I-TASSER results

I-TASSER results for job id Rv2175c

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

Input Sequence in FASTA format

>protein (146 residues)
MPGRAPGSTLARVGSIPAGDDVLDPDEPTYDLPRVAELLGVPVSKVAQQLREGHLVAVRR
AGGVVIPQVFFTNSGQVVKSLPGLLTILHDGGYRDTEIMRWLFTPDPSLTITRDGSRDAV
SNARPVDALHAHQAREVVRRAQAMAY

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MPGRAPGSTLARVGSIPAGDDVLDPDEPTYDLPRVAELLGVPVSKVAQQLREGHLVAVRRAGGVVIPQVFFTNSGQVVKSLPGLLTILHDGGYRDTEIMRWLFTPDPSLTITRDGSRDAVSNARPVDALHAHQAREVVRRAQAMAY
Prediction	CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHCCEEEEEHCCEEHCCHHHHCCCCCHCCCCCCHHHHHHHCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHHCCHHHHHHHHHHHCC
Conf.Score	99999987644456788776777888876799999999899889999999989589999899788544546599865587663455555479999999999867898888877776667778994999987865799999998769
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MPGRAPGSTLARVGSIPAGDDVLDPDEPTYDLPRVAELLGVPVSKVAQQLREGHLVAVRRAGGVVIPQVFFTNSGQVVKSLPGLLTILHDGGYRDTEIMRWLFTPDPSLTITRDGSRDAVSNARPVDALHAHQAREVVRRAQAMAY
Prediction	75453455413404514254531457442140440063272535303410564300002376323001300367342152041002003224143620042013434513344444444445121031046644430333047468
	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

                   |                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHCCEEEEEHCCEEHCCHHHHCCCCCHCCCCCCHHHHHHHCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHHCCHHHHHHHHHHHCC
MPGRAPGSTLARVGSIPAGDDVLDPDEPTYDLPRVAELLGVPVSKVAQQLREGHLVAVRRAGGVVIPQVFFTNSGQVVKSLPGLLTILHDGGYRDTEIMRWLFTPDPSLTITRDGSRDAVSNARPVDALHAHQAREVVRRAQAMAY

2kfsA

1.00

3.71

MUSTER

MPGRAPGSTLARVGSIPAGDDVLDPDEPTYDLPRVAELLGVPVSKVAQQLREGHLVAVRRAGGVVIPQVFFTNSGQVVKSLPGLLTILHDGGYRDTEIMRWLFTPDPSLTITRDGSRDAVSNARPVDALHAHQAREVVRRAQAMAY

2kfsA

1.00

6.05

dPPAS

MPGRAPGSTLARVGSIPAGDDVLDPDEPTYDLPRVAELLGVPVSKVAQQLREGHLVAVRRAGGVVIPQVFFTNSGQVVKSLPGLLTILHDGGYRDTEIMRWLFTPDPSLTITRDGSRDAVSNARPVDALHAHQAREVVRRAQAMAY

2kfsA

1.00

5.99

wdPPAS

MPGRAPGSTLARVGSIPAGDDVLDPDEPTYDLPRVAELLGVPVSKVAQQLREGHLVAVRRAGGVVIPQVFFTNSGQVVKSLPGLLTILHDGGYRDTEIMRWLFTPDPSLTITRDGSRDAVSNARPVDALHAHQAREVVRRAQAMAY

2kfsA

1.00

0.99

4.02

wMUSTER

-PGRAPGSTLARVGSIPAGDDVLDPDEPTYDLPRVAELLGVPVSKVAQQLREGHLVAVRRAGGVVIPQVFFTNSGQVVKSLPGLLTILHDGGYRDTEIMRWLFTPDPSLTITRDGSRDAVSNARPVDALHAHQAREVVRRAQAMAY

2kfsA

1.00

5.56

wPPAS

MPGRAPGSTLARVGSIPAGDDVLDPDEPTYDLPRVAELLGVPVSKVAQQLREGHLVAVRRAGGVVIPQVFFTNSGQVVKSLPGLLTILHDGGYRDTEIMRWLFTPDPSLTITRDGSRDAVSNARPVDALHAHQAREVVRRAQAMAY

2kfsA

1.00

11.95

dPPAS2

MPGRAPGSTLARVGSIPAGDDVLDPDEPTYDLPRVAELLGVPVSKVAQQLREGHLVAVRRAGGVVIPQVFFTNSGQVVKSLPGLLTILHDGGYRDTEIMRWLFTPDPSLTITRDGSRDAVSNARPVDALHAHQAREVVRRAQAMAY

