I-TASSER results

I-TASSER results for job id Rv0759c

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

Input Sequence in FASTA format

>seq (110 residues)
MAFLTIEPMTQGHTLVVPRAEIDHWQNVDPALFGRVMSVSQLIGKAVCRAFSTQRAGMII
AGLEVPHLHIHVFPTRSLSDFGFANVDRNPSPGSLDEAQAKIRAALAQLA

Predicted Secondary Structure

Sequence	20 40 60 80 100 \| \| \| \| \| MAFLTIEPMTQGHTLVVPRAEIDHWQNVDPALFGRVMSVSQLIGKAVCRAFSTQRAGMIIAGLEVPHLHIHVFPTRSLSDFGFANVDRNPSPGSLDEAQAKIRAALAQLA
Prediction	CCCCCCCCCCCCEEEEHCHHHCCEEHCCCHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEEHCCCCCEEEEEEHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHC
Conf.Score	86677678889868987654443334499999999999999999999997588866899975579966899985998655688888999999999999999999999979
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 \| \| \| \| \| MAFLTIEPMTQGHTLVVPRAEIDHWQNVDPALFGRVMSVSQLIGKAVCRAFSTQRAGMIIAGLEVPHLHIHVFPTRSLSDFGFANVDRNPSPGSLDEAQAKIRAALAQLA
Prediction	73103143435210000036203413504562143024004400410462160620000001321322000001144264241543547345641551164026205748
	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

CCCCCCCCCCCCEEEEHCHHHCCEEHCCCHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEEHCCCCCEEEEEEHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHC
MAFLTIEPMTQGHTLVVPRAEIDHWQNVDPALFGRVMSVSQLIGKAVCRAFSTQRAGMIIAGLEVPHLHIHVFPTRSLSDFGFANVDRNPSPGSLDEAQAKIRAALAQLA

