I-TASSER results

I-TASSER results for job id Rv1159A

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

Input Sequence in FASTA format

>protein (94 residues)
MAVLTDEQVDAALHDLNGWQRAGGVLRRSIKFPTFMAGIDAVRRVAERAEEVNHHPDIDI
RWRTVTFALVTHAVGGITENDIAMAHDIDAMFGA

Predicted Secondary Structure

Sequence	20 40 60 80 \| \| \| \| MAVLTDEQVDAALHDLNGWQRAGGVLRRSIKFPTFMAGIDAVRRVAERAEEVNHHPDIDIRWRTVTFALVTHAVGGITENDIAMAHDIDAMFGA
Prediction	CCCCCHHHHHHHHHHCCCCEEHCCEEEEEEEHCCHHHHHHHHHHHHHHHHHHCCCCCEEEHCCEEEEEEEEHCCCCCCHHHHHHHHHHHHHHHC
Conf.Score	9999899999999869997998899999999699999999999999999998999868998679999999976999788999999999999859
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 \| \| \| \| MAVLTDEQVDAALHDLNGWQRAGGVLRRSIKFPTFMAGIDAVRRVAERAEEVNHHPDIDIRWRTVTFALVTHAVGGITENDIAMAHDIDAMFGA
Prediction	8651467315622771653635664041404063154013003300520574712040204344030202023243016302500530361278
	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

                   |                   |                   |                   |

Sec.Str
Seq

CCCCCHHHHHHHHHHCCCCEEHCCEEEEEEEHCCHHHHHHHHHHHHHHHHHHCCCCCEEEHCCEEEEEEEEHCCCCCCHHHHHHHHHHHHHHHC
MAVLTDEQVDAALHDLNGWQRAGGVLRRSIKFPTFMAGIDAVRRVAERAEEVNHHPDIDIRWRTVTFALVTHAVGGITENDIAMAHDIDAMFGA

2ebbA

0.33

0.99

4.34

MUSTER

M-RLTEEEVQALLEKADGWKLADRWIVKKYRFQDYLQGIEFVRRIAAISENANHHPFISIDYKLITVKLSSWRAKGLTKLDFDLAKQYDEVYNQ

2ebbA

0.32

0.99

8.12

dPPAS

-MRLTEEEVQALLEKADGWKLADEWIVKKYRFQDYLQGIEFVRRIAAISENANHHPFISIDYKLITVKLSSWRAKGLTKLDFDLAKQYDEVYNQ

2ebbA

0.33

0.99

6.82

wdPPAS

M-RLTEEEVQALLEKADGWKLADEWIVKKYRFQDYLQGIEFVRRIAAISENANHHPFISIDYKLITVKLSSWRAKGLTKLDFDLAKQYDEVYNQ

2ebbA

0.33

0.32

0.98

5.33

wMUSTER

--RLTEEEVQALLEKADGWKLADEWIVKKYRFQDYLQGIEFVRRIAAISENANHHPFISIDYKLITVKLSSWRAKGLTKLDFDLAKQYDEVYNQ

2ebbA

0.33

0.99

5.23

wPPAS

M-RLTEEEVQALLEKADGWKLADEWIVKKYRFQDYLQGIEFVRRIAAISENANHHPFISIDYKLITVKLSSWRAKGLTKLDFDLAKQYDEVYNQ

2ebbA

0.32

0.99

9.90

dPPAS2

-MRLTEEEVQALLEKADGWKLADEWIVKKYRFQDYLQGIEFVRRIAAISENANHHPFISIDYKLITVKLSSWRAKGLTKLDFDLAKQYDEVYNQ

2ebbA

0.33

0.99

5.00

PPAS

M-RLTEEEVQALLEKADGWKLADEWIVKKYRFQDYLQGIEFVRRIAAISENANHHPFISIDYKLITVKLSSWRAKGLTKLDFDLAKQYDEVYNQ

2ebbA

0.33

0.99

5.55

Env-PPAS

M-RLTEEEVQALLEKADGWKLADEWIVKKYRFQDYLQGIEFVRRIAAISENANHHPFISIDYKLITVKLSSWRAKGLTKLDFDLAKQYDEVYNQ

3jstA

0.37

0.36

0.99

4.21

MUSTER

MNRLTESEMNEALRALDGWQKVDGAITRSFKFKDFSTAFGFMAQAALYAEKLDHHPEWFNAYNRVDVTLATHSENGVTELDIKMARKMNAIAG-

3jstA

0.35

0.99

7.84

dPPAS

RNRLTESEMNEALRALDGWQKVDGAITRSFKFKDFSTAFGFMAQAALYAEKLDHHPEWFNAYNRVDVTLATHSENGVTELDIKMARKMNAIAG-

(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 1 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 = 0.5±0.5Å

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	2ebbA	0.965	0.59	0.323	0.989
2	3jstA	0.919	1.04	0.344	0.989
3	1ru0A	0.881	1.55	0.287	1.000
4	1f93A	0.867	1.58	0.290	0.989
5	2v6uA	0.856	1.74	0.277	1.000
6	1usoB	0.721	1.35	0.368	0.808
7	4lowA	0.699	1.82	0.225	0.808
8	5fxdA	0.643	3.00	0.109	0.883
9	1ahvA	0.643	3.11	0.075	0.894
10	1diqA	0.638	2.92	0.054	0.883

(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	0.54	10	1dcpA	HBI	Rep, Mult	53,54,55,70,71,72,73
2	0.27	6	1f93A	III	Rep, Mult	36,37,40,43,44,47,51
3	0.10	2	1f93B	III	Rep, Mult	43,46,47,50
4	0.06	2	1usm0	III	Rep, Mult	35,36,39,43,46,50,55,56,57,58,59,60,61,62
5	0.02	1	1in0B	HG	Rep, Mult	41,88,92

