I-TASSER results

I-TASSER results for job id Rv0333

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

Input Sequence in FASTA format

>protein (124 residues)
MTTSEIATVLAWHDALNAADIETLVALSTDDIDIGDAHGAVQGHDALRGWASSLTTTAEL
GRMYVHHGVVVVEQKITSGEDPGIARTGAAAFRVVQDHVASVFRHEDLASALAATELTED
DLVD

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MTTSEIATVLAWHDALNAADIETLVALSTDDIDIGDAHGAVQGHDALRGWASSLTTTAELGRMYVHHGVVVVEQKITSGEDPGIARTGAAAFRVVQDHVASVFRHEDLASALAATELTEDDLVD
Prediction	CCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEHCCCCCCCHHHHHHHHHHHHHCCEEEEEEEEEHCCEEEEEEEHCCCCCCCCCCCEEEEEEEHCCEEEEEEHCCCHHHHHHHHCCCHHHHCC
Conf.Score	9778999999999998787599999985899688589987457999999999979858887899969899999875688988887546789999999999999757689999998999888569
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MTTSEIATVLAWHDALNAADIETLVALSTDDIDIGDAHGAVQGHDALRGWASSLTTTAELGRMYVHHGVVVVEQKITSGEDPGIARTGAAAFRVVQDHVASVFRHEDLASALAATELTEDDLVD
Prediction	7645423302311421466314203423357152333733352252025106736142422312144210002343534656544433121020344302312415414501431614574348
	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

                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEHCCCCCCCHHHHHHHHHHHHHCCEEEEEEEEEHCCEEEEEEEHCCCCCCCCCCCEEEEEEEHCCEEEEEEHCCCHHHHHHHHCCCHHHHCC
MTTSEIATVLAWHDALNAADIETLVALSTDDIDIGDAHGAVQGHDALRGWASSLTTTAELGRMYVHHGVVVVEQKITSGEDPGIARTGAAAFRVVQDHVASVFRHEDLASALAATELTEDDLVD

5aihA

0.23

0.22

0.93

1.55

MUSTER

MT--PLETVQLFLARVNALDLDGACALLAEDVVYDNPMPTVHGRAAARAFLSQLPIDWETHAIAATGGTVLTERTDRFTLADGRTLAVMGAFDVADGSITAWRDYFDLGQFMAQMAP-------

5aifA

0.17

0.16

0.93

1.51

dPPAS

MT--PIETVTAFIAHWNSGDMEAMYDLCAEDVVWHIPMEPIAGKPAMRAAVEGFMCDWQVHAIAANGATVLTERTDGFTFTNGRRATVMGTFECAERRIIAWRDYFDMLEFQREFAG-------

4u13A

0.21

0.17

0.82

1.76

wdPPAS

FQSD-LPDIVNYFDADSCNDTDALSETFAPDAVVEDEGARHQGVVAILRWWVAA-YVAEPLESTVDGDKALVRAKVS-GRFPGSPVTLTYSFTIKDGRIARLEIQ-------------------

5aihA

0.22

0.20

0.92

1.72

wMUSTER

--MTPLETVQLFLARVNALDLDGACALLAEDVVYDNPMPTVHGRAAARAFLSQLPIDWETHAIAATGGTVLTERTDRFTLADGRTLAVMGAFDVADGSITAWRDYFDLGQFMAQMA--------

5aifA

0.18

0.16

0.89

1.77

wPPAS

MT--PIETVTAFIAHWNSGDMEAMYDLCAEDVVW-IPMEPIAGKPAMRAAVEGF-CDWQVHAIAANGATVLTERTDGFTFTNGRRATVMGTFECAERRIIAWRDYDEFQREFAG----------

5aifA

0.18

0.16

0.90

2.27

dPPAS2

MT--PIETVTAFIAHWNSGDMEAMYDLCAEDVVWHNPMEPIAGKPAMRAAVEGFMCDWQVHAIAANGATVLTERTDGFTFTNGRRATVMGTFECAERRIIAWRDYLEFQREFAG----------

5aihA

0.23

0.21

0.93

1.76

PPAS

MT--PLETVQLFLARVNALDLDGACALLAEDVVYDNPMPTVHGRAAARAFLSATAIDWETHAIAATGGTVLTERTDRFTLADGRTLAVMGAFDVADGSITAWRDYFDLGQFMAQMAP-------