3p0tA

0.85

1.00

3.17

MUSTER

VAFLTIEPMTQGHTLVVPREEIDNWQDVDSAAFNRVMGVSQLIGKAVCKAFRTERSGLIIAGLEVPHLHVHVFPTRSLSDFGFANVDRNPSPESLDEAQAKIKAALAQLA

3p0tA

0.85

1.00

5.09

dPPAS

VAFLTIEPMTQGHTLVVPREEIDNWQDVDSAAFNRVMGVSQLIGKAVCKAFRTERSGLIIAGLEVPHLHVHVFPTRSLSDFGFANVDRNPSPESLDEAQAKIKAALAQLA

3p0tA

0.85

1.00

5.06

wdPPAS

VAFLTIEPMTQGHTLVVPREEIDNWQDVDSAAFNRVMGVSQLIGKAVCKAFRTERSGLIIAGLEVPHLHVHVFPTRSLSDFGFANVDRNPSPESLDEAQAKIKAALAQLA

3p0tA

0.85

1.00

3.48

wMUSTER

VAFLTIEPMTQGHTLVVPREEIDNWQDVDSAAFNRVMGVSQLIGKAVCKAFRTERSGLIIAGLEVPHLHVHVFPTRSLSDFGFANVDRNPSPESLDEAQAKIKAALAQLA

3p0tA

0.85

1.00

3.45

wPPAS

VAFLTIEPMTQGHTLVVPREEIDNWQDVDSAAFNRVMGVSQLIGKAVCKAFRTERSGLIIAGLEVPHLHVHVFPTRSLSDFGFANVDRNPSPESLDEAQAKIKAALAQLA

3p0tA

0.85

1.00

6.66

dPPAS2

VAFLTIEPMTQGHTLVVPREEIDNWQDVDSAAFNRVMGVSQLIGKAVCKAFRTERSGLIIAGLEVPHLHVHVFPTRSLSDFGFANVDRNPSPESLDEAQAKIKAALAQLA

3p0tA

0.85

1.00

3.51

PPAS

VAFLTIEPMTQGHTLVVPREEIDNWQDVDSAAFNRVMGVSQLIGKAVCKAFRTERSGLIIAGLEVPHLHVHVFPTRSLSDFGFANVDRNPSPESLDEAQAKIKAALAQLA

3p0tA

0.85

1.00

3.76

Env-PPAS

VAFLTIEPMTQGHTLVVPREEIDNWQDVDSAAFNRVMGVSQLIGKAVCKAFRTERSGLIIAGLEVPHLHVHVFPTRSLSDFGFANVDRNPSPESLDEAQAKIKAALAQLA

3lb5C

0.32

0.30

0.94

2.34

MUSTER

IAFMDIMPQAPGHTLVIPKKGSRNLLDADTETLFPVIKAVQKIAKAVKKAFQADGITVMQSQQTVYHLHFHIIPRMEGIELTPN---IITPTEILEENAKKIRAAL----

1y23B

0.27

0.26

0.99

3.83

dPPAS

LAFLDISQVTKGHTLVIPKTHIENVYEFTDELAKQYFHAVPKIARAIRDEFEPIGLNTLNAGQSVFHYHMHIIPRYGKGDAVWKTHADDYKPEDLQNISSSIAKRLASS-

(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=1.58

Estimated TM-score = 0.93±0.06

Estimated RMSD = 1.3±1.3Å

Download Model 2

C-score=-3.50

Download Model 3

C-score=-3.77

Download Model 4

C-score=-5.00

Download Model 5

C-score=-3.67

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	3p0tA	0.966	0.75	0.855	1.000
2	2eo4A	0.855	1.59	0.209	0.936
3	3lb5C	0.829	1.63	0.324	0.927
4	3o0mA	0.825	1.74	0.311	0.936
5	3anoA	0.788	2.42	0.179	0.946
6	3i24A	0.783	2.41	0.183	0.991
7	3i4sA	0.780	2.26	0.140	0.973
8	5l0lA	0.779	1.99	0.129	0.918
9	5cs2A	0.777	1.92	0.208	0.918
10	3nrdA	0.768	2.10	0.167	0.927

(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	0.61	54	1av5B	AP2	Rep, Mult	3,4,5,6,7,15,61,63,64,65,69,71
2	0.09	10	2eo4A	ZN	Rep, Mult	21,67
3	0.05	5	2fhiA	IB2	Rep, Mult	4,5,15,57,58,59,61,64,65,69,71,73
4	0.04	5	3lb5D	UNL	Rep, Mult	3,4,5,6,15
5	0.04	5	3anoA	PO4	Rep, Mult	61,63,64,65,69,71
6	0.01	2	3llj0	III	Rep, Mult	9,25,26,28,30,31,34,35,38,41,54,55,56,57,58,59,60,61,71,76,77,78
7	0.01	2	1h3uB	NAG	Rep, Mult	3,17,69
8	0.01	1	3oheA	CA	Rep, Mult	31,34
9	0.01	1	1y23B	MG	Rep, Mult	105,108
10	0.01	1	1fitA	FRU	Rep, Mult	50,51,52

