I-TASSER results

I-TASSER results for job id Rv2036

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

Input Sequence in FASTA format

>protein (213 residues)
MIAADDDTEKSMMDMARAERAELAAFLTTLTLQQWETPSLCAGWSVKEVVAHMISYEDLG
VFGLLKRFAKGRIVRANEVGVDEFAGLSPQELADYVGRHLQPRGLTAGFGGMIALVDGMI
HHQDIRRPLGQPRTIPAQRLDRVLRLMPKNPRLRARPRIKGLRLRATDLDWTIGTGPEVT
GPGEALLMAMAGRPAAVSDLSGPGKPTLAGRLG

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| MIAADDDTEKSMMDMARAERAELAAFLTTLTLQQWETPSLCAGWSVKEVVAHMISYEDLGVFGLLKRFAKGRIVRANEVGVDEFAGLSPQELADYVGRHLQPRGLTAGFGGMIALVDGMIHHQDIRRPLGQPRTIPAQRLDRVLRLMPKNPRLRARPRIKGLRLRATDLDWTIGTGPEVTGPGEALLMAMAGRPAAVSDLSGPGKPTLAGRLG
Prediction	CCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCHHHCCCCCCCCCCCHHHHHHHHHHHCCHHHHHHHHHHCCCCCHHHHHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCEEEHCCCCCEEEHCCCCEEHCHHHHHHHHHCCCCCCCEEEHCCHHHHHHHHC
Conf.Score	998888767899999999999999999859977768999999998999999886454445666666654688656679999999889999999999987888888887665466557777777764467998999999999999998765555566777657875689766776676567689999999989987765566585699998869
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| MIAADDDTEKSMMDMARAERAELAAFLTTLTLQQWETPSLCAGWSVKEVVAHMISYEDLGVFGLLKRFAKGRIVRANEVGVDEFAGLSPQELADYVGRHLQPRGLTAGFGGMIALVDGMIHHQDIRRPLGQPRTIPAQRLDRVLRLMPKNPRLRARPRIKGLRLRATDLDWTIGTGPEVTGPGEALLMAMAGRPAAVSDLSGPGKPTLAGRLG
Prediction	744546623540142034004301510570467426322305503022000100122332122203431444144124300442273315200420353253342223332322002010010200102435262345003201411343341324431320313366341322424504230210000003153234516256253036228
	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

CCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCHHHCCCCCCCCCCCHHHHHHHHHHHCCHHHHHHHHHHCCCCCHHHHHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCEEEHCCCCCEEEHCCCCEEHCHHHHHHHHHCCCCCCCEEEHCCHHHHHHHHC
MIAADDDTEKSMMDMARAERAELAAFLTTLTLQQWETPSLCAGWSVKEVVAHMISYEDLGVFGLLKRFAKGRIVRANEVGVDEFAGLSPQELADYVGRHLQPRGLTAGFGGMIALVDGMIHHQDIRRPLGQPRTIPAQRLDRVLRLMPKNPRLRARPRIKGLRLRATDLDWTIGTGPEVTGPGEALLMAMAGRPAAVSDLSGPGKPTLAGRLG

2nsgA

0.16

0.98

1.66

MUSTER

MTTFHDLPLEERLTLARLGTSHYSRQLSLVDNAEFGEHSLLEGWTRSHLIAAVAYNAIALCNLMHWANTGEETPEARNEEIAYGSTLNPDALRNLHEHSVQGRTVPASETLWMRSREVWIHAVDLGAVATFG-DIPEVILRTLAAEITQKWT--SQGAGEGLVLLDEPSSTRYPAAPGVSGSLAGIVRYAAGRGSDGVTSSTGEVPEPPRW--

2nsgA

0.15

0.99

2.01

dPPAS

MTTFHDLPLEERLTLARLGTSHYSRQLSLVDNAEFGEHSLLEGWTRSHLIAAVAYNAIALCNLMHWANTGEETPEARNEEIAYGSTLNPDALRNLHEHSAQGRTVPASETLWMRSREVWIHAVDLGAVATFG-DIPEVILRTLAAEITQKWTSQGAGEGLVLLDEPSSTRYPAAPGQDVSGSLAGIVRYAAGRGSDGVTSSTGEVPEPPRW--