2k54A

0.16

0.15

0.94

1.80

Env-PPAS

MNSEIELPVQKQLEAYNARDIDAFMAWWADDCQYYAFGNAAEIRVRHIERFKEPDLYGELLTRVIVGNVVIDHETVTRNPEGKGEVDVACIYEVENGRIAKAWFKIGEPRIVSQKS--------

5aifA

0.18

0.16

0.92

1.53

MUSTER

MT--PIETVTAFIAHWNSGDMEAMYDLCAEDVVWHNIPMPIAGKPAMRAAVEGFMCDWQVHAIAANGATVLTERTDGFTFTNGRRATVMGTFECAERRIIAWRDYFDMLEFQREFA--------

5aihA

0.23

0.22

0.93

1.48

dPPAS

MT--PLETVQLFLARVNALDLDGACALLAEDVVYDNPMPTVHGRAAARAFLSQLPIDWETHAIAATGGTVLTERTDRFTLADGRTLAVMGAFDVADGSITAWRDYFDLGQFMAQMAP-------

(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=-0.17

Estimated TM-score = 0.69±0.12

Estimated RMSD = 4.7±3.1Å

Download Model 2

C-score=-2.33

Download Model 3

C-score=-2.30

Download Model 4

C-score=-5.00

Download Model 5

C-score=-1.16

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	5aihA	0.850	1.59	0.217	0.927
2	5aifA	0.824	1.72	0.148	0.927
3	1tuhA	0.810	1.82	0.181	0.935
4	5cxoA	0.797	2.15	0.158	0.911
5	3wmdA	0.792	2.06	0.148	0.919
6	3i0yA	0.791	1.94	0.155	0.927
7	3rgaA	0.789	2.13	0.218	0.919
8	3ebtA	0.782	1.95	0.150	0.911
9	1nu3B	0.782	2.24	0.168	0.952
10	2bngC	0.778	2.50	0.161	0.935

(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	0.39	61	5kp1A	EQU	Rep, Mult	12,36,54,74,76,78,87,90,102,106
2	0.07	11	2inxA	FFP	Rep, Mult	12,16,36,74,89,90,102,104
3	0.05	8	4j8tA	DOG	Rep, Mult	13,16,24,36,50,51,89,102,104,106,111
4	0.04	6	3h3hA	UNL	Rep, Mult	12,16,34,51,54,91
5	0.01	2	3junB	AJD	Rep, Mult	20,24,47,50,51,53,57,59
6	0.01	2	1gybB	III	Rep, Mult	31,33,40,41,42,100
7	0.01	1	1nu3A	VPR	Rep, Mult	50,54,56,76,78,104,106,111,122
8	0.01	1	3en8A	CA	Rep, Mult	30,31
9	0.01	1	3fkaA	UNL	Rep, Mult	16,34,47,50,51,104
10	0.01	1	2bngB	CA	Rep, Mult	1,96

