I-TASSER results

I-TASSER results for job id Rv1331

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

Input Sequence in FASTA format

>protein (101 residues)
MAVVSAPAKPGTTWQRESAPVDVTDRAWVTIVWDDPVNLMSYVTYVFQKLFGYSEPHATK
LMLQVHNEGKAVVSAGSRESMEVDVSKLHAAGLWATMQQDR

Predicted Secondary Structure

Sequence	20 40 60 80 100 \| \| \| \| \| MAVVSAPAKPGTTWQRESAPVDVTDRAWVTIVWDDPVNLMSYVTYVFQKLFGYSEPHATKLMLQVHNEGKAVVSAGSRESMEVDVSKLHAAGLWATMQQDR
Prediction	CCCCCCCCCCCCEEEEEHCCCCCCCCCEEEEEHCCCCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHCEEEEEEHCHHHHHHHHHHHHHCCCEEEEEHCC
Conf.Score	99988888998667776544457899858999779999757999999999899999999999999875858999876588999999999669879997689
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 \| \| \| \| \| MAVVSAPAKPGTTWQRESAPVDVTDRAWVTIVWDDPVNLMSYVTYVFQKLFGYSEPHATKLMLQVHNEGKAVVSAGSRESMEVDVSKLHAAGLWATMQQDR
Prediction	75644555556454456466565555302000110731324100300341072447403400240145030201313454034205404734140423568
	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

                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCCCCCCCCCCEEEEEHCCCCCCCCCEEEEEHCCCCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHCEEEEEEHCHHHHHHHHHHHHHCCCEEEEEHCC
MAVVSAPAKPGTTWQRESAPVDVTDRAWVTIVWDDPVNLMSYVTYVFQKLFGYSEPHATKLMLQVHNEGKAVVSAGSRESMEVDVSKLHAAGLWATMQQDR

