I-TASSER results

I-TASSER results for job id Rv2179c

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

Input Sequence in FASTA format

>protein (168 residues)
MRYFYDTEFIEDGHTIELISIGVVAEDGREYYAVSTEFDPERAGSWVRTHVLPKLPPPAS
QLWRSRQQIRLDLEEFLRIDGTDSIELWAWVGAYDHVALCQLWGPMTALPPTVPRFTREL
RQLWEDRGCPRMPPRPRDVHDALVDARDQLRRFRLITSTDDAGRGAAR

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MRYFYDTEFIEDGHTIELISIGVVAEDGREYYAVSTEFDPERAGSWVRTHVLPKLPPPASQLWRSRQQIRLDLEEFLRIDGTDSIELWAWVGAYDHVALCQLWGPMTALPPTVPRFTRELRQLWEDRGCPRMPPRPRDVHDALVDARDQLRRFRLITSTDDAGRGAAR
Prediction	CEEEEEEEHCCCCCCCEEEEEEEHCCCCCEEEEEHCCCCHHHHCHHHHHHHHHCCCCCCCHHHCCHHHHHHHHHHHHHCCCCCCCEEEEHCCCCHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCC
Conf.Score	989998565489998668999998589987999857899788758999987655899987555789999999999997589999589985555558999999887555775577665568999999799888878899986899999999999999998765677789
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MRYFYDTEFIEDGHTIELISIGVVAEDGREYYAVSTEFDPERAGSWVRTHVLPKLPPPASQLWRSRQQIRLDLEEFLRIDGTDSIELWAWVGAYDHVALCQLWGPMTALPPTVPRFTRELRQLWEDRGCPRMPPRPRDVHDALVDARDQLRRFRLITSTDDAGRGAAR
Prediction	630000001165564140000000254244001103614474025003620143045463533442540252025004447753010000123210000020024146125512410440242146364471365374411002004302531410452364555568
	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

                   |                   |                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CEEEEEEEHCCCCCCCEEEEEEEHCCCCCEEEEEHCCCCHHHHCHHHHHHHHHCCCCCCCHHHCCHHHHHHHHHHHHHCCCCCCCEEEEHCCCCHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCC
MRYFYDTEFIEDGHTIELISIGVVAEDGREYYAVSTEFDPERAGSWVRTHVLPKLPPPASQLWRSRQQIRLDLEEFLRIDGTDSIELWAWVGAYDHVALCQLWGPMTALPPTVPRFTRELRQLWEDRGCPRMPPRPRDVHDALVDARDQLRRFRLITSTDDAGRGAAR

4hecA

0.99

0.90

0.91

3.40

MUSTER

VRYFYDTEFIEDGHTIELISIGVVAEDGREYYAVSTEFDPERAGSWVRTHVLPKLPPPASQLWRSRQQIRLDLEEFLRIDGTDSIELWAWVGAYDHVALCQLWGPMTALPPTVPRFTRELRQLWEDRGCPRMPP-----HDALVDARDQLRRFRLITS----------

4hecA

0.99

0.90

0.91

5.11

dPPAS

VRYFYDTEFIEDGHTIELISIGVVAEDGREYYAVSTEFDPERAGSWVRTHVLPKLPPPASQLWRSRQQIRLDLEEFLRIDGTDSIELWAWVGAYDHVALCQLWGPMTALPPTVPRFTRELRQLWEDRGCPRMPP-----HDALVDARDQLRRFRLITS----------

4hecA

0.99

0.90

0.91

6.30

wdPPAS

VRYFYDTEFIEDGHTIELISIGVVAEDGREYYAVSTEFDPERAGSWVRTHVLPKLPPPASQLWRSRQQIRLDLEEFLRIDGTDSIELWAWVGAYDHVALCQLWGPMTALPPTVPRFTRELRQLWEDRGCPRMP-----PHDALVDARDQLRRFRLITS----------

4hecA

0.99

0.90

0.91

4.12

wMUSTER

VRYFYDTEFIEDGHTIELISIGVVAEDGREYYAVSTEFDPERAGSWVRTHVLPKLPPPASQLWRSRQQIRLDLEEFLRIDGTDSIELWAWVGAYDHVALCQLWGPMTALPPTVPRFTRELRQLWEDRGCPRMPP-----HDALVDARDQLRRFRLITS----------

