61	3e1eC

Consensus prediction of GO terms

Molecular Function	GO:0016290
GO-Score	0.50
Biological Processes	GO:0072329	GO:0042178	GO:0032048	GO:0035338	GO:0006631	GO:0043491	GO:1902108
GO-Score	0.57	0.57	0.51	0.50	0.50	0.33	0.33
Cellular Component	GO:0005759	GO:0005743	GO:0005829	GO:0005758	GO:0032587
GO-Score	0.50	0.33	0.33	0.33	0.33

(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.