I-TASSER results

I-TASSER results for job id Rv1503c

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

Input Sequence in FASTA format

>protein (182 residues)
DFLLRAEILREKGTNRSRFLRNEVDKYTWQDKGSSYLPSELVAAFLWAQFEEAERITRIR
LDLWNRYHESFESLEQRGLLRRPIIPQGCSHNAHMYYVLLAPSADREEVLARLTSEGIGA
VFHYVPLHDSPAGRRYGRTNGNLTVTNDVASRLIRLPMWVGLQEVDQSRVVEALTRILTL
RA

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| DFLLRAEILREKGTNRSRFLRNEVDKYTWQDKGSSYLPSELVAAFLWAQFEEAERITRIRLDLWNRYHESFESLEQRGLLRRPIIPQGCSHNAHMYYVLLAPSADREEVLARLTSEGIGAVFHYVPLHDSPAGRRYGRTNGNLTVTNDVASRLIRLPMWVGLQEVDQSRVVEALTRILTLRA
Prediction	HHHHHHHHHHHHCCCCCHHHCCCCCCEEEEHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCEEEEEEEEHCCCCHHHHHHHHHHHHCCCEEEEHCCCCCCHHHHHHCCCCCCCHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHCC
Conf.Score	58999999999899876455688865799976667896599999999999999999999999999999998668887875588878998766899999968987599999999998998588656887898899879998889589999987544568999999999999999999998659
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| DFLLRAEILREKGTNRSRFLRNEVDKYTWQDKGSSYLPSELVAAFLWAQFEEAERITRIRLDLWNRYHESFESLEQRGLLRRPIIPQGCSHNAHMYYVLLAPSADREEVLARLTSEGIGAVFHYVPLHDSPAGRRYGRTNGNLTVTNDVASRLIRLPMWVGLQEVDQSRVVEALTRILTLRA
Prediction	72052043026332433434545343131210130021410000002022630451163045005203620571675430420423762400000010204567405401521474745142142102303003624265331220241043000320237334620531051025006648
	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

HHHHHHHHHHHHCCCCCHHHCCCCCCEEEEHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCEEEEEEEEHCCCCHHHHHHHHHHHHCCCEEEEHCCCCCCHHHHHHCCCCCCCHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHCC
DFLLRAEILREKGTNRSRFLRNEVDKYTWQDKGSSYLPSELVAAFLWAQFEEAERITRIRLDLWNRYHESFESLEQRGLLRRPIIPQGCSHNAHMYYVLLAPSADREEVLARLTSEGIGAVFHYVPLHDSPAGRRYGRTNGNLTVTNDVASRLIRLPMWVGLQEVDQSRVVEALTRILTLRA

4lc3A

0.25

0.24

0.97

2.95

MUSTER

DEAVLAQKYRLQGITRT-----GFDGMDCDVLGGKYNLTDVAARVGLGQLPHLERFTAQRRALARAYFAAFDGGAAAKLGVGLPVAEFENGNWHMFLVTLPLTITRAEFMAQMKERGIGTGIHYPAIHLFTLYRARGFKEGMFPHAERYGASTVTLPLFTQMTEGDVRRVVDAVNQICEQYG

4k2bA2

0.17

0.15

0.89

5.92

dPPAS

EVEDILNTLTEVLPTG------------------KFTSDNLQAAIGLERMKYLSLNNFKRLFLADRYITQLAELQNKGYIELPELSED--HVWHLFPIKVRTEDRADIMTKLNEDFGVQTDVYYILSHMQKPLVQDKYAGLQLVHTEKAHSQVLHLPLYPSFTLEEQDRVMEGLFHVIKQEI

4k2bA2

0.19

0.16

0.87

5.24

wdPPAS

EVEDILNTLTEVLP--------------------KFTSDNLQAAIGLERMKYLSLNNFKRLFLADRYITQLAELQNKGYIELPELSED--HVWHLFPIKVRTE-DRADIMTKLNED-VQTDVYYILSHMQKPLVQDKYAGLQLVHTEKAHSQVLHLPLYPSFTLEEQDRVMEGLFHVIKQEI

4lc3A

0.25

0.24

0.97

3.45

wMUSTER

DEAVLAQKYRLQGITRT-----GFDGMDCDVLGGKYNLTDVAARVGLGQLPHLERFTAQRRALARAYFAAFDGGAAAKLGVGLPVAEFENGNWHMFLVTLPLTITRAEFMAQMKERGIGTGIHYPAIHLFTLYRARGFKEGMFPHAERYGASTVTLPLFTQMTEGDVRRVVDAVNQICEQYG