	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	3hwoA	0.515	4.02	0.082	0.809	5.4.4.2	46
2	0.060	1i7qA	0.534	4.01	0.104	0.809	4.1.3.27	NA
3	0.060	2fitA	0.759	2.36	0.206	0.918	3.6.1.29	NA
4	0.060	1c8bA	0.517	3.29	0.031	0.727	3.4.24.78	NA
5	0.060	3c20B	0.495	4.13	0.068	0.791	2.7.2.4	58
6	0.060	1vgyA	0.506	4.10	0.054	0.827	3.5.1.18	NA
7	0.060	1z84A	0.710	2.90	0.095	0.918	2.7.7.12	61,67,69
8	0.060	2pofA	0.549	3.20	0.128	0.746	3.6.1.26	69
9	0.060	3gb0A	0.504	3.99	0.118	0.791	3.4.11.-	NA
10	0.060	2a4mC	0.503	3.96	0.094	0.773	6.1.1.2	41
11	0.060	1pytB	0.492	4.10	0.064	0.846	3.4.17.1	NA
12	0.060	3dgvA	0.412	5.09	0.065	0.782	3.4.17.20	NA
13	0.060	3bznA	0.501	4.24	0.103	0.827	5.4.4.2	NA
14	0.060	2dlcX	0.494	3.92	0.102	0.773	6.1.1.1	NA
15	0.060	1yi8A	0.407	4.91	0.078	0.791	6.1.1.2	NA
16	0.060	2g5fA	0.516	4.39	0.051	0.836	5.4.4.2	71
17	0.060	2dhtA	0.502	3.99	0.038	0.782	1.1.1.42	NA
18	0.060	3rhnA	0.582	2.58	0.217	0.754	3.-.-.-	3,8,15,65,71
19	0.060	2p4sA	0.506	4.50	0.052	0.864	2.4.2.1	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	0.65	0.966	0.75	0.85	1.00	3p0tA	GO:0003824
1	0.35	0.784	2.68	0.17	0.95	3anoB	GO:0000166 GO:0003824 GO:0003877 GO:0005524 GO:0005886 GO:0015967 GO:0016740 GO:0016779 GO:0040007
2	0.31	0.825	1.74	0.31	0.94	3o0mA	GO:0000166 GO:0003824 GO:0004081 GO:0016787 GO:0046872
3	0.30	0.829	1.63	0.32	0.93	3lb5C	GO:0003824
4	0.29	0.771	2.10	0.20	0.92	2fitA	GO:0000166 GO:0003824 GO:0005634 GO:0005737 GO:0005739 GO:0005829 GO:0006163 GO:0006351 GO:0006355 GO:0006915 GO:0009117 GO:0016787 GO:0031625 GO:0032435 GO:0042802 GO:0047710 GO:0070062 GO:0072332
5	0.29	0.780	2.26	0.14	0.97	3i4sA	GO:0003824
6	0.28	0.788	2.42	0.18	0.95	3anoA	GO:0000166 GO:0003824 GO:0003877 GO:0005524 GO:0005886 GO:0015967 GO:0016740 GO:0016779 GO:0040007
7	0.28	0.855	1.59	0.21	0.94	2eo4A	GO:0003824 GO:0046872
8	0.27	0.663	1.64	0.19	0.75	3l7xA	GO:0003824 GO:0046872
9	0.27	0.777	1.92	0.21	0.92	5cs2A	GO:0003824 GO:0008270 GO:0016787 GO:0047710
10	0.26	0.589	2.57	0.21	0.75	3n1sJ	GO:0000166 GO:0003824 GO:0005829 GO:0016787 GO:0043530 GO:0055130
11	0.24	0.796	2.05	0.16	0.95	3nrdA	GO:0003824
12	0.19	0.612	2.02	0.28	0.71	3oxkA	GO:0000166 GO:0003824 GO:0005634 GO:0005737 GO:0016787
13	0.19	0.577	2.97	0.23	0.77	4eguA	GO:0003824 GO:0046872
14	0.16	0.587	1.95	0.23	0.67	4zglD	GO:0003824
15	0.16	0.582	2.58	0.20	0.75	5i2fA	GO:0000118 GO:0000166 GO:0003824 GO:0005080 GO:0005634 GO:0005737 GO:0005856 GO:0005886 GO:0006351 GO:0006355 GO:0006915 GO:0007165 GO:0009154 GO:0016787 GO:0050850 GO:0070062 GO:0072332
16	0.16	0.573	2.65	0.20	0.75	4njxA	GO:0000166 GO:0003824 GO:0005730 GO:0005739 GO:0006629 GO:0006694 GO:0006915 GO:0016787
17	0.14	0.768	1.82	0.21	0.89	1emsA	GO:0000166 GO:0003824 GO:0006139 GO:0006807 GO:0008152 GO:0016787 GO:0016810 GO:0047710
18	0.14	0.571	2.75	0.17	0.75	1xquB	GO:0003824
19	0.13	0.477	1.28	0.26	0.52	4zglE	GO:0003824
20	0.13	0.730	2.77	0.16	0.95	2oikC	GO:0003824 GO:0046872
21	0.11	0.700	3.10	0.13	0.93	3jb9c	GO:0003824 GO:0005634 GO:0005681 GO:0005684 GO:0006397 GO:0008380 GO:0045292
22	0.08	0.671	1.79	0.23	0.75	3imiA	GO:0003824 GO:0046872
23	0.08	0.644	2.20	0.17	0.75	3ksvA	GO:0003824 GO:0046872
24	0.07	0.664	2.25	0.22	0.76	1y23B	GO:0003824

Consensus prediction of GO terms

Molecular Function	GO:0044389	GO:0005524	GO:0003877	GO:0046872	GO:0004081
GO-Score	0.59	0.35	0.35	0.31	0.31
Biological Processes	GO:2000112	GO:0097193	GO:0032434	GO:0072331	GO:1901799	GO:0010468	GO:0072521	GO:1903506	GO:0040007	GO:0015967
GO-Score	0.59	0.59	0.59	0.59	0.59	0.59	0.59	0.59	0.35	0.35
Cellular Component	GO:0043231	GO:0031988	GO:1903561	GO:0044444	GO:0005886
GO-Score	0.59	0.59	0.59	0.59	0.35

(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.