2wa8C

0.25

0.24

0.96

3.78

MUSTER

---TNDWLDFDQLAEEKVRDALKPPSMYKVILVNDDYTPMEFVIDVLQKFFSYDVERATQLMLAVHYQGKAICGVFTAEVAETKVAMVNKYPLLCTLEKA-

2wa8C

0.25

0.24

0.96

7.18

dPPAS

---TNDWLDFDQLAEEKVRDALKPPSMYKVILVNDDYTPMEFVIDVLQKFFSYDVERATQLMLAVHYQGKAICGVFTAEVAETKVAMVNKYPLLCTLEKA-

2wa8C

0.25

0.24

0.96

6.67

wdPPAS

---TNDWLDFDQLAEEKVRDALKPPSMYKVILVNDDYTPMEFVIDVLQKFFSYDVERATQLMLAVHYQGKAICGVFTAEVAETKVAMVNKYPLLCTLEKA-

2wa8C

0.25

0.24

0.95

4.33

wMUSTER

----NDWLDFDQLAEEKVRDALKPPSMYKVILVNDDYTPMEFVIDVLQKFFSYDVERATQLMLAVHYQGKAICGVFTAEVAETKVAMVNKYPLLCTLEKA-

2wa8C

0.25

0.24

0.96

5.13

wPPAS

---TNDWLDFDQLAEEKVRDALKPPSMYKVILVNDDYTPMEFVIDVLQKFFSYDVERATQLMLAVHYQGKAICGVFTAEVAETKVAMVNKYPLLCTLEKA-

2wa8C

0.25

0.24

0.96

11.73

dPPAS2

---TNDWLDFDQLAEEKVRDALKPPSMYKVILVNDDYTPMEFVIDVLQKFFSYDVERATQLMLAVHYQGKAICGVFTAEVAETKVAMVNKYPLLCTLEKA-

2wa8C

0.25

0.24

0.96

4.80

PPAS

---TNDWLDFDQLAEEKVRDALKPPSMYKVILVNDDYTPMEFVIDVLQKFFSYDVERATQLMLAVHYQGKAICGVFTAEVAETKVAMVNKYPLLCTLEKA-

2wa8C

0.25

0.24

0.96

4.66

Env-PPAS

---TNDWLDFDQLAEEKVRDALKPPSMYKVILVNDDYTPMEFVIDVLQKFFSYDVERATQLMLAVHYQGKAICGVFTAEVAETKVAMVNKYPLLCTLEKA-

3gq1A

0.28

0.22

0.78

3.48

MUSTER

---------------------TQKPSLYRVLILNDDYTPMEFVVYVLERFFNKSREDATRIMLHVHQNGVGVCGVYTYEVAETKVAQVIDSPLQCTMEKD-

4yjmA

0.22

0.17

0.78

6.96

dPPAS

---------------------LERPKLYKVMLLNDDYTPREFVTVVLKAVFRMSEDTGRRVMMTAHRFGSAVVVVCERDIAETKAKEATDLPLMFTTEPE-

(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=1.13

Estimated TM-score = 0.87±0.07

Estimated RMSD = 1.9±1.6Å

Download Model 2

C-score=-0.79

Download Model 3

C-score=0.66

Download Model 4

C-score=-2.96

Download Model 5

C-score=-4.56

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	2wa8C	0.923	0.78	0.247	0.960
2	1rqvA	0.576	2.69	0.138	0.772
3	1dd4A	0.568	2.85	0.156	0.733
4	3ip4B1	0.540	3.23	0.086	0.802
5	1mwrB	0.527	3.25	0.087	0.782
6	2q43A	0.516	3.77	0.042	0.802
7	3h0rE3	0.515	3.22	0.111	0.782
8	2dy1A	0.514	3.71	0.054	0.802
9	1htoX2	0.513	3.55	0.054	0.762
10	1f1hL	0.507	3.51	0.011	0.752

(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	0.86	50	3g1bB	III	Rep, Mult	33,34,35,36,37,38,39,40,43,62,65,66,94
2	0.07	4	3g1bB	MG	Rep, Mult	29,31,98
3	0.01	1	1mbx1	III	Rep, Mult	24,28,49,77,79,82,83,84,86,87
4	0.01	1	1ctf0	III	Rep, Mult	48,51,52,53,54,56,57,64,70,71,72,73,74,75
5	0.01	1	1mbuD	YBT	Rep, Mult	54,56

