I-TASSER results

I-TASSER results for job id Rv0813c

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

Input Sequence in FASTA format

>protein (226 residues)
MSSGAGSDATGAGGVHAAGSGDRAVAAAVERAKATAARNIPAFDDLPVPADTANLREGAD
LNNALLALLPLVGVWRGEGEGRGPDGDYRFGQQIVVSHDGGDYLNWESRSWRLTATGDYQ
EPGLREAGFWRFVADPYDPSESQAIELLLAHSAGYVELFYGRPRTQSSWELVTDALARSR
SGVLVGGAKRLYGIVEGGDLAYVEERVDADGGLVPHLSARLSRFVG

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 220 \| \| \| \| \| \| \| \| \| \| \| MSSGAGSDATGAGGVHAAGSGDRAVAAAVERAKATAARNIPAFDDLPVPADTANLREGADLNNALLALLPLVGVWRGEGEGRGPDGDYRFGQQIVVSHDGGDYLNWESRSWRLTATGDYQEPGLREAGFWRFVADPYDPSESQAIELLLAHSAGYVELFYGRPRTQSSWELVTDALARSRSGVLVGGAKRLYGIVEGGDLAYVEERVDADGGLVPHLSARLSRFVG
Prediction	CCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHCCEEEEEEEEHCCCCCCEEEEEEEEEHCCCCCEEEEEEEEEHCCCCCCCCCCEEEEEEEEHCCCCCCCCCCCEEEEEEHCCCCEEEEEEEEHCCCCEEEEEHCCEEHCCCCCCCCCEEEEEEEHCCCCEEEEEEEHCCCCCCHCEEEEEEEEHCC
Conf.Score	9999999888888888889889999999999998656689988889998777778889999988988875465899988884898876557899999689996689999998488988788764678899977888888999869999987999799998787689879999765776688865555589999867995899999874999974568999998589
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 220 \| \| \| \| \| \| \| \| \| \| \| MSSGAGSDATGAGGVHAAGSGDRAVAAAVERAKATAARNIPAFDDLPVPADTANLREGADLNNALLALLPLVGVWRGEGEGRGPDGDYRFGQQIVVSHDGGDYLNWESRSWRLTATGDYQEPGLREAGFWRFVADPYDPSESQAIELLLAHSAGYVELFYGRPRTQSSWELVTDALARSRSGVLVGGAKRLYGIVEGGDLAYVEERVDADGGLVPHLSARLSRFVG
Prediction	8455455545567554442414510541464157146241341671313422341544370362020002001303141416247461512130302253433030102013135555444213301000103454555646330100002331200012032466530302242233154155045042202015534011112122573502420303045268
	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                 220

                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHCCEEEEEEEEHCCCCCCEEEEEEEEEHCCCCCEEEEEEEEEHCCCCCCCCCCEEEEEEEEHCCCCCCCCCCCEEEEEEHCCCCEEEEEEEEHCCCCEEEEEHCCEEHCCCCCCCCCEEEEEEEHCCCCEEEEEEEHCCCCCCHCEEEEEEEEHCC
MSSGAGSDATGAGGVHAAGSGDRAVAAAVERAKATAARNIPAFDDLPVPADTANLREGADLNNALLALLPLVGVWRGEGEGRGPDGDYRFGQQIVVSHDGGDYLNWESRSWRLTATGDYQEPGLREAGFWRFVADPYDPSESQAIELLLAHSAGYVELFYGRPRTQSSWELVTDALARSRSGVLVGGAKRLYGIVEGGDLAYVEERVDADGGLVPHLSARLSRFVG

2fwvA

1.00

0.84

3.52

MUSTER

--------------------------AAVERAKATAARNIPAFDDLPVPADTANLREGADLNNALLALLPLVGVWRGEGEGRGPDGDYRFGQQIVVSHDGGDYLNWESRSWRLTATGDYQEPGLREAGFWRFVA----------IELLLAHSAGYVELFYGRPRTQSSWELVTDALARSRSGVLVGGAKRLYGIVEGGDLAYVEERVDADGGLVPHLSARLSRFVG

