I-TASSER results

I-TASSER results for job id Rv3361c

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

Input Sequence in FASTA format

>protein (183 residues)
MQQWVDCEFTGRDFRDEDLSRLHTERAMFSECDFSGVNLAESQHRGSAFRNCTFERTTLW
HSTFAQCSMLGSVFVACRLRPLTLDDVDFTLAVLGGNDLRGLNLTGCRLRETSLVDTDLR
KCVLRGADLSGARTTGARLDDADLRGATVDPVLWRTASLVGARVDVDQAVAFAAAHGLCL
AGG

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| MQQWVDCEFTGRDFRDEDLSRLHTERAMFSECDFSGVNLAESQHRGSAFRNCTFERTTLWHSTFAQCSMLGSVFVACRLRPLTLDDVDFTLAVLGGNDLRGLNLTGCRLRETSLVDTDLRKCVLRGADLSGARTTGARLDDADLRGATVDPVLWRTASLVGARVDVDQAVAFAAAHGLCLAGG
Prediction	CHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCC
Conf.Score	745647988899999999999866788668999999999998788988899999998889986789888898889998899877888889988899888998788988899989998889988889999999899999999999998788988888867788668999999999879977799
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| MQQWVDCEFTGRDFRDEDLSRLHTERAMFSECDFSGVNLAESQHRGSAFRNCTFERTTLWHSTFAQCSMLGSVFVACRLRPLTLDDVDFTLAVLGGNDLRGLNLTGCRLRETSLVDTDLRKCVLRGADLSGARTTGARLDDADLRGATVDPVLWRTASLVGARVDVDQAVAFAAAHGLCLAGG
Prediction	756647143541334614454032540425504263033660446403263032651456514465154543344403045034751446413454044651447514455145553546514165332643447434274342352404503055044663444362024104125136678
	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

CHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCC
MQQWVDCEFTGRDFRDEDLSRLHTERAMFSECDFSGVNLAESQHRGSAFRNCTFERTTLWHSTFAQCSMLGSVFVACRLRPLTLDDVDFTLAVLGGNDLRGLNLTGCRLRETSLVDTDLRKCVLRGADLSGARTTGARLDDADLRGATVDPVLWRTASLVGARVDVDQAVAFAAAHGLCLAGG

2bm5A

1.00

6.72

MUSTER

MQQWVDCEFTGRDFRDEDLSRLHTERAMFSECDFSGVNLAESQHRGSAFRNCTFERTTLWHSTFAQCSMLGSVFVACRLRPLTLDDVDFTLAVLGGNDLRGLNLTGCRLRETSLVDTDLRKCVLRGADLSGARTTGARLDDADLRGATVDPVLWRTASLVGARVDVDQAVAFAAAHGLCLAGG

2bm5A

1.00

8.24

dPPAS

MQQWVDCEFTGRDFRDEDLSRLHTERAMFSECDFSGVNLAESQHRGSAFRNCTFERTTLWHSTFAQCSMLGSVFVACRLRPLTLDDVDFTLAVLGGNDLRGLNLTGCRLRETSLVDTDLRKCVLRGADLSGARTTGARLDDADLRGATVDPVLWRTASLVGARVDVDQAVAFAAAHGLCLAGG

2bm5A

1.00

8.13

wdPPAS

MQQWVDCEFTGRDFRDEDLSRLHTERAMFSECDFSGVNLAESQHRGSAFRNCTFERTTLWHSTFAQCSMLGSVFVACRLRPLTLDDVDFTLAVLGGNDLRGLNLTGCRLRETSLVDTDLRKCVLRGADLSGARTTGARLDDADLRGATVDPVLWRTASLVGARVDVDQAVAFAAAHGLCLAGG

2bm5A

1.00

0.99

7.00

wMUSTER

-QQWVDCEFTGRDFRDEDLSRLHTERAMFSECDFSGVNLAESQHRGSAFRNCTFERTTLWHSTFAQCSMLGSVFVACRLRPLTLDDVDFTLAVLGGNDLRGLNLTGCRLRETSLVDTDLRKCVLRGADLSGARTTGARLDDADLRGATVDPVLWRTASLVGARVDVDQAVAFAAAHGLCLAGG

2bm5A

1.00

5.44

wPPAS

MQQWVDCEFTGRDFRDEDLSRLHTERAMFSECDFSGVNLAESQHRGSAFRNCTFERTTLWHSTFAQCSMLGSVFVACRLRPLTLDDVDFTLAVLGGNDLRGLNLTGCRLRETSLVDTDLRKCVLRGADLSGARTTGARLDDADLRGATVDPVLWRTASLVGARVDVDQAVAFAAAHGLCLAGG

2bm5A

1.00

7.69

dPPAS2

MQQWVDCEFTGRDFRDEDLSRLHTERAMFSECDFSGVNLAESQHRGSAFRNCTFERTTLWHSTFAQCSMLGSVFVACRLRPLTLDDVDFTLAVLGGNDLRGLNLTGCRLRETSLVDTDLRKCVLRGADLSGARTTGARLDDADLRGATVDPVLWRTASLVGARVDVDQAVAFAAAHGLCLAGG