2kfsA

1.00

5.04

PPAS

MPGRAPGSTLARVGSIPAGDDVLDPDEPTYDLPRVAELLGVPVSKVAQQLREGHLVAVRRAGGVVIPQVFFTNSGQVVKSLPGLLTILHDGGYRDTEIMRWLFTPDPSLTITRDGSRDAVSNARPVDALHAHQAREVVRRAQAMAY

2kfsA

1.00

5.92

Env-PPAS

MPGRAPGSTLARVGSIPAGDDVLDPDEPTYDLPRVAELLGVPVSKVAQQLREGHLVAVRRAGGVVIPQVFFTNSGQVVKSLPGLLTILHDGGYRDTEIMRWLFTPDPSLTITRDGSRDAVSNARPVDALHAHQAREVVRRAQAMAY

2kfsA1

1.00

0.71

2.41

MUSTER

MPGRAPGSTLARVGSIPAGDDVLDPDEPTYDLPRVAELLGVPVSKVAQQLREGHLVAVRRAGGVVIPQVFFTNSGQVVKSLPGLLTILHDGGYRDTEIMRWLFT------------------------------------------

2kfsA1

1.00

0.71

4.34

dPPAS

MPGRAPGSTLARVGSIPAGDDVLDPDEPTYDLPRVAELLGVPVSKVAQQLREGHLVAVRRAGGVVIPQVFFTNSGQVVKSLPGLLTILHDGGYRDTEIMRWLFT------------------------------------------

(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=2.00

Estimated TM-score = 0.99±0.04

Estimated RMSD = 1.0±1.0Å

Download Model 2

C-score=-4.39

Download Model 3

C-score=-4.47

Download Model 4

C-score=-5.00

Download Model 5

C-score=-5.00

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	2kfsA	0.985	0.75	1.000	1.000
2	1b25A	0.483	4.77	0.074	0.815
3	1eflA	0.480	4.72	0.081	0.815
4	2qfzA	0.476	4.74	0.045	0.788
5	3qyeA	0.472	5.13	0.066	0.829
6	2haeA	0.472	4.89	0.067	0.794
7	2dvmA	0.472	4.78	0.092	0.794
8	5hjnA	0.470	4.87	0.022	0.788
9	1o0sA1	0.470	4.90	0.081	0.815
10	1aorA	0.468	4.76	0.079	0.815

(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	0.21	10	1znnB	SO4	Rep, Mult	136,139,140
2	0.07	3	2wieC	CVM	Rep, Mult	81,84,88
3	0.04	2	1c6dA	KR	Rep, Mult	88,98,101,126,129,140
4	0.02	1	4o6mA	MPG	Rep, Mult	88,101
5	0.02	1	2d2mD	OXY	Rep, Mult	133,137
6	0.02	1	1p8j0	III	Rep, Mult	56,58,59,126
7	0.02	1	3o72C	OXY	Rep, Mult	90,139
8	0.02	1	3fcsC	IMD	Rep, Mult	103,133
9	0.02	1	1aorB	SF4	Rep, Mult	69,71,99,103
10	0.02	1	2wpnB	SF4	Rep, Mult	59,68
11	0.02	1	2yl8A	MN	Rep, Mult	31,77