2fwvA

1.00

0.84

6.29

dPPAS

--------------------------AAVERAKATAARNIPAFDDLPVPADTANLREGADLNNALLALLPLVGVWRGEGEGRGPDGDYRFGQQIVVSHDGGDYLNWESRSWRLTATGDYQEPGLREAGFWRFVA----------IELLLAHSAGYVELFYGRPRTQSSWELVTDALARSRSGVLVGGAKRLYGIVEGGDLAYVEERVDADGGLVPHLSARLSRFVG

2fwvA

1.00

0.84

7.44

wdPPAS

--------------------------AAVERAKATAARNIPAFDDLPVPADTANLREGADLNNALLALLPLVGVWRGEGEGRGPDGDYRFGQQIVVSHDGGDYLNWESRSWRLTATGDYQEPGLREAGFWRFVA----------IELLLAHSAGYVELFYGRPRTQSSWELVTDALARSRSGVLVGGAKRLYGIVEGGDLAYVEERVDADGGLVPHLSARLSRFVG

2fwvA

1.00

0.84

4.35

wMUSTER

--------------------------AAVERAKATAARNIPAFDDLPVPADTANLREGADLNNALLALLPLVGVWRGEGEGRGPDGDYRFGQQIVVSHDGGDYLNWESRSWRLTATGDYQEPGLREAGFWRFVA----------IELLLAHSAGYVELFYGRPRTQSSWELVTDALARSRSGVLVGGAKRLYGIVEGGDLAYVEERVDADGGLVPHLSARLSRFVG

2fwvA

1.00

0.84

6.19

wPPAS

--------------------------AAVERAKATAARNIPAFDDLPVPADTANLREGADLNNALLALLPLVGVWRGEGEGRGPDGDYRFGQQIVVSHDGGDYLNWESRSWRLTATGDYQEPGLREAGFWRFVA----------IELLLAHSAGYVELFYGRPRTQSSWELVTDALARSRSGVLVGGAKRLYGIVEGGDLAYVEERVDADGGLVPHLSARLSRFVG

2fwvA

1.00

0.84

10.69

dPPAS2

--------------------------AAVERAKATAARNIPAFDDLPVPADTANLREGADLNNALLALLPLVGVWRGEGEGRGPDGDYRFGQQIVVSHDGGDYLNWESRSWRLTATGDYQEPGLREAGFWRFVA----------IELLLAHSAGYVELFYGRPRTQSSWELVTDALARSRSGVLVGGAKRLYGIVEGGDLAYVEERVDADGGLVPHLSARLSRFVG

2fwvA

1.00

0.84

5.16

PPAS

--------------------------AAVERAKATAARNIPAFDDLPVPADTANLREGADLNNALLALLPLVGVWRGEGEGRGPDGDYRFGQQIVVSHDGGDYLNWESRSWRLTATGDYQEPGLREAGFWRFVA----------IELLLAHSAGYVELFYGRPRTQSSWELVTDALARSRSGVLVGGAKRLYGIVEGGDLAYVEERVDADGGLVPHLSARLSRFVG

2fwvA

1.00

0.84

6.12

Env-PPAS

--------------------------AAVERAKATAARNIPAFDDLPVPADTANLREGADLNNALLALLPLVGVWRGEGEGRGPDGDYRFGQQIVVSHDGGDYLNWESRSWRLTATGDYQEPGLREAGFWRFVA----------IELLLAHSAGYVELFYGRPRTQSSWELVTDALARSRSGVLVGGAKRLYGIVEGGDLAYVEERVDADGGLVPHLSARLSRFVG

2fr2A

0.30

0.20

0.68

2.38

MUSTER

-----------------------------------------------------------DLAPALQALSPLLGSWAGRGAGKYPTIPFEYLEEVVFAHVGKPFLTYTQQTRAVAD----GKPLHSETGYLRVCRP-------GCVELVLAHPSGITEIEVGTYSTGDVIELELSTIGLAPTAKEVTALDRSYRID-GDELSYSLQMRAVGQPLQDHLAAVLHRQR-