	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	0.584	2ebbA	0.965	0.59	0.323	0.989	4.2.1.96	54,55,81
2	0.581	3jstA	0.919	1.04	0.344	0.989	4.2.1.96	54,55,72,81
3	0.574	2v6uA	0.856	1.74	0.277	1.000	4.2.1.96	54,55,72,81
4	0.188	2acyA	0.553	2.52	0.088	0.723	3.6.1.7	43
5	0.165	1ru0A	0.881	1.55	0.287	1.000	4.2.1.96	54,55,72,81
6	0.066	1w2iA	0.539	2.53	0.091	0.702	3.6.1.7	NA
7	0.066	2fhmA	0.512	2.74	0.077	0.692	3.6.1.7	NA
8	0.060	1tlbA	0.606	3.20	0.065	0.957	1.3.3.3	82
9	0.060	3ju5C	0.586	2.94	0.084	0.872	2.7.3.3	18
10	0.060	1u6rA	0.604	3.02	0.092	0.915	2.7.3.2	NA
11	0.060	1m5hC	0.599	2.50	0.072	0.798	2.3.1.101	58
12	0.060	1qk1A	0.564	3.42	0.047	0.904	2.7.3.2	NA
13	0.060	1cpbB	0.289	4.71	0.038	0.553	3.4.17.2	NA
14	0.060	1f93A	0.867	1.58	0.290	0.989	4.2.1.96	55,56,82
15	0.060	3dgvA	0.571	3.87	0.097	0.947	3.4.17.20	NA
16	0.060	3fcrA	0.605	3.46	0.067	0.947	2.6.1.-	NA
17	0.060	1cpbA	0.359	3.66	0.081	0.617	3.4.17.2	NA
18	0.060	1eqrA	0.584	3.27	0.068	0.894	6.1.1.12	NA
19	0.060	2cghB	0.624	3.16	0.055	0.968	6.3.4.15	NA
20	0.060	3d66A	0.581	3.94	0.065	0.957	3.4.17.20	NA
21	0.060	2ewnA	0.636	2.94	0.065	0.915	6.3.4.15	NA
22	0.060	1bibA	0.615	3.24	0.096	0.968	6.3.4.15	NA
23	0.060	2c1cA	0.594	4.00	0.064	0.979	3.4.17.2	NA
24	0.060	1lfwA	0.609	3.52	0.091	0.851	3.4.13.3	NA
25	0.060	2gl6A	0.479	3.87	0.053	0.777	2.7.3.2	27

(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	0.57	0.965	0.59	0.32	0.99	2ebbA	GO:0006729 GO:0008124 GO:0016829
1	0.51	0.877	1.57	0.29	1.00	1f93A	GO:0003713 GO:0004505 GO:0005634 GO:0005654 GO:0005737 GO:0006351 GO:0006355 GO:0006558 GO:0006729 GO:0008124 GO:0016829 GO:0042802 GO:0043496 GO:0045893 GO:0051289 GO:0051291 GO:0055114 GO:0070062
2	0.49	0.919	1.04	0.34	0.99	3jstA	GO:0006729 GO:0008124 GO:0016829
3	0.49	0.856	1.74	0.28	1.00	2v6uA	GO:0006729 GO:0008124 GO:0016829
4	0.42	0.874	1.59	0.29	1.00	4c45A	GO:0004505 GO:0005634 GO:0005739 GO:0006729 GO:0008124 GO:0016829 GO:0045893 GO:0051289 GO:0051291 GO:0055114
5	0.40	0.881	1.55	0.29	1.00	1ru0A	GO:0004505 GO:0005634 GO:0005739 GO:0006729 GO:0008124 GO:0016829 GO:0045893 GO:0051289 GO:0051291 GO:0055114
6	0.33	0.721	1.35	0.37	0.81	1usoB	GO:0006729 GO:0008124 GO:0016829
7	0.31	0.699	1.82	0.23	0.81	4lowA	GO:0006729 GO:0008124
8	0.14	0.497	2.62	0.10	0.66	1dtjC	GO:0000398 GO:0003676 GO:0003723 GO:0005634 GO:0044822
9	0.06	0.309	4.81	0.03	0.62	3p6cA	GO:0001816 GO:0005215 GO:0005504 GO:0005634 GO:0005737 GO:0005811 GO:0005829 GO:0006469 GO:0006810 GO:0008289 GO:0019433 GO:0042632 GO:0045892 GO:0050727 GO:0050729 GO:0050872 GO:0050873 GO:0070062 GO:0071285
10	0.06	0.308	4.79	0.03	0.61	2qm9A	GO:0001816 GO:0005215 GO:0005504 GO:0005634 GO:0005654 GO:0005737 GO:0006469 GO:0006810 GO:0008289 GO:0042632 GO:0045892 GO:0050727 GO:0050729 GO:0050872 GO:0050873 GO:0070062 GO:0071285 GO:0071356
11	0.06	0.389	4.01	0.04	0.68	2jlbA	GO:0046872
12	0.06	0.347	4.31	0.05	0.60	3kf8A
13	0.06	0.316	3.77	0.02	0.49	5dpoA

Consensus prediction of GO terms

Molecular Function	GO:0008124	GO:0004505	GO:0003713	GO:0042802
GO-Score	0.97	0.72	0.51	0.51
Biological Processes	GO:0006729	GO:0055114	GO:0051289	GO:0045893	GO:0051291	GO:0006558	GO:0043496
GO-Score	0.97	0.72	0.72	0.72	0.72	0.51	0.51
Cellular Component	GO:0005654	GO:0070062	GO:0005739
GO-Score	0.51	0.51	0.42

(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.