I-TASSER results

I-TASSER results for job id Rv3278c

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

Input Sequence in FASTA format

>protein (172 residues)
MSYPENVLAAGEQVVLHRHPHWNRLIWPVVVLVLLTGLAAFGSGFVNSTPWQQIAKNVIH
AVIWGIWLVIVGWLTLWPFLSWLTTHFVVTNRRVMFRHGVLTRSGIDIPLARINSVEFRD
RIFERIFRTGTLIIESASQDPLEFYNIPRLREVHALLYHEVFDTLGSDESPS

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MSYPENVLAAGEQVVLHRHPHWNRLIWPVVVLVLLTGLAAFGSGFVNSTPWQQIAKNVIHAVIWGIWLVIVGWLTLWPFLSWLTTHFVVTNRRVMFRHGVLTRSGIDIPLARINSVEFRDRIFERIFRTGTLIIESASQDPLEFYNIPRLREVHALLYHEVFDTLGSDESPS
Prediction	CCCHHHHCCCCCEEEEEHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHEEEEEEHCCEEEEEHCCEEEEEEEEEEEEEEEEEEHCCHHHHHHCCEEEEEEHCCCCCEEEHCCCCHHHHHHHHHHHHHCCCCCCCCCC
Conf.Score	9875675789968999856658999999999999999999999998665544456789999999999999999999999987445899989999999755787689997334787788859888775957999997899969985889999999999999986777888999
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MSYPENVLAAGEQVVLHRHPHWNRLIWPVVVLVLLTGLAAFGSGFVNSTPWQQIAKNVIHAVIWGIWLVIVGWLTLWPFLSWLTTHFVVTNRRVMFRHGVLTRSGIDIPLARINSVEFRDRIFERIFRTGTLIIESASQDPLEFYNIPRLREVHALLYHEVFDTLGSDESPS
Prediction	7623563137413011413321311233233333333333333221333333433333333233333333333332221233332302024520223311034433403143045043533202212210302030335461305305405401520362156457667648
	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

                   |                   |                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCHHHHCCCCCEEEEEHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHEEEEEEHCCEEEEEHCCEEEEEEEEEEEEEEEEEEHCCHHHHHHCCEEEEEEHCCCCCEEEHCCCCHHHHHHHHHHHHHCCCCCCCCCC
MSYPENVLAAGEQVVLHRHPHWNRLIWPVVVLVLLTGLAAFGSGFVNSTPWQQIAKNVIHAVIWGIWLVIVGWLTLWPFLSWLTTHFVVTNRRVMFRHGVLTRSGIDIPLARINSVEFRDRIFERIFRTGTLIIESASQDPLEFYNIPRLREVHALLYHEVFDTLGSDESPS

1h2sB

0.15

0.05

0.35

1.55

dPPAS2

---------------------GAVFIFVGALTVLFGAIAYGEVTAAAATGDAAAVQEAAVSAILGLIILLGINLGLVAATL-------------------------------------------------------------------------------------------

2axtZ

0.10

0.03

0.34

1.48

dPPAS2

----------------------MTILFQLALAALVILSFVMVIGVPVAYASDRSKQLIFLGSGLWIALVLVVGVLNFFVV--------------------------------------------------------------------------------------------

5fvmA

0.12

0.99

0.67

MUSTER

IHQPNQTVSRSLSLLADLKAHPQALVYPLTVAIKVSRQRAALSIIDKMRMHSPKLVNQAELVSDELIRVAVLWHELWYEGLEDASRQFFGEHNTTLEPLHEMLKRGPETLREISFQNSFGRDLNDAYEWVLNYKRTKDINNLN-QAWDIYYNVFRRISRKLPQLQTQHVSPK

1h2sB

0.15

0.05

0.35

0.87

dPPAS

---------------------GAVFIFVGALTVLFGAIAYGEVTAAAATGDAAAVQEAAVSAILGLIILLGINLGLVAATL-------------------------------------------------------------------------------------------

2axtZ

0.10

0.03

0.34

0.88

wdPPAS

----------------------MTILFQLALAALVILSFVMVIGVPVAYASWDRSKQLIFLGSGLWIALVLVVGVLNFFVV-------------------------------------------------------------------------------------------

3zbpA2

0.12

0.11

0.90

0.73

wMUSTER

------------SVVIGSYDSDISLRNSSGSLKTFEGVSSVSMIINYHENVEGIPQSMVNQNILEVLNALVILF-LMDITNWAHFH--VPVQTVQLHVCFDRQEAQAIL-DPISIASLYTD-PDRDVSISTVTTGYADPEKFVINGL-SIEDIRKRLEERREMMNRAKANMR

3dcxA

0.19

0.09

0.49

0.80

wPPAS

LGP----IGDNEQLALAYRVI----------------------------------------------------------------DFVFTNKRLILID---KVSYHSVPYKAITHFEVETA------GTAELKLWISGQKDKELKKGTDVVGIQKTIANFSL----------