2fr2A

0.30

0.20

0.68

4.04

dPPAS

-----------------------------------------------------------DLAPALQALSPLLGSWAGRGAGKYPTIPFEYLEEVVFAHVGKPFLTYTQQTRAVAD----GKPLHSETGYLRVCR-------PGCVELVLAHPSGITEIEVGTYSTGDVIELELSTIGLAPTAKEVTALDRSYRID-GDELSYSLQMRAVGQPLQDHLAAVLHRQR-

(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=0.08

Estimated TM-score = 0.72±0.11

Estimated RMSD = 5.4±3.4Å

Download Model 2

C-score=-0.42

Download Model 3

C-score=-0.23

Download Model 4

C-score=-0.69

Download Model 5

C-score=-1.86

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	2fwvA	0.836	0.43	1.000	0.841
2	2fr2A	0.626	1.79	0.294	0.677
3	3ia8A	0.625	1.71	0.205	0.668
4	2q4nA	0.605	1.82	0.291	0.655
5	1i78A	0.525	3.53	0.031	0.655
6	4tq2A	0.514	3.67	0.103	0.655
7	1k24A	0.512	3.76	0.049	0.646
8	4yl7A	0.498	4.78	0.092	0.726
9	5ekqA	0.493	4.41	0.027	0.704
10	3kvnX	0.490	4.80	0.048	0.735

(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	0.40	6	3emmA	HEM	Rep, Mult	88,90,110,124,151,155,185,186,188,190,204,206,216,217
2	0.05	1	1ujwA	UUU	Rep, Mult	107,125,126,127,150
3	0.05	1	1tlzB	URI	Rep, Mult	90,108,110,124,126
4	0.05	1	3rgnA	MG	Rep, Mult	191,193,194,200,201
5	0.05	1	1ab00	III	Rep, Mult	73,74,95,97,99,107,109,223
6	0.05	1	1uynX	CXE	Rep, Mult	127,129,131,148,150