4k2bA2

0.19

0.16

0.87

2.92

wPPAS

EVEDILNTLTEVLP--------------------KFTSDNLQAAIGLERMKYLSLNNFKRLFLADRYITQLAELQNKGYIELPELSED--HVWHLFPIKVRT-EDRADIMTKLNED-VQTDVYYILSHMQKPLVQDKYAGLQLVHTEKAHSQVLHLPLYPSFTLEEQDRVMEGLFHVIKQEI

4k2bA2

0.17

0.15

0.89

6.34

dPPAS2

EVEDILNTLTEVLPTG------------------KFTSDNLQAAIGLERMKYLSLNNFKRLFLADRYITQLAELQNKGYIELPELSED--HVWHLFPIKVRTEDRADIMTKLNEDFGVQTDVYYILSHMQKPLVQDKYAGLQLVHTEKAHSQVLHLPLYPSFTLEEQDRVMEGLFHVIKQEI

4k2bA2

0.19

0.16

0.88

2.50

PPAS

EVEDILNTLTEVLPTG------------------KFTSDNLQAAIGLERMKYLSLNNFKRLFLADRYITQLAELQNKGYIELPELSED--HVWHLFPIKVRT-EDRADIMTKLNEDFVQTDVYYILSHMQKPLVQDKYAGLQLVHTEKAHSQVLHLPLYPSFTLEEQDRVMEGLFHVIKQEI

4k2bA2

0.19

0.16

0.88

3.83

Env-PPAS

EVEDILNTLTEVLPTG------------------KFTSDNLQAAIGLERMKYLSLNNFKRLFLADRYITQLAELQNKGYIELPELSED--HVWHLFPIKVRT-EDRADIMTKLNEDFVQTDVYYILSHMQKPLVQDKYAGLQLVHTEKAHSQVLHLPLYPSFTLEEQDRVMEGLFHVIKQEI

4qgrA

0.24

0.22

0.91

2.79

MUSTER

ELADTLRSVLFHGKGE--------TQYDNVRIGINSRLDTIQAAVLLEKLAILEDEMEARDRIARRYNEALKDV-----VKVPELPAGNRSAWAQYSIESEN---RDGLKAQLQAEGIPSVIYYKPLHLQTAYKHYSVAPGGLPVSESLPSRILSLPMHPYLSEADQDKIIGVIRGFHGKK-

4lc3A

0.25

0.24

0.97

5.47

dPPAS

DEAVLAQKYRLQGITRT-----GFDGMDCDVLGGKYNLTDVAARVGLGQLPHLERFTAQRRALARAYFAAFDGGAAAKLGVGLPVAEFENGNWHMFLVTLPLTITRAEFMAQMKERGIGTGIHYPAIHLFTLYRARGFKEGMFPHAERYGASTVTLPLFTQMTEGDVRRVVDAVNQICEQYG

(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=0.90

Estimated TM-score = 0.84±0.08

Estimated RMSD = 3.4±2.4Å

Download Model 2

C-score=-0.91

Download Model 3

C-score=-3.51

Download Model 4

C-score=-3.99

Download Model 5

C-score=-4.75

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	4lc3A	0.912	1.52	0.249	0.973
2	2fniA	0.843	1.93	0.162	0.951
3	3dr4C	0.827	1.99	0.256	0.923
4	1b9iA	0.811	2.30	0.145	0.945
5	3bcxA	0.808	2.83	0.180	0.951
6	2po3A	0.802	2.28	0.193	0.912
7	2ogaA	0.800	2.25	0.234	0.918
8	4k2bA	0.798	2.53	0.169	0.945
9	3frkA	0.794	1.93	0.210	0.890
10	1mdoA	0.794	2.16	0.239	0.896

(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	0.18	14	2ogaA	PGU	Rep, Mult	12,35,37
2	0.12	10	2po3B	T4K	Rep, Mult	123,124
3	0.08	7	3dr7D	GPD	Rep, Mult	94,119,121,124
4	0.07	6	3frkB	TQP	Rep, Mult	94,121,123,124
5	0.06	5	2ogaA	PGU	Rep, Mult	12,26,27,35,37
6	0.05	5	3b8xB	G4M	Rep, Mult	119,121,124
7	0.04	3	3dr7B	GPD	Rep, Mult	26,27
8	0.02	3	4iy7D	PYR	Rep, Mult	63,160,162,163,164
9	0.02	2	4xk83	CLA	Rep, Mult	68,71
10	0.01	1	4zdoD	NUC	Rep, Mult	112,116,176
11	0.01	1	3i54D	CMP	Rep, Mult	61,65
12	0.01	1	3kgxA	MG	Rep, Mult	66,70,168
13	0.01	1	3ju7B	CA	Rep, Mult	51
14	0.01	1	4jtdB	PGW	Rep, Mult	56,157,158
15	0.01	1	2dglD	BR	Rep, Mult	56,160
16	0.01	1	2gmsA	MG	Rep, Mult	162,165