2x2vA

0.05

0.02

0.35

1.44

dPPAS2

-----------------------AFLGAAIAAGLAAVAGAIAVAIIVKATILRGTLQTLMFIGVPLAEAVPIIAIVISLLILF-----------------------------------------------------------------------------------------

4d6wA2

0.12

0.11

0.93

0.96

PPAS

IAFPENTKLDWKPVTKNTRYCPLQSDGAQVLTSEIQRILDYSLCQNTWDKVERKEP-----------LSPLDLSYLASKSPGKGLAYTVINGTLSFAHTRYVRMWIDGPVLEPKGKRESPSGISSDI-FKYGDMEIGPNGLLKTAGFPWHLIGMGIVDNELHELSEANPLDH

4xb1A2

0.07

0.06

0.95

0.72

Env-PPAS

IGVLRENLLGENIKRIDAVVNASTTFILTKMSEGKTLDDAIEEAKSLGILEEDPSKDIDGIDAYYKAKILHWVSYGEPPEEEERLGIRVRDARNVRLVAQVSKGKISVKPRKLS----SDNPLLVEGVQNAAVIRTNNLGEVILKGRVTASGVFTDIIKATLKFPNLR----

(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 4 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=-4.36

Estimated TM-score = 0.26±0.08

Estimated RMSD = 15.6±3.3Å

Download Model 2

C-score=-4.50

Download Model 3

C-score=-4.76

Download Model 4

C-score=-4.85

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	3cqyA	0.493	4.74	0.069	0.767
2	5d92D	0.485	3.69	0.044	0.663
3	4p96A	0.480	4.31	0.053	0.727
4	4av3A	0.480	4.03	0.051	0.669
5	3agrA	0.480	5.13	0.019	0.791
6	5fbyA2	0.474	4.88	0.045	0.738
7	3qbwA	0.473	4.54	0.070	0.727
8	5id6A	0.469	5.36	0.064	0.802
9	4a01A	0.467	4.86	0.026	0.767
10	4xydA	0.467	4.33	0.046	0.704

(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	0.05	3	2nwwB	TB1	Rep, Mult	138,140,150,153,154,157
2	0.05	3	2nwlA	ASP	Rep, Mult	153,154,157
3	0.04	2	3ag3A	PEK	Rep, Mult	25,29,83
4	0.04	2	4m70Q	III	Rep, Mult	31,34,35,38,60,61,65,68,69,72,79
5	0.04	2	4fe1L	CLA	Rep, Mult	68,71,79
6	0.04	2	5dwkA	78N	Rep, Mult	39,63,66,67,70,75
7	0.04	2	2hgrH	NUC	Rep, Mult	112,125,127
8	0.04	2	1v54D	DMU	Rep, Mult	74,77
9	0.04	2	2nwxB	ASP	Rep, Mult	113,137,154,157,158,161
10	0.02	1	4d2eC	78M	Rep, Mult	29,32,73,74,77
11	0.02	1	1mz9B	VDY	Rep, Mult	59,62,66
12	0.02	1	3a0hK	CLA	Rep, Mult	41,45
13	0.02	1	2e7yB	ZN	Rep, Mult	19,21,168
14	0.02	1	4r7cA	GLY	Rep, Mult	29,33,73
15	0.02	1	3h87B	IMD	Rep, Mult	124,125
16	0.02	1	3db1D	PO4	Rep, Mult	97,98,103
17	0.02	1	1ij6A	CA	Rep, Mult	134,136,138,140