2nsgA

0.17

0.16

0.97

3.59

wdPPAS

MTTFHDLPLEERLTLARLGTSHYSRQLSLVDNAEFGEHSLLEGWTRSHLIAAVAYNAIALCNLMHWANTGEVSPEARNEEIAYGSTLNPDALRNLHEHSAQGRTVPASETLWMRSREVWIHAVDLGAVATFG-DIPEVILRTLAAEITQKWT--SQGAGEGLVLLDEPSSTRYPAAPGVSGSLAGIVRYAAGRGSDGVTSSTGEVPE----PP

2nsgA

0.16

0.15

0.96

2.02

wMUSTER

-TTFHDLPLEERLTLARLGTSHYSRQLSLVDNAEFGEHSLLEGWTRSHLIAAVAYNAIALCNLMHWANTGEVSPEARNEEIAYGSTLNPDALRNLHEHSVQGRTVPASETLWMRSREVWIHAVDLGAVATFG-DIPEVILRTLAAEITQKWT--SQGAGEGLVLLDEPSSTRYPAAPGVSGSLAGIVRYAAGRGSDGVTSSTGEVP-----PP

2nsgA

0.16

0.15

0.96

3.33

wPPAS

MTTFHDLPLEERLTLARLGTSHYSRQLSLVDNAEFGEHSLLEGWTRSHLIAAVAYNAIALCNLMHWANTGEVSPEARNEEIAYGSTLNPDALRNLHEHSAQGRTVPASETLWMRSREVWIHAVDLGAVATFG-DIPEVILRTLAAEITQKWT--SQGAGEGLVLLDEPSSYPAAPGQDVSGSLAGIVRYAAGRGSDGVTSSTGE------EPP

2nsgA

0.17

0.16

0.94

5.42

dPPAS2

MTTFHDLPLEERLTLARLGTSHYSRQLSLVDNAEFGEHSLLEGWTRSHLIAAVAYNAIALCNLMHWANTGEETPEARNEEIAYGSTLNPDALRNLHEHSAQGRTVPASETLWMRSREVWIHAVDLGAVATFG-DIPEVILRTLAAEITQKWTSQG--AGEGLVLLDEPSSTRYPAAPGVSGSLAGIVRYAAGRGSDGVTSST----------G

2nsgA

0.16

0.15

0.95

2.27

PPAS

MTTFHDLPLEERLTLARLGTSHYSRQLSLVDNAEFGEHSLLEGWTRSHLIAAVAYNAIALCNLMHWANTGEVSPEARNEEIAYGSTLNPDALRNLHEHSAQGRTVPASETLWMRSREVWIHAVDLGAVATFG-DIPEVILRTLAAEITQKWT--SQGAGEGLVLLDEPSSTRYPAAPGVSGSLAGIVRYAAGRGSDGVTSSTGE-------VP

2nsgA

0.15

0.99

2.80

Env-PPAS

MTTFHDLPLEERLTLARLGTSHYSRQLSLVDNAEFGEHSLLEGWTRSHLIAAVAYNAIALCNLMHWANTGEVSPEARNEEIAYGSTLNPDALRNLHEHSAQGRTVPASETLWMRSREVWIHAVDLGAVATFG-DIPEVILRTLAAEITQKWTSQGAGEGLVLLDEPSSTRYPAAPGQDVSGSLAGIVRYAAGRGSDGVTSSTGEVPEPPRW--

2nsgA1

0.16

0.09

0.61

0.88

MUSTER

MTTFHDLPLEERLTLARLGTSHYSRQLSLVDNAEFGEHSLLEGWTRSHLIAAVAYNAIALCNLMHWANTGEETPEARNEEIAYGSTLNPDALRNLHEHSAQGRTVPASETLWMRSREVWIHAVDLG-AVA-----------------------------------------------------------------------------------