4hecA

0.99

0.90

0.91

6.15

wPPAS

VRYFYDTEFIEDGHTIELISIGVVAEDGREYYAVSTEFDPERAGSWVRTHVLPKLPPPASQLWRSRQQIRLDLEEFLRIDGTDSIELWAWVGAYDHVALCQLWGPMTALPPTVPRFTRELRQLWEDRGCPRMPP-----HDALVDARDQLRRFRLITS----------

4hecA

0.99

0.90

0.91

16.00

dPPAS2

VRYFYDTEFIEDGHTIELISIGVVAEDGREYYAVSTEFDPERAGSWVRTHVLPKLPPPASQLWRSRQQIRLDLEEFLRIDGTDSIELWAWVGAYDHVALCQLWGPMTALPPTVPRFTRELRQLWEDRGCPRMPP-----HDALVDARDQLRRFRLITS----------

4hecA

0.99

0.90

0.91

5.36

PPAS

VRYFYDTEFIEDGHTIELISIGVVAEDGREYYAVSTEFDPERAGSWVRTHVLPKLPPPASQLWRSRQQIRLDLEEFLRIDGTDSIELWAWVGAYDHVALCQLWGPMTALPPTVPRFTRELRQLWEDRGCPRMPP-----HDALVDARDQLRRFRLITS----------

4hecA

0.99

0.90

0.91

5.60

Env-PPAS

VRYFYDTEFIEDGHTIELISIGVVAEDGREYYAVSTEFDPERAGSWVRTHVLPKLPPPASQLWRSRQQIRLDLEEFLRIDGTDSIELWAWVGAYDHVALCQLWGPMTALPPTVPRFTRELRQLWEDRGCPRMPP-----HDALVDARDQLRRFRLITS----------

1wljA

0.17

0.15

0.93

1.21

MUSTER

EVVAMDCEMVGPHRESGLARCSLVNVHGAVLYDKFIRPE-GEITDYR--TRVSGVTPQHMVGATPFAVARLEILQLLKGK-----LVVGHDLKHDFQALKEDMSGYTLLWREAKL--VSLRVLSERLLHKSIQNS-LLGHSSVEDARATMELYQISQRIRAR-RGLPR

1wljA

0.14

0.13

0.90

1.03

dPPAS

EVVAMDCEMVGPHRESGLARCSLVNVHGAVLYDKFIEGEITDYRTRVSGVTPQHMVGAT-----PFAVARLEILQLLKGK-----LVVGHDLKHDFQALK------EDMSGYTIYDTSTDRLLWREAKLVSLIQNSLLGHSSVEDARATMELYQISQRIRARRGLPRL

(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=1.63

Estimated TM-score = 0.94±0.05

Estimated RMSD = 1.9±1.6Å

Download Model 2

C-score=-1.87

Download Model 3

C-score=-0.05

Download Model 4

C-score=-1.83

Download Model 5

C-score=-2.90

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	4hecA	0.891	0.78	0.987	0.911
2	2f96A	0.767	3.12	0.130	0.958
3	5l7zA	0.756	3.34	0.093	0.946
4	2gbzA	0.755	2.92	0.145	0.946
5	2d5rA	0.749	3.40	0.123	0.970
6	4rg8A	0.749	3.23	0.088	0.946
7	2p51A	0.745	3.58	0.146	0.976
8	2is3A	0.743	3.14	0.125	0.934
9	3d45A	0.740	3.29	0.086	0.934
10	5cy4A	0.738	2.96	0.128	0.929

(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	0.52	82	1j53A	MN	Rep, Mult	6,7,8,145
2	0.16	33	3g10A	MN	Rep, Mult	6,90,95
3	0.16	30	2iocB	D5M	Rep, Mult	6,7,8,9,11,44,46,47,50,51,94,145
4	0.02	3	4okkA	MG	Rep, Mult	5,6,89,90,145,149
5	0.01	3	5dk5A	MES	Rep, Mult	8,50,51,141,145
6	0.00	1	3ngyD	III	Rep, Mult	65,67,68,71,75
7	0.00	1	4okeB	MG	Rep, Mult	37,65,66,67

