I-TASSER results

I-TASSER results for job id Rv3755c

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

Input Sequence in FASTA format

>protein (199 residues)
MNAVPSDLTPRVWPAMLTWRAQDISRMESVRVQLSGKRIRANGRIVAAATANNPAFGAHY
DLQTDETGATKRFGLTVTLAERERQLAIARDEENMWLVTDHQGERRAAYNGALDIDLVFS
PFFNALPIRRLGLHERAESIALPVVYVNVPEMSVDAATVSYTSEGRLDGIKLRSPVADTT
VTVDSDGFIVDYPGLAERM

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| MNAVPSDLTPRVWPAMLTWRAQDISRMESVRVQLSGKRIRANGRIVAAATANNPAFGAHYDLQTDETGATKRFGLTVTLAERERQLAIARDEENMWLVTDHQGERRAAYNGALDIDLVFSPFFNALPIRRLGLHERAESIALPVVYVNVPEMSVDAATVSYTSEGRLDGIKLRSPVADTTVTVDSDGFIVDYPGLAERM
Prediction	CCCCCCCCCCCCCEEEEEEEHCCCCCEEEEEEEEHCCEEEEEEEEEEEHCCCCCCEEEEEEEEHCCCCEEEEEEEEEEHCCCEEEEEEEHCCCCCEEEHCCCCCHCCCCCCCEEEEEEHCCCCCCHHHHHHCCCCCCCEEEEEEEEEHCCCCEEEEEEEEEEHCCCCCEEEEEHCCEEEEEEHCCCCEEEHCCHHHEHC
Conf.Score	9988888887766589999865789857999999699899999999975789985899999998799769999999998785689999996999789977998565567998578887585555456676566767755789899998899879999999997799878999978858999985998598778445439
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| MNAVPSDLTPRVWPAMLTWRAQDISRMESVRVQLSGKRIRANGRIVAAATANNPAFGAHYDLQTDETGATKRFGLTVTLAERERQLAIARDEENMWLVTDHQGERRAAYNGALDIDLVFSPFFNALPIRRLGLHERAESIALPVVYVNVPEMSVDAATVSYTSEGRLDGIKLRSPVADTTVTVDSDGFIVDYPGLAERM
Prediction	8645457444331311030343625210201034576403020100023466341010302030356130230203033364423030322661302143574443450520110001302310020021240364455350300102036142552413033356542031314514240402650002303420535
	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

                   |                   |                   |                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCCCCCCCCCCCEEEEEEEHCCCCCEEEEEEEEHCCEEEEEEEEEEEHCCCCCCEEEEEEEEHCCCCEEEEEEEEEEHCCCEEEEEEEHCCCCCEEEHCCCCCHCCCCCCCEEEEEEHCCCCCCHHHHHHCCCCCCCEEEEEEEEEHCCCCEEEEEEEEEEHCCCCCEEEEEHCCEEEEEEHCCCCEEEHCCHHHEHC
MNAVPSDLTPRVWPAMLTWRAQDISRMESVRVQLSGKRIRANGRIVAAATANNPAFGAHYDLQTDETGATKRFGLTVTLAERERQLAIARDEENMWLVTDHQGERRAAYNGALDIDLVFSPFFNALPIRRLGLHERAESIALPVVYVNVPEMSVDAATVSYTSEGRLDGIKLRSPVADTTVTVDSDGFIVDYPGLAERM

2h1tA

0.25

0.23

0.91

2.98

MUSTER

-------SRDRLYTWAGLWRSPSS---SWEALRLEDDQAESQLRAPD--ERSGLPYQLDYRLRWDADWHLREAVFHVESETGVRKLHLLADGRGHWQDG--DGEALPAFDGCLDIDIWPSPFTNTFPIRRLGLAD-GQRAEIRALYIEAPALEPRS-RQAYTRLDA-SHYLYENSAFKAVLLVDEQGLVIDYPGLFQRL

2h1tA

0.25

0.23

0.92

4.70

dPPAS

-------SRDRLYTWAGLWRSPSSS---WEALRLEDDQAESQLRAPD--ERSGLPYQLDYRLRWDADWHLREAVFHVESETGVRKLHLLADGRGHWQDG--DGEALPAFDGCLDIDIWPSPFTNTFPIRRLGLAD-GQRAEIRALYIEAPALEPRS-RQAYTRLDASHYLYENGSAFKAVLLVDEQGLVIDYPGLFQRL