	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	2q2rA	0.433	5.80	0.086	0.726	2.7.1.2	NA
2	0.060	3b9jC	0.328	5.97	0.044	0.597	1.17.3.2,1.17.1.4	76
3	0.060	3b9jI	0.258	5.57	0.025	0.434	1.17.1.4,1.17.3.2	133
4	0.060	3kvnX	0.490	4.80	0.048	0.735	3.1.1.1	69
5	0.060	2iirA	0.424	6.02	0.066	0.748	2.7.2.1	NA
6	0.060	1h7aA	0.403	5.39	0.049	0.673	1.17.4.2	196
7	0.060	1a4eA	0.425	4.17	0.077	0.589	1.11.1.6	NA
8	0.060	1im0A	0.445	5.01	0.055	0.686	3.1.1.32,3.1.1.4	108
9	0.060	1i78A	0.525	3.53	0.031	0.655	3.4.23.49	NA
10	0.060	1jrpB	0.365	5.54	0.059	0.611	1.17.1.4	NA
11	0.060	1iphA	0.424	5.51	0.038	0.699	1.11.1.6	NA
12	0.060	1jroB	0.402	6.21	0.041	0.712	1.1.1.204	NA
13	0.060	1x3mA	0.422	5.77	0.073	0.717	2.7.2.15,2.7.2.-	2
14	0.060	2e20A	0.422	5.74	0.073	0.712	2.7.2.15	66
15	0.060	1rm6A	0.403	5.63	0.030	0.637	1.3.99.20	NA
16	0.060	2ckjA	0.343	5.82	0.056	0.584	1.17.1.4,1.17.3.2	NA
17	0.060	1oacB	0.406	5.45	0.045	0.655	1.4.3.21,1.4.3.6	NA
18	0.060	2iufA	0.404	5.76	0.061	0.686	1.11.1.6	NA
19	0.060	2wgqB	0.412	5.40	0.035	0.655	1.4.3.21	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	0.66	0.836	0.43	1.00	0.84	2fwvA	GO:0005886 GO:0006810
1	0.34	0.626	1.79	0.29	0.68	2fr2A	GO:0006810
2	0.29	0.650	1.70	0.20	0.69	3ia8A	GO:0003676 GO:0003677 GO:0046872
3	0.28	0.622	1.75	0.29	0.67	3wjeB	GO:0005737 GO:0005829 GO:0006810
4	0.20	0.514	3.67	0.10	0.65	4tq2A	GO:0016829 GO:0017009
5	0.12	0.485	3.35	0.09	0.60	3bdrA	GO:0016829 GO:0017006 GO:0017009
6	0.10	0.413	4.76	0.05	0.62	2vdfA	GO:0004190 GO:0006508
7	0.07	0.512	3.76	0.05	0.65	1k24A	GO:0004190 GO:0006508 GO:0046872
8	0.07	0.440	4.91	0.04	0.65	2x4mA	GO:0004175 GO:0004190 GO:0006508 GO:0007599 GO:0008233 GO:0009279 GO:0016020 GO:0016021 GO:0016787 GO:0042730
9	0.06	0.525	3.53	0.03	0.65	1i78A	GO:0004175 GO:0004190 GO:0004252 GO:0006508 GO:0008233 GO:0009279 GO:0016020 GO:0016021 GO:0016787 GO:0031230
10	0.06	0.360	6.15	0.07	0.67	1l8kA	GO:0004721 GO:0004725 GO:0004726 GO:0005178 GO:0005634 GO:0005654 GO:0005737 GO:0005783 GO:0005793 GO:0005886 GO:0006470 GO:0008285 GO:0008286 GO:0010804 GO:0010888 GO:0016020 GO:0016311 GO:0016787 GO:0016791 GO:0019901 GO:0019905 GO:0030183 GO:0030217 GO:0030218 GO:0030971 GO:0035335 GO:0042059 GO:0042512 GO:0042518 GO:0042524 GO:0042527 GO:0042593 GO:0045650 GO:0045722 GO:0046627 GO:0050728 GO:0050860 GO:0050922 GO:0060334 GO:0060336 GO:0060339 GO:0061099 GO:0070104 GO:0070373 GO:1902202 GO:1902206 GO:1902212 GO:1902215 GO:1902227 GO:1902233 GO:1902237 GO:1903899 GO:2000587
11	0.06	0.322	6.40	0.03	0.61	1acoA	GO:0003994 GO:0005506 GO:0005634 GO:0005739 GO:0006099 GO:0006101 GO:0008152 GO:0016829 GO:0043209 GO:0046872 GO:0051536 GO:0051539
12	0.06	0.343	5.83	0.03	0.59	1pytB	GO:0004180 GO:0004181 GO:0005576 GO:0005615 GO:0006508 GO:0008233 GO:0008237 GO:0008270 GO:0016787 GO:0046872
13	0.06	0.337	5.42	0.03	0.56	2c14A	GO:0003824 GO:0004655 GO:0005829 GO:0006779 GO:0006782 GO:0006783 GO:0008270 GO:0016829 GO:0033014 GO:0046872
14	0.06	0.330	5.87	0.07	0.57	4q2hA	GO:0016853 GO:0047580
15	0.06	0.281	6.27	0.07	0.51	1e3dA	GO:0008901 GO:0009375 GO:0046872 GO:0051536 GO:0051538 GO:0051539 GO:0055114
16	0.06	0.317	5.70	0.05	0.54	4dwoA	GO:0005737 GO:0016311 GO:0016787 GO:0016791 GO:0044283 GO:0046872
17	0.06	0.279	5.81	0.05	0.48	1tu7A	GO:0004364 GO:0008152 GO:0016740
18	0.06	0.292	5.96	0.05	0.52	3opnA	GO:0003723 GO:0008168 GO:0032259

Consensus prediction of GO terms

Molecular Function	GO:0043169	GO:1901363	GO:0097159
GO-Score	0.58	0.55	0.55
Biological Processes	GO:0006810	GO:0017007
GO-Score	0.84	0.39
Cellular Component	GO:0005886	GO:0044444
GO-Score	0.66	0.56

(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.