	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	0.527	2gbzA	0.755	2.92	0.145	0.946	3.1.-.-	8,140
2	0.428	2is3B	0.663	2.72	0.126	0.792	3.1.13.-	8,140
3	0.168	1w0hA	0.737	3.22	0.121	0.934	3.1.11.-	95,143
4	0.093	1fxxA	0.753	3.13	0.087	0.958	3.1.11.1	8,140
5	0.067	2p51A	0.745	3.58	0.146	0.976	3.1.13.4	6,143,147
6	0.060	2guiA	0.709	3.00	0.135	0.881	2.7.7.7	8,140
7	0.060	1hjrC	0.469	4.35	0.065	0.702	3.1.22.4	6,99,148
8	0.060	2o4iA	0.733	3.18	0.133	0.923	3.1.11.2	6,8,94,99,145
9	0.060	1q8iA	0.624	3.74	0.133	0.839	2.7.7.7	76,146
10	0.060	2jguA	0.636	3.65	0.103	0.851	2.7.7.7	70,74
11	0.060	2ajqA	0.598	3.07	0.109	0.762	2.7.7.7	70,101
12	0.060	1s5jA	0.648	3.36	0.123	0.845	2.7.7.7	NA
13	0.060	2oa8B	0.732	3.12	0.133	0.923	3.1.11.2	6,8,94,145
14	0.060	2p1jB	0.584	3.66	0.129	0.756	2.7.7.7	NA
15	0.060	1tgoA	0.639	3.37	0.097	0.845	2.7.7.7	113
16	0.060	1cjyA	0.467	4.88	0.051	0.744	3.1.1.4,3.1.1.5	NA
17	0.060	1whvA	0.222	4.74	0.096	0.363	3.1.13.4	101
18	0.060	2zf5Y	0.471	4.89	0.041	0.798	2.7.1.30	NA
19	0.060	3flcX	0.433	4.73	0.086	0.714	2.7.1.30	98
20	0.060	1wljA	0.686	3.12	0.101	0.881	3.1.13.1	8,140
21	0.060	2gv9B	0.634	3.53	0.135	0.851	2.7.7.7	29,135,145
22	0.060	2a1rB	0.747	3.27	0.081	0.946	3.1.13.4	9,10
23	0.060	3hz6A	0.477	4.86	0.048	0.786	2.7.1.17	49