2h1tA

0.25

0.23

0.91

5.12

wdPPAS

-----SRDRL------YTWAGLRSPSSSWEALRLEDDQAESQLRAPD--ERSGLPYQLDYRLRWDADWHLREAVFHVESETGVRKLHLLADGRGHWQDG--DGEALPAFDGCLDIDIWPSPFTNTFPIRRLGLAD-GQRAEIRALYIEAPALEPRS-RQAYTRLDA-SHYLYENSAFKAVLLVDEQGLVIDYPGLFQRL

2h1tA

0.25

0.23

0.91

3.57

wMUSTER

--------RDRLYTWAGLWRSPSS---SWEALRLEDDQAESQLRAPD--ERSGLPYQLDYRLRWDADWHLREAVFHVESETGVRKLHLLADGRGHWQDG--DGEALPAFDGCLDIDIWPSPFTNTFPIRRLGLAD-GQRAEIRALYIEAPALEPRS-RQAYTRLDA-SHYLYENSAFKAVLLVDEQGLVIDYPGLFQRL

2h1tA

0.25

0.23

0.91

5.04

wPPAS

-------SRDRLYTWAGLWRSPSS---SWEALRLEDDQAESQLRAPD--ERSGLPYQLDYRLRWDADWHLREAVFHVESETGVRKLHLLADGRGHWQDG--DGEALPAFDGCLDIDIWPSPFTNTFPIRRLGLAD-GQRAEIRALYIEAPALEPRS-RQAYTRLDA-SHYLYENSAFKAVLLVDEQGLVIDYPGLFQRL

2h1tA

0.25

0.23

0.91

12.90

dPPAS2

-------SRDRLYTWAGLWRSPSS---SWEALRLEDDQAESQLRAPD--ERSGLPYQLDYRLRWDADWHLREAVFHVESETGVRKLHLLADGRGHWQDG--DGEALPAFDGCLDIDIWPSPFTNTFPIRRLGLAD-GQRAEIRALYIEAPALEPRS-RQAYTRLDA-SHYLYENSAFKAVLLVDEQGLVIDYPGLFQRL

2h1tA

0.25

0.23

0.91

4.24

PPAS

-------SRDRLYTWAGLWRSPSS---SWEALRLEDDQAESQLRAPD--ERSGLPYQLDYRLRWDADWHLREAVFHVESETGVRKLHLLADGRGHWQDG--DGEALPAFDGCLDIDIWPSPFTNTFPIRRLGLA-DGQRAEIRALYIEAPALEPRS-RQAYTRL-DASHYLYENSAFKAVLLVDEQGLVIDYPGLFQRL

2h1tA

0.25

0.23

0.91

6.19

Env-PPAS

-------SRDRLYTWAGLWRSPSS---SWEALRLEDDQAESQLRAPD--ERSGLPYQLDYRLRWDADWHLREAVFHVESETGVRKLHLLADGRGHWQDG--DGEALPAFDGCLDIDIWPSPFTNTFPIRRLGLA-DGQRAEIRALYIEAPALEPRS-RQAYTRL-DASHYLYENSAFKAVLLVDEQGLVIDYPGLFQRL

2h1tA2

0.33

0.14

0.42

1.33

MUSTER

-----------------------------------------------------------------------------------------------------------------DIDIWPSPFTNTFPIRRLGLAD-GQRAEIRALYIEAPALEPRS-RQAYTRLDA-SHYLYENSAFKAVLLVDEQGLVIDYPGLFQRL

2h1tA2

0.32

0.14

0.42

2.18

dPPAS

-----------------------------------------------------------------------------------------------------------------DIDIWPSPFTNTFPIRRLGLAD-GQRAEIRALYIEAPALEPRS-RQAYTRLDASHYLYENGSAFKAVLLVDEQGLVIDYPGLFQRL

(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=0.93

Estimated TM-score = 0.84±0.08

Estimated RMSD = 3.5±2.4Å

Download Model 2

C-score=0.41

Download Model 3

C-score=0.11

Download Model 4

C-score=-5.00

Download Model 5

C-score=-0.08

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	2h1tA	0.885	1.03	0.247	0.915
2	4d51A	0.541	4.34	0.046	0.739
3	3fidA	0.536	3.83	0.051	0.704
4	1uynX	0.533	3.89	0.045	0.704
5	3kvnX2	0.523	3.84	0.099	0.704
6	3aehA	0.514	3.70	0.070	0.683
7	2jqyA	0.514	4.39	0.061	0.749
8	3qq2A	0.503	3.86	0.032	0.683
9	4rl8A	0.500	4.20	0.075	0.699
10	1lshA	0.497	3.71	0.026	0.653