2nsgA1

0.13

0.09

0.71

1.29

dPPAS

MTTFHDLPLEERLTLARLGTSHYSRQLSLVDNAEFGEHSLLEGWTRSHLIAAVAYNAIALCNLMHWANTGEETPEARNEEIAYGSTLNPDALRNLHEHSVARLDVAWRETSEDAWSHE------VLTAQGRTVPASETLWMRSREVWIHAVDLGAVA--------------------------------------------------------

(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 2 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=0.56

Estimated TM-score = 0.79±0.09

Estimated RMSD = 4.3±2.9Å

Download Model 2

C-score=-3.31

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	2nsgA	0.919	1.45	0.154	0.977
2	4x8bA	0.566	4.35	0.092	0.779
3	5cofA	0.503	2.77	0.119	0.596
4	4n6cA	0.491	2.86	0.090	0.592
5	1ogyA	0.490	5.59	0.059	0.859
6	2nyaA	0.489	5.66	0.063	0.859
7	5civA	0.486	2.91	0.123	0.582
8	5cogA	0.484	2.82	0.100	0.582
9	1h0hA	0.484	5.88	0.074	0.855
10	2z1qB	0.482	4.59	0.073	0.700

(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	0.55	8	2nsfA	ZN	Rep, Mult	52,117,121
2	0.10	2	2z1qB	FAD	Rep, Mult	30,49,125,126,127