	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	2cb1A	0.611	2.88	0.114	0.769	4.2.99.10	NA
2	0.060	3caiA	0.605	3.50	0.109	0.791	2.6.1.-	NA
3	0.060	1n8pC	0.608	3.31	0.123	0.802	4.4.1.1	NA
4	0.060	2zc0A	0.595	3.42	0.109	0.758	2.6.1.44	NA
5	0.060	2jg2A	0.587	3.07	0.074	0.742	2.3.1.50	67
6	0.060	2c7tA	0.740	3.42	0.158	0.967	2.6.1.-	NA
7	0.060	3if2A	0.603	3.39	0.114	0.769	2.6.1.-	NA
8	0.060	2hzpA	0.588	3.92	0.116	0.808	3.7.1.3	NA
9	0.060	1qgnA	0.590	3.09	0.101	0.758	2.5.1.48	67
10	0.060	1pg8A	0.605	3.51	0.123	0.797	4.4.1.11	NA
11	0.060	2r2nA	0.586	3.74	0.102	0.786	2.6.1.39,2.6.1.7	NA
12	0.060	2wk8B	0.576	3.28	0.128	0.731	2.3.-.-	68
13	0.060	1cl1B	0.601	3.25	0.099	0.780	4.4.1.8	NA
14	0.060	1p3wB	0.621	3.62	0.126	0.819	2.8.1.7	NA
15	0.060	1cs1A	0.607	3.09	0.077	0.786	2.5.1.48	NA
16	0.060	1gc0B	0.586	3.46	0.128	0.769	4.4.1.11	NA
17	0.060	2qlrA	0.586	3.70	0.101	0.791	2.6.1.39,2.6.1.7	NA
18	0.060	3a2bA	0.587	3.02	0.090	0.731	2.3.1.50	68
19	0.060	1b9hA	0.812	2.27	0.145	0.945	4.2.1.-	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	0.26	0.800	2.25	0.23	0.92	2ogaA	GO:0003824 GO:0008483 GO:0016740 GO:0017000 GO:0030170 GO:0033068
1	0.22	0.827	1.99	0.26	0.92	3dr4C	GO:0003824 GO:0008483 GO:0009103 GO:0009243 GO:0016740
2	0.21	0.912	1.52	0.25	0.97	4lc3A	GO:0003824
3	0.19	0.843	1.93	0.16	0.95	2fniA	GO:0003824 GO:0008483 GO:0016740
4	0.19	0.782	2.73	0.12	0.93	2gmsA	GO:0003824 GO:0008483 GO:0016740
5	0.17	0.812	2.27	0.14	0.95	1b9hA	GO:0003824 GO:0016740 GO:0016829 GO:0017000
6	0.17	0.802	2.28	0.19	0.91	2po3A	GO:0003824
7	0.16	0.804	2.33	0.17	0.95	4k2mA	GO:0003824 GO:0008483 GO:0016740 GO:0017000 GO:0030170
8	0.16	0.816	2.12	0.24	0.92	1mdxA	GO:0003824 GO:0006629 GO:0008483 GO:0009103 GO:0009245 GO:0016740 GO:0046493 GO:0046677 GO:0099621
9	0.16	0.808	2.83	0.18	0.95	3bcxA	GO:0003824 GO:0008483 GO:0016740
10	0.15	0.792	2.64	0.45	0.95	4zahA	GO:0003824 GO:0009246 GO:0016740 GO:0019180 GO:0030170
11	0.15	0.786	2.33	0.19	0.92	3uwcA	GO:0003824 GO:0008483 GO:0016740
12	0.15	0.794	1.93	0.21	0.89	3frkA	GO:0003824
13	0.14	0.769	2.15	0.20	0.88	3ju7A	GO:0003824
14	0.14	0.756	2.52	0.24	0.90	4qgrA	GO:0003824 GO:0008483 GO:0016740
15	0.14	0.763	2.44	0.19	0.91	4zasA	GO:0003824
16	0.14	0.740	3.42	0.16	0.97	2c7tA	GO:0003824 GO:0008483 GO:0016740 GO:0017000
17	0.13	0.776	2.42	0.13	0.91	4ztcA	GO:0003824 GO:0006486 GO:0008483 GO:0016740 GO:0047302
18	0.13	0.758	2.08	0.25	0.86	3nu7B	GO:0000271 GO:0003824 GO:0008483 GO:0009103 GO:0009243 GO:0016740 GO:0030170 GO:0071555

Consensus prediction of GO terms

Molecular Function	GO:0008483	GO:0048037	GO:0043168
GO-Score	0.62	0.52	0.52
Biological Processes	GO:0030639	GO:1901336	GO:0033067	GO:0009103	GO:0046402
GO-Score	0.52	0.52	0.52	0.44	0.44
Cellular Component
GO-Score

(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.