(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	2zf4E	PPY	Rep, Mult	32,34,41,123,192,196,198
2	0.06	3	4uzsC	POL	Rep, Mult	184,189
3	0.04	2	2qtkA	C8E	Rep, Mult	31,40,60
4	0.04	2	3ehbB	HEA	Rep, Mult	128,181
5	0.04	2	4qjsU	MG	Rep, Mult	125,129
6	0.04	2	2y2xA	C8E	Rep, Mult	29,57,58,59,76,83
7	0.02	1	3c9zA	UUU	Rep, Mult	53,100
8	0.02	1	3gdeA	PO4	Rep, Mult	44,166,171
9	0.02	1	1l8tA	MG	Rep, Mult	25,191
10	0.02	1	2gufA	MPG	Rep, Mult	34,35,36,37,38,63,72,73,89,97,99
11	0.02	1	4dsyA	UUU	Rep, Mult	52,124
12	0.02	1	1htwA	MG	Rep, Mult	111,116
13	0.02	1	2ikfA	MG	Rep, Mult	114,116
14	0.02	1	2aepA	GLC	Rep, Mult	74,75,87,147,148
15	0.02	1	1pj2A	NAI	Rep, Mult	130,132
16	0.02	1	1uynX	CXE	Rep, Mult	43,45,56,58
17	0.02	1	2zegB	IMD	Rep, Mult	114,151,184

	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	1kitA	0.456	5.38	0.061	0.769	3.2.1.18	NA
2	0.060	1uv4A	0.443	4.76	0.083	0.694	3.2.1.99	189
3	0.060	2aepA	0.455	4.85	0.048	0.724	3.2.1.18	65
4	0.060	2d0vA	0.445	5.64	0.041	0.799	1.1.99.8	NA
5	0.060	1eusA	0.439	4.90	0.077	0.699	3.2.1.18	NA
6	0.060	1ingA	0.454	4.73	0.062	0.714	3.2.1.18	164
7	0.060	1vlbA	0.462	5.13	0.068	0.749	1.2.99.7	NA
8	0.060	1w6sC	0.438	5.64	0.047	0.794	1.1.99.8	NA
9	0.060	1lrwA	0.443	5.62	0.041	0.794	1.1.99.8	NA
10	0.060	2agsA	0.442	5.41	0.035	0.759	3.2.1.18	41
11	0.060	1v0zA	0.456	4.81	0.041	0.719	3.2.1.18	NA
12	0.060	1nn2A	0.454	4.73	0.055	0.714	3.2.1.18	NA
13	0.060	1eutA	0.444	4.91	0.039	0.699	3.2.1.18	NA
14	0.060	1n63B	0.446	5.86	0.066	0.809	1.2.99.2	NA
15	0.060	1usrA	0.466	4.64	0.045	0.714	3.2.1.18	59,189,198
16	0.060	1kb0A	0.465	5.72	0.054	0.834	1.1.99.-	NA
17	0.060	3kvnX	0.516	4.00	0.037	0.699	3.1.1.1	NA
18	0.060	1t3qB	0.460	5.13	0.074	0.749	1.3.99.17	NA
19	0.060	1eurA	0.441	4.94	0.039	0.699	3.2.1.18	82