	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	1xmeA	0.454	5.02	0.083	0.715	1.9.3.1	NA
2	0.060	2occN	0.443	5.00	0.050	0.704	1.9.3.1	35
3	0.060	3hq2B	0.440	3.92	0.044	0.622	3.4.24.-	135
4	0.060	2hv7A	0.445	5.23	0.080	0.785	5.2.1.8	37
5	0.060	2fr0A	0.450	4.85	0.032	0.750	2.3.1.94	NA
6	0.060	1occA	0.441	4.81	0.056	0.704	1.9.3.1	NA
7	0.060	3iayA	0.458	4.78	0.033	0.704	2.7.7.7	NA
8	0.060	3e08A	0.432	4.45	0.059	0.645	1.13.11.11	32,77
9	0.060	2c6fA	0.434	4.27	0.026	0.622	3.4.15.1	135,158
10	0.060	1obbA	0.436	5.24	0.051	0.756	3.2.1.20	NA
11	0.060	1clqA	0.412	5.04	0.053	0.669	2.7.7.7	158
12	0.060	2ixpB	0.448	5.12	0.094	0.779	5.2.1.8	NA
13	0.060	1p7cB	0.431	5.09	0.058	0.727	2.7.1.21	NA
14	0.060	2d1fA	0.436	5.27	0.045	0.744	4.2.3.1	NA
15	0.060	1osnA	0.455	4.61	0.055	0.704	2.7.1.21	NA
16	0.060	1h16A	0.432	5.04	0.020	0.680	2.3.1.54	NA
17	0.060	2epoA	0.438	5.01	0.062	0.686	3.2.1.52	NA
18	0.060	2pmzQ	0.442	5.01	0.020	0.715	2.7.7.6	141,153
19	0.060	1p6xA	0.463	4.72	0.046	0.715	2.7.1.21	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	0.07	0.442	5.20	0.05	0.76	4zfvA	GO:0005524 GO:0006040 GO:0009254 GO:0016301 GO:0016310 GO:0016740 GO:0016773
1	0.07	0.490	3.76	0.04	0.67	5d92B	GO:0000166 GO:0008654 GO:0016020 GO:0016021 GO:0016740 GO:0016780 GO:0046872
2	0.07	0.468	4.72	0.06	0.75	3qbxB	GO:0000166 GO:0005524 GO:0005975 GO:0006040 GO:0009254 GO:0016301 GO:0016310 GO:0016740 GO:0016773 GO:0097175
3	0.07	0.465	4.86	0.06	0.74	4mo5A	GO:0000166 GO:0005524 GO:0005975 GO:0006040 GO:0009254 GO:0016301 GO:0016310 GO:0016740 GO:0016773 GO:0097175
4	0.07	0.465	5.10	0.04	0.78	4jepA	GO:0005576 GO:0016787 GO:0017111 GO:0020003
5	0.07	0.474	4.95	0.09	0.76	3cqyA	GO:0000166 GO:0005524 GO:0005975 GO:0006040 GO:0009254 GO:0016301 GO:0016310 GO:0016740 GO:0016773 GO:0097175
6	0.07	0.454	4.15	0.09	0.67	4mndA	GO:0003824 GO:0008152 GO:0008654 GO:0016020 GO:0016021 GO:0016740 GO:0016779 GO:0016780 GO:0046872
7	0.07	0.455	4.33	0.06	0.68	4o6mB	GO:0000166 GO:0008654 GO:0016020 GO:0016021 GO:0016740 GO:0016780 GO:0046872
8	0.07	0.480	5.13	0.02	0.79	3agrA	GO:0005576 GO:0016787 GO:0017111
9	0.07	0.440	5.22	0.04	0.76	4jepB	GO:0005576 GO:0016787 GO:0017111 GO:0020003
10	0.07	0.468	5.19	0.03	0.79	4kh6B	GO:0005576 GO:0016787 GO:0017111 GO:0020003
11	0.06	0.414	4.44	0.09	0.65	3ihuA	GO:0003677 GO:0003700 GO:0006351 GO:0006355
12	0.06	0.434	4.05	0.06	0.63	3fmsA	GO:0003677 GO:0003700 GO:0006351 GO:0006355 GO:0046872
13	0.06	0.400	4.74	0.05	0.65	3c7jA	GO:0003700 GO:0006355
14	0.06	0.412	4.46	0.07	0.65	2di3A	GO:0003677 GO:0003700 GO:0006351 GO:0006355 GO:0046872
15	0.06	0.410	4.46	0.08	0.63	1h9tA	GO:0000062 GO:0003677 GO:0003700 GO:0005737 GO:0005829 GO:0006351 GO:0006355 GO:0006629 GO:0006631 GO:0019217 GO:0019395 GO:0045723 GO:0045892 GO:0045893
16	0.06	0.361	5.52	0.04	0.63	3zx3B	GO:0000166 GO:0005524 GO:0005615 GO:0008021 GO:0009986 GO:0010238 GO:0010332 GO:0010996 GO:0014069 GO:0016020 GO:0016021 GO:0016323 GO:0016787 GO:0016887 GO:0031000 GO:0032496 GO:0033198 GO:0033602 GO:0035456 GO:0035457 GO:0042802 GO:0043005 GO:0043025 GO:0043262 GO:0043278 GO:0051260 GO:0071222 GO:0071275 GO:0071356 GO:0097060 GO:1903576 GO:2001170
17	0.06	0.357	5.47	0.05	0.66	4br5A	GO:0000166 GO:0016020 GO:0016021 GO:0016787
18	0.06	0.363	5.23	0.07	0.62	4ipiA	GO:0003824 GO:0016051 GO:0046872

Consensus prediction of GO terms

Molecular Function	GO:0035639	GO:0032559	GO:0016772	GO:0032550
GO-Score	0.37	0.37	0.37	0.37
Biological Processes	GO:0000270	GO:0006796
GO-Score	0.37	0.37
Cellular Component	GO:0016021	GO:0020003
GO-Score	0.07	0.07

(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.