(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	0.67	0.921	1.11	0.98	0.96	4hecB	GO:0000287 GO:0003676 GO:0004518 GO:0004527 GO:0004532 GO:0008408 GO:0016787 GO:0040007 GO:0046872 GO:0090305 GO:0090503
1	0.52	0.742	3.16	0.11	0.95	2igiA	GO:0000175 GO:0003676 GO:0004518 GO:0004527 GO:0005737 GO:0005829 GO:0006259 GO:0006401 GO:0008310 GO:0016787 GO:0016788 GO:0016896 GO:0034611 GO:0046872 GO:0090305 GO:0090501 GO:0090503
2	0.38	0.751	2.87	0.14	0.93	3tr8A	GO:0000175 GO:0003676 GO:0004518 GO:0004527 GO:0005737 GO:0016787 GO:0016788 GO:0016896 GO:0090305 GO:0090503
3	0.35	0.755	2.92	0.14	0.95	2gbzA	GO:0000175 GO:0003676 GO:0004518 GO:0004527 GO:0005737 GO:0016787 GO:0016788 GO:0016896 GO:0090305 GO:0090503
4	0.33	0.777	3.19	0.13	0.98	2f96A	GO:0000287 GO:0003676 GO:0004518 GO:0004527 GO:0004540 GO:0006396 GO:0008033 GO:0016787 GO:0016896 GO:0046872 GO:0090305 GO:0090501 GO:0090503
5	0.31	0.703	2.96	0.14	0.86	3ngyC	GO:0000287 GO:0003676 GO:0004518 GO:0004527 GO:0004540 GO:0005829 GO:0006396 GO:0008033 GO:0016787 GO:0016896 GO:0046872 GO:0090305 GO:0090501 GO:0090503
6	0.29	0.745	3.19	0.13	0.95	1j9aA	GO:0000175 GO:0003676 GO:0004518 GO:0004527 GO:0005737 GO:0016787 GO:0016788 GO:0016896 GO:0090305 GO:0090503
7	0.28	0.749	2.98	0.13	0.94	5cy4C	GO:0003676 GO:0004518 GO:0004527 GO:0005737 GO:0016787 GO:0016788 GO:0016896 GO:0090305 GO:0090503
8	0.26	0.710	3.26	0.11	0.91	5fkvD	GO:0003676 GO:0003677 GO:0003887 GO:0004518 GO:0004527 GO:0006260 GO:0016740 GO:0016779 GO:0016787 GO:0044776 GO:0045004 GO:0046872 GO:0071897 GO:0090305
9	0.23	0.749	3.23	0.09	0.95	4rg8A	GO:0003676 GO:0004518 GO:0004527 GO:0004529 GO:0006281 GO:0006974 GO:0008852 GO:0016787 GO:0046872 GO:0090305
10	0.22	0.584	3.66	0.13	0.76	2p1jB	GO:0003676 GO:0003677 GO:0003824 GO:0003887 GO:0004518 GO:0004527 GO:0005737 GO:0006260 GO:0006261 GO:0008408 GO:0016740 GO:0016779 GO:0016787 GO:0071897 GO:0090305
11	0.15	0.788	3.17	0.13	0.98	3v9xB	GO:0000287 GO:0003676 GO:0004518 GO:0004527 GO:0004540 GO:0005829 GO:0006396 GO:0008033 GO:0016787 GO:0016896 GO:0046872 GO:0090305 GO:0090501 GO:0090503
12	0.14	0.751	3.33	0.08	0.95	2a1sC	GO:0000166 GO:0000184 GO:0000289 GO:0003676 GO:0003723 GO:0003730 GO:0004518 GO:0004527 GO:0004535 GO:0005634 GO:0005730 GO:0005737 GO:0005829 GO:0006402 GO:0007292 GO:0009451 GO:0016787 GO:0019901 GO:0043488 GO:0044822 GO:0046872 GO:0090305 GO:0090503
13	0.14	0.751	3.48	0.12	0.98	4gmjB	GO:0000175 GO:0000289 GO:0000290 GO:0000932 GO:0003676 GO:0003700 GO:0003723 GO:0004518 GO:0004527 GO:0004532 GO:0004535 GO:0004871 GO:0005634 GO:0005654 GO:0005737 GO:0005829 GO:0005975 GO:0006351 GO:0006355 GO:0006417 GO:0006977 GO:0007165 GO:0008284 GO:0008285 GO:0010629 GO:0016020 GO:0016787 GO:0030014 GO:0031047 GO:0033962 GO:0035195 GO:0043928 GO:0045944 GO:0046872 GO:0060213 GO:0061014 GO:0090305 GO:0090503 GO:1900153
14	0.13	0.752	3.20	0.08	0.96	4js4A	GO:0000175 GO:0000287 GO:0000738 GO:0003676 GO:0003677 GO:0003697 GO:0004518 GO:0004527 GO:0004529 GO:0006281 GO:0006308 GO:0006974 GO:0008310 GO:0008852 GO:0016787 GO:0046872 GO:0051575 GO:0090503
15	0.13	0.745	3.58	0.15	0.98	2p51A	GO:0000289 GO:0003676 GO:0003723 GO:0003729 GO:0004518 GO:0004527 GO:0004535 GO:0005634 GO:0005737 GO:0005829 GO:0006351 GO:0006355 GO:0016787 GO:0030014 GO:0030015 GO:0046872 GO:0090305 GO:0090503
16	0.12	0.741	3.38	0.15	0.97	4b8cA	GO:0000175 GO:0000289 GO:0000932 GO:0003676 GO:0003723 GO:0004518 GO:0004527 GO:0005634 GO:0005737 GO:0006351 GO:0006355 GO:0006357 GO:0006368 GO:0016787 GO:0030015 GO:0032968 GO:0046872 GO:0090305 GO:0090503
17	0.12	0.725	3.34	0.07	0.94	3c95A	GO:0000175 GO:0000287 GO:0000738 GO:0003676 GO:0003677 GO:0003697 GO:0004518 GO:0004527 GO:0004529 GO:0006281 GO:0006308 GO:0006974 GO:0008310 GO:0008852 GO:0016787 GO:0046872 GO:0051575 GO:0090503
18	0.11	0.727	3.30	0.09	0.92	3d45B	GO:0000166 GO:0000184 GO:0000289 GO:0003676 GO:0003723 GO:0004518 GO:0004527 GO:0004535 GO:0005634 GO:0005730 GO:0005737 GO:0006402 GO:0016787 GO:0019901 GO:0044822 GO:0046872 GO:0090305 GO:0090503

Consensus prediction of GO terms

Molecular Function	GO:0003676	GO:0000175	GO:0000287	GO:0034611	GO:0008310
GO-Score	0.96	0.81	0.78	0.52	0.52
Biological Processes	GO:0090503	GO:0040007	GO:0006401	GO:0006259	GO:0008033
GO-Score	0.96	0.67	0.52	0.52	0.33
Cellular Component	GO:0005829
GO-Score	0.52

(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.