(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	0.10	0.525	3.65	0.08	0.69	3qq2B	GO:0005576 GO:0007155 GO:0009279 GO:0009405 GO:0009986 GO:0016020 GO:0016021 GO:0019867 GO:0042597
1	0.10	0.536	3.83	0.05	0.70	3fidA	GO:0046872
2	0.07	0.514	3.70	0.07	0.68	3aehA	GO:0004175 GO:0004252 GO:0005576 GO:0006508 GO:0008233 GO:0008236 GO:0009279 GO:0009405 GO:0009986 GO:0016020 GO:0016021 GO:0016787 GO:0019867 GO:0042597
3	0.07	0.533	3.89	0.04	0.70	1uynX	GO:0004252 GO:0006508
4	0.07	0.509	4.50	0.05	0.72	3pgrA	GO:0006810 GO:0006869 GO:0009279 GO:0015483 GO:0015718 GO:0015909 GO:0016020 GO:0016021 GO:0022834 GO:0055085
5	0.07	0.539	4.26	0.03	0.74	4v3gA	GO:0016021 GO:0098657
6	0.07	0.516	4.00	0.04	0.70	3kvnX	GO:0006629 GO:0008610 GO:0009247 GO:0009279 GO:0016020 GO:0016021 GO:0016298 GO:0016787 GO:0016788 GO:0042710 GO:0044010 GO:0048870 GO:0052689 GO:0071973 GO:0071978
7	0.07	0.506	3.73	0.02	0.68	3sloA	GO:0004175 GO:0004252 GO:0005576 GO:0006508 GO:0008233 GO:0008236 GO:0009279 GO:0009405 GO:0009986 GO:0016020 GO:0016021 GO:0016787 GO:0019867 GO:0042597
8	0.06	0.385	6.06	0.08	0.72	3e74B	GO:0000256 GO:0004038 GO:0005737 GO:0006144 GO:0008270 GO:0009442 GO:0016787 GO:0016810 GO:0046872 GO:0050897
9	0.06	0.361	5.81	0.04	0.64	3j0eH	GO:0000166 GO:0003746 GO:0003924 GO:0005525 GO:0005622 GO:0005737 GO:0005829 GO:0006412 GO:0006414
10	0.06	0.285	6.58	0.07	0.57	3fpjB	GO:0030410 GO:0030418 GO:0046872 GO:0051536 GO:0051539
11	0.06	0.308	6.34	0.06	0.62	3fcxB	GO:0005737 GO:0005788 GO:0016023 GO:0016787 GO:0016788 GO:0018738 GO:0031410 GO:0046294 GO:0047374 GO:0052689 GO:0070062 GO:1901687
12	0.06	0.346	5.89	0.03	0.64	4ohqB	GO:0003824 GO:0004807 GO:0005739 GO:0005829 GO:0006094 GO:0006096 GO:0006642 GO:0008152 GO:0009507 GO:0009536 GO:0009570 GO:0009579 GO:0009658 GO:0009941 GO:0016853 GO:0019253 GO:0019563 GO:0032504 GO:0046166 GO:0048046 GO:0080022
13	0.06	0.326	5.39	0.08	0.55	2a6wB	GO:0000139 GO:0001948 GO:0005783 GO:0005789 GO:0005794 GO:0006810 GO:0006888 GO:0015031 GO:0016020 GO:0016021 GO:0030134 GO:0030246 GO:0046872
14	0.06	0.328	5.23	0.04	0.54	1m4yA	GO:0003824 GO:0004298 GO:0005737 GO:0005839 GO:0006508 GO:0008152 GO:0008233 GO:0009376 GO:0016787 GO:0030163 GO:0046872 GO:0051603
15	0.06	0.296	5.98	0.02	0.55	4w8iA	GO:0003824 GO:0008117 GO:0016829 GO:0016831 GO:0019752 GO:0030170
16	0.06	0.304	4.72	0.04	0.48	1a0kA	GO:0003779 GO:0003785 GO:0005618 GO:0005634 GO:0005730 GO:0005737 GO:0005819 GO:0005829 GO:0005856 GO:0005886 GO:0005938 GO:0008154 GO:0009506 GO:0009524 GO:0009826 GO:0010229 GO:0015629 GO:0042989 GO:0048046 GO:0048366 GO:0048527
17	0.06	0.315	6.08	0.03	0.58	3ak5A	GO:0004175 GO:0004252 GO:0005576 GO:0006508 GO:0008233 GO:0008236 GO:0009279 GO:0009405 GO:0009986 GO:0016020 GO:0016021 GO:0016787 GO:0019867 GO:0042597
18	0.06	0.308	5.64	0.07	0.56	3gygA

Consensus prediction of GO terms

Molecular Function	GO:0004252	GO:0046872	GO:0022834	GO:0015483
GO-Score	0.13	0.10	0.07	0.07
Biological Processes	GO:0051704
GO-Score	0.32
Cellular Component	GO:0030313	GO:0019867	GO:0044462	GO:0031224
GO-Score	0.43	0.43	0.43	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.