	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	1euzF	0.432	5.20	0.080	0.815	1.4.1.3	95
2	0.060	2aw5B	0.446	4.33	0.047	0.733	1.1.1.40	NA
3	0.060	1hrdA	0.439	5.07	0.107	0.808	1.4.1.2	79,84
4	0.060	2ecfA	0.433	4.82	0.075	0.726	3.4.14.5	NA
5	0.060	2dvmA	0.472	4.78	0.092	0.794	1.1.1.38	NA
6	0.060	2hldK	0.412	4.75	0.045	0.678	3.6.3.14	NA
7	0.060	1gytJ	0.436	5.14	0.045	0.822	3.4.11.1	128
8	0.060	1thmA	0.450	4.31	0.085	0.664	3.4.21.66	NA
9	0.060	2gepA	0.425	4.29	0.040	0.664	1.8.1.2	NA
10	0.060	1ah2A	0.395	4.52	0.032	0.630	3.4.21.-	NA
11	0.060	3bx1B	0.432	4.38	0.055	0.657	3.4.21.62	44
12	0.060	2tohA	0.446	5.24	0.050	0.829	1.14.16.2	37
13	0.060	1ltuA	0.427	5.27	0.050	0.788	1.14.16.1	NA
14	0.060	1dbiA	0.445	4.19	0.109	0.657	3.4.21.-	NA
15	0.060	1aupA	0.444	5.11	0.073	0.822	1.4.1.2	NA
16	0.060	3e2tA	0.449	5.00	0.044	0.801	1.14.16.4	NA
17	0.060	1gq2A	0.406	5.20	0.029	0.753	1.1.1.40	NA
18	0.060	1g72A	0.416	5.32	0.038	0.781	1.1.99.8	NA
19	0.060	1bvuA	0.391	5.02	0.063	0.706	1.4.1.3	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	0.88	0.985	0.75	1.00	1.00	2kfsA	GO:0003677 GO:0018107 GO:0019217
1	0.11	0.406	5.20	0.03	0.75	1gq2A	GO:0004470 GO:0004471 GO:0004473 GO:0005737 GO:0006108 GO:0008948 GO:0016491 GO:0046872 GO:0051287 GO:0055114
2	0.07	0.473	4.61	0.07	0.77	3qybA	GO:0005096 GO:0005622 GO:0005737 GO:0006886 GO:0012505 GO:0016192 GO:0017137 GO:0030659 GO:0031338 GO:0031339 GO:0031988 GO:0032869 GO:0061024 GO:0070062 GO:0090630
3	0.07	0.483	4.77	0.07	0.82	1b25A	GO:0009055 GO:0016491 GO:0016625 GO:0046872 GO:0051536 GO:0051539 GO:0055114
4	0.07	0.415	5.21	0.06	0.75	2qq8A	GO:0005096 GO:0005776 GO:0005794 GO:0005829 GO:0006886 GO:0010507 GO:0017137 GO:0019901 GO:0031338 GO:0055037 GO:0071955 GO:0090630 GO:1902017 GO:2000785
5	0.07	0.458	4.83	0.04	0.78	2g77A	GO:0005096 GO:0005794 GO:0005795 GO:0006886 GO:0016192 GO:0017137 GO:0031338 GO:0090630
6	0.07	0.425	5.45	0.10	0.79	3nv9A	GO:0004470 GO:0004471 GO:0006108 GO:0051287 GO:0055114
7	0.07	0.472	4.78	0.09	0.79	2dvmA	GO:0000166 GO:0004470 GO:0004471 GO:0006108 GO:0051287 GO:0055114
8	0.07	0.434	5.05	0.04	0.76	3dzxA	GO:0005096 GO:0005622 GO:0006886 GO:0012505 GO:0017137 GO:0031338 GO:0071889 GO:0090630 GO:1902017
9	0.06	0.437	5.04	0.06	0.79	1vl6B	GO:0000166 GO:0004470 GO:0004471 GO:0006108 GO:0008948 GO:0016491 GO:0046872 GO:0051287 GO:0055114
10	0.06	0.473	4.93	0.07	0.80	1vl6A	GO:0000166 GO:0004470 GO:0004471 GO:0006108 GO:0008948 GO:0016491 GO:0046872 GO:0051287 GO:0055114
11	0.06	0.272	5.69	0.02	0.53	4axsA	GO:0006525 GO:0008804 GO:0016301 GO:0016310 GO:0016740
12	0.06	0.445	4.44	0.04	0.72	2a9fA	GO:0004470 GO:0004471 GO:0006108 GO:0016491 GO:0046872 GO:0051287 GO:0055114
13	0.06	0.476	4.74	0.04	0.79	2qfzA	GO:0005096 GO:0005622 GO:0006886 GO:0012505 GO:0017137 GO:0031338 GO:0042803 GO:0071889 GO:0090630 GO:1902017
14	0.06	0.453	4.83	0.06	0.77	3hzjC	GO:0005096 GO:0005634 GO:0005769 GO:0005794 GO:0006886 GO:0017137 GO:0031338 GO:0032880 GO:0090630
15	0.06	0.454	4.74	0.05	0.76	4p17B	GO:0005096 GO:0005622 GO:0006886 GO:0012505 GO:0017137 GO:0031338 GO:0090630
16	0.06	0.397	5.22	0.06	0.72	3wjaB	GO:0004470 GO:0004471 GO:0004473 GO:0005737 GO:0005739 GO:0005829 GO:0005975 GO:0006108 GO:0006741 GO:0008948 GO:0009055 GO:0009725 GO:0009743 GO:0016491 GO:0030145 GO:0043531 GO:0046872 GO:0050661 GO:0051262 GO:0051287 GO:0055114 GO:1902031
17	0.06	0.472	5.13	0.07	0.83	3qyeA	GO:0005096 GO:0005622 GO:0005634 GO:0005829 GO:0006886 GO:0012505 GO:0017137 GO:0031338 GO:0032880 GO:0061024 GO:0090630 GO:1902017
18	0.06	0.468	4.76	0.08	0.82	1aorA	GO:0009055 GO:0016491 GO:0016625 GO:0033726 GO:0046872 GO:0051536 GO:0051539 GO:0055114

Consensus prediction of GO terms

Molecular Function	GO:0003677	GO:0043169
GO-Score	0.88	0.34
Biological Processes	GO:0019217	GO:0018107
GO-Score	0.88	0.88
Cellular Component	GO:0044424
GO-Score	0.34

(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.