	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	2nyaA	0.489	5.66	0.063	0.859	1.7.99.4	NA
2	0.060	2xaaA	0.418	5.39	0.053	0.695	1.1.1.1	NA
3	0.060	2ipyA	0.323	5.69	0.015	0.545	4.2.1.3	NA
4	0.060	1u2zC	0.424	5.85	0.063	0.756	2.1.1.43	24,27,50,125,135
5	0.060	2ivfA	0.418	5.70	0.048	0.723	1.17.99.2	95
6	0.060	1kqfA	0.478	5.97	0.069	0.855	1.2.1.2	NA
7	0.060	1rjwA	0.414	5.49	0.054	0.685	1.1.1.1	NA
8	0.060	1l7qA	0.378	5.81	0.050	0.671	3.1.1.1	122
9	0.060	1thgA	0.423	5.78	0.043	0.742	3.1.1.3	NA
10	0.060	1q16A	0.449	5.81	0.064	0.779	1.7.99.4	NA
11	0.060	3co8A	0.422	5.25	0.052	0.681	5.1.1.1	NA
12	0.060	1q6xA	0.354	6.20	0.037	0.662	2.3.1.6	NA
13	0.060	1e3eA	0.349	6.17	0.066	0.653	1.1.1.1	NA
14	0.060	2d1rA	0.412	5.90	0.021	0.737	1.13.12.7	NA
15	0.060	2fj0A	0.420	5.85	0.026	0.728	3.1.1.1	NA
16	0.060	2ow6A	0.413	5.95	0.051	0.737	3.2.1.114	NA
17	0.060	1vfsA	0.415	5.40	0.122	0.690	5.1.1.1	NA
18	0.060	1h0hA	0.484	5.88	0.074	0.855	1.2.1.2	NA
19	0.060	1cjyA	0.410	5.80	0.061	0.732	3.1.1.4,3.1.1.5	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	0.49	0.916	1.48	0.16	0.98	2nsfA	GO:0046872
1	0.07	0.566	4.35	0.09	0.78	4x8bA	GO:0004497 GO:0005506 GO:0016491 GO:0016705 GO:0046872 GO:0052699 GO:0055114
2	0.07	0.490	2.95	0.10	0.59	5cogB	GO:0005634 GO:0005737 GO:0006312
3	0.06	0.309	6.00	0.04	0.53	3b8gA	GO:0004042 GO:0005737 GO:0006526 GO:0008080 GO:0008652 GO:0016740 GO:0016746
4	0.06	0.307	6.55	0.04	0.60	2akzA	GO:0000015 GO:0000287 GO:0001917 GO:0004634 GO:0005615 GO:0005622 GO:0005737 GO:0005829 GO:0005886 GO:0006094 GO:0006096 GO:0016020 GO:0016829 GO:0043025 GO:0043204 GO:0043209 GO:0046872 GO:0061621 GO:0070062
5	0.06	0.329	5.45	0.04	0.53	2y3cA	GO:0046872
6	0.06	0.325	5.94	0.04	0.57	3amgB	GO:0004553 GO:0005576 GO:0005975 GO:0006073 GO:0008152 GO:0008422 GO:0009251 GO:0009986 GO:0016787 GO:0016798
7	0.06	0.339	5.38	0.06	0.57	5dn1A	GO:0000105 GO:0000162 GO:0003824 GO:0003949 GO:0004640 GO:0005622 GO:0005737 GO:0008152 GO:0008652 GO:0009073 GO:0016853
8	0.06	0.313	6.15	0.03	0.59	2qsgA	GO:0000111 GO:0000122 GO:0003677 GO:0003684 GO:0003697 GO:0005634 GO:0005737 GO:0005829 GO:0006265 GO:0006281 GO:0006289 GO:0006298 GO:0006974 GO:0043161 GO:0071942 GO:1990165
9	0.06	0.288	6.37	0.03	0.55	2x7gA	GO:0000166 GO:0000245 GO:0000287 GO:0001525 GO:0004672 GO:0004674 GO:0005524 GO:0005634 GO:0005654 GO:0005730 GO:0005737 GO:0006397 GO:0006468 GO:0008284 GO:0008380 GO:0010628 GO:0016301 GO:0016310 GO:0016740 GO:0030154 GO:0035063 GO:0035556 GO:0043525 GO:0044822 GO:0045070 GO:0045071 GO:0045087 GO:0045787 GO:0048024 GO:0071889
10	0.06	0.330	5.75	0.08	0.57	1y1hX	GO:0005783 GO:0005788 GO:0006687 GO:0016491 GO:0042803 GO:0043687 GO:0046872 GO:0055114
11	0.06	0.309	6.28	0.07	0.56	4a82A	GO:0000166 GO:0005524 GO:0005886 GO:0006810 GO:0016020 GO:0016021 GO:0016787 GO:0016887 GO:0042626 GO:0055085
12	0.06	0.337	5.75	0.08	0.58	3fwnA	GO:0004616 GO:0005829 GO:0006098 GO:0016491 GO:0019521 GO:0042802 GO:0042803 GO:0055114
13	0.06	0.266	5.59	0.04	0.46	4hkaA	GO:0004833 GO:0006569 GO:0006727 GO:0016491 GO:0019441 GO:0019442 GO:0020037 GO:0046872 GO:0048072 GO:0051213 GO:0055114 GO:0070189 GO:1901216
14	0.06	0.287	4.80	0.04	0.43	2kvpA	GO:0001726 GO:0003779 GO:0005178 GO:0005200 GO:0005737 GO:0005815 GO:0005856 GO:0005886 GO:0005925 GO:0007016 GO:0007044 GO:0007155 GO:0009986 GO:0016020 GO:0017166 GO:0030054 GO:0030274 GO:0030866 GO:0032403 GO:0032587 GO:0042995 GO:0051015 GO:0070062 GO:0070527
15	0.06	0.289	6.57	0.05	0.58	1y4jB	GO:0005783 GO:0005788 GO:0043687 GO:0046872
16	0.06	0.306	6.10	0.04	0.56	2q17E	GO:0046872
17	0.06	0.256	5.92	0.05	0.46	4meeA	GO:0005576 GO:0007155 GO:0009279 GO:0009405 GO:0009986 GO:0016020 GO:0016021 GO:0019867 GO:0042597
18	0.06	0.240	5.91	0.04	0.43	4gh8A	GO:0004146 GO:0005829 GO:0006545 GO:0006730 GO:0009165 GO:0016491 GO:0031427 GO:0042493 GO:0046654 GO:0046677 GO:0050661 GO:0055114

Consensus prediction of GO terms

Molecular Function	GO:0046872
GO-Score	0.55
Biological Processes	GO:0052699	GO:0006312	GO:0006094	GO:0061621	GO:0006526
GO-Score	0.07	0.07	0.06	0.06	0.06
Cellular Component	GO:0044424
GO-Score	0.36

(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.