	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	0.224	1hkxA	0.659	2.91	0.101	0.879	2.7.11.17	15
2	0.219	1e3vB	0.774	2.10	0.112	0.911	5.3.3.1	36
3	0.155	1o7hB	0.728	2.81	0.050	0.927	1.14.12.12	19
4	0.074	3e99A	0.694	2.79	0.077	0.895	1.14.12.10	NA
5	0.060	1k1xA	0.469	4.07	0.031	0.734	2.4.1.25	108
6	0.060	1l7kB	0.481	4.40	0.080	0.758	5.1.3.3	NA
7	0.060	1z45A	0.491	4.58	0.094	0.815	5.1.3.2,5.1.3.3	NA
8	0.060	2ux0A	0.664	2.64	0.103	0.863	2.7.11.17	NA
9	0.060	1kv9A	0.482	4.24	0.048	0.766	1.1.99.-	NA
10	0.060	2x4mA	0.469	4.29	0.069	0.798	3.4.23.48	77
11	0.060	2uv8G	0.487	3.84	0.095	0.758	2.3.1.86	NA
12	0.060	3gzxB	0.722	2.91	0.092	0.927	1.14.12.18	60
13	0.060	3en1B	0.721	2.97	0.092	0.935	1.14.12.3,1.14.12.11	27
14	0.060	2wyhA	0.474	4.14	0.078	0.774	3.2.1.24	NA
15	0.060	4stdA	0.773	2.86	0.097	1.000	4.2.1.94	NA
16	0.060	1bglA	0.465	4.28	0.029	0.782	3.2.1.23	NA
17	0.060	8choA	0.765	2.22	0.191	0.911	5.3.3.1	15,25,27,36,48
18	0.060	2v7oA	0.315	4.50	0.051	0.548	2.7.11.17	14
19	0.060	3lrkA	0.485	4.35	0.043	0.782	3.2.1.22	NA
20	0.060	3mwxA	0.472	4.50	0.061	0.815	5.1.3.3	NA
21	0.060	2cirA	0.500	4.01	0.020	0.782	5.1.3.15	NA
22	0.060	2aaaA	0.475	3.86	0.027	0.718	3.2.1.1	NA
23	0.060	1yiqA	0.488	4.35	0.038	0.790	1.1.99.-	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	0.38	0.727	2.53	0.22	0.90	1buqA	GO:0004769 GO:0005622 GO:0006629 GO:0006810 GO:0008202 GO:0016853
1	0.33	0.793	2.02	0.16	0.91	5cxoB	GO:0016787
2	0.32	0.802	2.06	0.17	0.96	4xbxC	GO:0016787 GO:0018744
3	0.31	0.783	2.17	0.12	0.91	3t8nB	GO:0004769 GO:0006629 GO:0008202 GO:0016853
4	0.31	0.818	2.21	0.18	0.99	4r9kC	GO:0016787 GO:0018744
5	0.30	0.744	2.39	0.13	0.89	4cdlA	GO:0004769 GO:0006629 GO:0008202 GO:0016853
6	0.29	0.797	2.25	0.21	0.93	4rzmB	GO:0016853 GO:0017000
7	0.29	0.779	2.17	0.14	0.91	2a15A	GO:0005622 GO:0006810 GO:0016853 GO:0032934 GO:0042803
8	0.29	0.795	2.08	0.15	0.92	3wmdB	GO:0016853
9	0.27	0.784	2.35	0.16	0.94	2bngC	GO:0004301 GO:0005886 GO:0016787 GO:0033963 GO:0097176
10	0.26	0.725	2.42	0.15	0.89	3lygA
11	0.11	0.707	2.16	0.19	0.82	4xb5A	GO:0005622 GO:0006810 GO:0007165 GO:0009579 GO:0009881 GO:0016020 GO:0016037 GO:0018298 GO:0030089 GO:0031404 GO:0042651 GO:0050896
12	0.11	0.707	2.18	0.17	0.82	1m98A	GO:0005622 GO:0006810 GO:0007165 GO:0009579 GO:0009881 GO:0016020 GO:0016037 GO:0018298 GO:0030089 GO:0031404 GO:0042651 GO:0050896
13	0.06	0.354	4.60	0.06	0.62	3aqbD	GO:0000287 GO:0008299 GO:0009234 GO:0016740 GO:0016765 GO:0036423 GO:0046872
14	0.06	0.303	5.74	0.03	0.65	1yw4A	GO:0006525 GO:0008152 GO:0008270 GO:0009017 GO:0016787 GO:0016788 GO:0019544 GO:0019545 GO:0046872
15	0.06	0.332	4.69	0.09	0.59	2yg8A	GO:0003824 GO:0006281 GO:0006284 GO:0008152 GO:0016798 GO:0019104
16	0.06	0.288	4.79	0.06	0.51	2e55A	GO:0000166 GO:0000287 GO:0003824 GO:0004845 GO:0004849 GO:0005525 GO:0005829 GO:0006206 GO:0006223 GO:0008152 GO:0008655 GO:0016740 GO:0016757 GO:0043097 GO:0044206
17	0.06	0.320	5.56	0.06	0.68	4wzzA	GO:0043190
18	0.06	0.330	4.75	0.08	0.63	2onkA	GO:0000166 GO:0005524 GO:0005886 GO:0006810 GO:0015412 GO:0015689 GO:0016020 GO:0016787 GO:0016887

Consensus prediction of GO terms

Molecular Function	GO:0004769	GO:0018744
GO-Score	0.57	0.53
Biological Processes	GO:0008202	GO:0006810
GO-Score	0.57	0.38
Cellular Component	GO:0005622
GO-Score	0.38

(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.