2bm5A

1.00

5.20

PPAS

MQQWVDCEFTGRDFRDEDLSRLHTERAMFSECDFSGVNLAESQHRGSAFRNCTFERTTLWHSTFAQCSMLGSVFVACRLRPLTLDDVDFTLAVLGGNDLRGLNLTGCRLRETSLVDTDLRKCVLRGADLSGARTTGARLDDADLRGATVDPVLWRTASLVGARVDVDQAVAFAAAHGLCLAGG

2bm5A

1.00

5.59

Env-PPAS

MQQWVDCEFTGRDFRDEDLSRLHTERAMFSECDFSGVNLAESQHRGSAFRNCTFERTTLWHSTFAQCSMLGSVFVACRLRPLTLDDVDFTLAVLGGNDLRGLNLTGCRLRETSLVDTDLRKCVLRGADLSGARTTGARLDDADLRGATVDPVLWRTASLVGARVDVDQAVAFAAAHGLCLAGG

2j8kA

0.25

0.23

0.94

5.78

MUSTER

VEKLRQLYAAGRDFSIVDLRGAVLENINLSGAILHGAMLDEANLQQANLSRADLSGATLNGADLRGANLSKADLSDAILDNAILEGAILDEAVLNQANLKAANLEQAILSHANIREADLSEANLEAADLSGADLAIADLHQANLHQAALERANLTGANLEDANLE-----------GTILEGG

4yc5A

0.44

0.99

7.39

dPPAS

GADLSYANLHHANLSRANLRSADLRNANLSHANLSGANLEEANLEAANLRGADLHEANLSGADLQEANLTQANLKDANLSDANLEQADLAGADLQGAVLDGANLHGANLNNANLSEAMLTRANLEQADLSGARTTGARLDDADLRGATVDPVLWRTASLVGARVDVDQAVAFAAAHGLCLA--

(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=2.00

Estimated TM-score = 0.99±0.04

Estimated RMSD = 1.4±1.3Å

Download Model 2

C-score=-4.01

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	2bm5A	0.953	1.17	1.000	1.000
2	4yc5A	0.942	1.17	0.442	0.989
3	3pssA	0.887	1.94	0.225	0.995
4	3du1X	0.881	2.31	0.194	0.984
5	2xtwA	0.868	2.48	0.203	0.995
6	2xt2A	0.863	2.18	0.155	0.989
7	2j8kA	0.835	2.36	0.221	0.940
8	2w7zB	0.823	2.57	0.080	0.951
9	3nawA	0.794	3.04	0.181	0.967
10	2v5iA	0.744	3.53	0.044	0.989

(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.)

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	0.125	1nhcA	0.682	3.94	0.073	0.978	3.2.1.15	88
2	0.103	1hg8A	0.698	3.83	0.066	0.984	3.2.1.15	88
3	0.066	1idjA	0.709	3.66	0.066	0.945	4.2.2.10	NA
4	0.066	1nhcE	0.697	3.79	0.055	0.967	3.2.1.15	86,106,131
5	0.066	1qcxA	0.708	3.57	0.066	0.945	4.2.2.10	NA
6	0.066	1kcdA	0.697	3.81	0.112	0.973	3.2.1.15	NA
7	0.066	1pclA	0.725	3.60	0.044	0.962	4.2.2.2	108
8	0.066	1jtaA	0.660	4.04	0.045	0.962	4.2.2.2	6
9	0.066	1ia5A	0.678	3.97	0.044	0.984	3.2.1.15	NA
10	0.066	1xg2A	0.686	3.55	0.056	0.923	3.1.1.11	NA
11	0.066	1oocB	0.673	3.55	0.056	0.934	4.2.2.2	85
12	0.066	2iq7A	0.672	3.93	0.073	0.973	3.2.1.15	NA
13	0.060	1ea0A	0.636	3.72	0.068	0.896	1.4.1.13	170
14	0.060	2vdcA	0.636	3.72	0.068	0.896	1.4.1.13	NA
15	0.060	2qx3A	0.682	3.84	0.055	0.945	4.2.2.2	33
16	0.060	2ntqB	0.684	3.93	0.067	0.940	3.1.1.11	66,100
17	0.060	1rmgA	0.695	4.00	0.055	1.000	3.2.1.-	58,118
18	0.060	1czfA	0.695	3.87	0.050	0.973	3.2.1.15	128
19	0.060	1ru4A	0.728	3.55	0.082	0.973	4.2.2.2	NA
20	0.060	1bheA	0.684	3.82	0.084	0.956	3.2.1.15	88
21	0.060	1airA	0.661	4.09	0.033	0.956	4.2.2.2	NA
22	0.060	2z8gB	0.681	4.15	0.110	0.989	3.2.1.57	63,85
23	0.060	1vblA	0.707	3.81	0.071	0.967	4.2.2.2	18,78
24	0.060	1k5cA	0.696	3.82	0.112	0.973	3.2.1.15	NA
25	0.060	2pecA	0.661	4.08	0.033	0.956	4.2.2.2	105
26	0.060	1qjvA	0.681	3.84	0.067	0.940	3.1.1.11	66,88
27	0.060	3b4nA	0.647	3.64	0.075	0.874	4.2.2.2	81,98
28	0.060	3h09B	0.715	3.49	0.090	0.973	3.4.21.72	118
29	0.060	1ofdA	0.625	3.95	0.056	0.907	1.4.7.1	NA
30	0.060	1llwA	0.629	3.97	0.062	0.913	1.4.7.1	NA
31	0.060	1bn8A	0.723	3.53	0.066	0.956	4.2.2.2	78

(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.

[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.