	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	1pcaA	0.480	2.88	0.100	0.653	3.4.17.1	NA
2	0.060	1darA	0.509	3.49	0.086	0.782	3.6.5.3	NA
3	0.060	1jqmB	0.475	3.58	0.033	0.743	3.6.5.3	NA
4	0.060	3fwmA	0.470	4.05	0.065	0.812	2.4.1.129,	NA
5	0.060	2ywfA	0.473	3.73	0.086	0.733	3.6.5.-	NA
6	0.060	2pffA	0.481	4.34	0.054	0.881	2.3.1.41,2.3.1.86	87
7	0.060	1eloA	0.505	3.47	0.086	0.782	3.6.5.3	NA
8	0.060	3ffzA	0.483	4.52	0.065	0.881	3.4.24.69	NA
9	0.060	1pytA	0.477	2.76	0.087	0.644	3.4.17.1	NA
10	0.060	2fy3A	0.472	4.30	0.060	0.871	2.3.1.6	NA
11	0.060	1h2rL	0.474	4.01	0.091	0.802	1.12.2.1	NA
12	0.060	1s0kA	0.456	4.56	0.064	0.891	3.2.1.18	54
13	0.060	1bg0A	0.504	3.48	0.071	0.772	2.7.3.3	NA
14	0.060	3fwlA	0.479	4.41	0.086	0.871	2.4.1.129	49
15	0.060	2e1rA	0.495	3.73	0.054	0.792	3.6.5.3	NA
16	0.060	2imwP	0.470	2.79	0.076	0.653	2.7.7.7	55
17	0.060	2j1qA	0.499	3.62	0.092	0.792	2.7.3.3	NA
18	0.060	3dnyT	0.493	4.13	0.044	0.842	3.6.5.3	NA
19	0.060	2np0A	0.398	4.83	0.032	0.852	3.4.24.69	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	0.50	0.904	0.90	0.25	0.95	3o2bC	GO:0006508 GO:0009408 GO:0030163 GO:0051087
1	0.43	0.737	1.08	0.28	0.78	3gq1A	GO:0006508 GO:0030163
2	0.35	0.728	1.05	0.23	0.78	4yjmA	GO:0006508 GO:0030163
3	0.12	0.563	2.36	0.13	0.73	1rquA	GO:0003735 GO:0005622 GO:0005829 GO:0005840 GO:0006412 GO:0022625 GO:0030529
4	0.11	0.576	2.75	0.16	0.74	1dd3A	GO:0003735 GO:0005622 GO:0005840 GO:0006412 GO:0022625 GO:0030529
5	0.08	0.679	1.68	0.19	0.76	4o2xA	GO:0005215 GO:0005363 GO:0006508 GO:0006810 GO:0006974 GO:0008233 GO:0008643 GO:0015768 GO:0016787 GO:0030163 GO:0030288 GO:0034289 GO:0042597 GO:0042956 GO:0043190 GO:0055052 GO:0060326 GO:1901982 GO:1990060
6	0.07	0.505	2.92	0.07	0.73	3ip4B	GO:0000166 GO:0005524 GO:0006412 GO:0016874 GO:0016884 GO:0050567
7	0.07	0.570	2.31	0.11	0.72	2ftcE	GO:0003735 GO:0005622 GO:0005739 GO:0005743 GO:0005762 GO:0005840 GO:0006412 GO:0030529 GO:0070124 GO:0070125
8	0.07	0.331	3.48	0.07	0.45	2d6fD	GO:0000166 GO:0004812 GO:0005524 GO:0005737 GO:0006412 GO:0016874 GO:0016884 GO:0050567
9	0.07	0.505	3.16	0.12	0.77	3al0B	GO:0000166 GO:0005524 GO:0006412 GO:0016874 GO:0016884 GO:0032543 GO:0050567 GO:0070681
10	0.07	0.551	2.09	0.14	0.67	2zjq5	GO:0003735 GO:0005622 GO:0005840 GO:0006412 GO:0022625 GO:0030529
11	0.07	0.488	3.25	0.09	0.75	4n0hB	GO:0000166 GO:0005524 GO:0005739 GO:0006412 GO:0016874 GO:0016884 GO:0030956 GO:0032543 GO:0050567 GO:0070681
12	0.07	0.284	4.10	0.03	0.52	4wj3B	GO:0000166 GO:0005524 GO:0006412 GO:0016874 GO:0016884 GO:0032543 GO:0050567 GO:0070681
13	0.07	0.526	3.62	0.06	0.83	1zq1C	GO:0000166 GO:0004812 GO:0005524 GO:0005737 GO:0006412 GO:0016874 GO:0016884 GO:0050567
14	0.07	0.361	4.72	0.02	0.64	3kfuF	GO:0000166 GO:0005524 GO:0006412 GO:0016874 GO:0016884 GO:0050567
15	0.06	0.383	3.48	0.04	0.59	4v9jBe	GO:0003735 GO:0005622 GO:0005840 GO:0006412 GO:0030529
16	0.06	0.382	3.22	0.14	0.53	2qnwA	GO:0006633 GO:0046872
17	0.06	0.354	3.02	0.11	0.49	2ehtA	GO:0000036 GO:0005737 GO:0006629 GO:0006631 GO:0006633 GO:0031177
18	0.06	0.330	4.03	0.03	0.54	1xlyB	GO:0003723 GO:0003729 GO:0005634 GO:0005737 GO:0005789 GO:0005934 GO:0006810 GO:0007533 GO:0008289 GO:0008298 GO:0051028

Consensus prediction of GO terms

Molecular Function	GO:0051087	GO:0005198
GO-Score	0.50	0.44
Biological Processes	GO:0006508	GO:0030163	GO:0009408	GO:0034645	GO:0010467	GO:0043043	GO:0044267
GO-Score	0.82	0.82	0.50	0.44	0.44	0.44	0.44
Cellular Component	GO:0015934	GO:0022626
GO-Score	0.44	0.44

(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.