I-TASSER results

I-TASSER results for job id Rv0678

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

Input Sequence in FASTA format

>protein (165 residues)
MSVNDGVDQMGAEPDIMEFVEQMGGYFESRSLTRLAGRLLGWLLVCDPERQSSEELATAL
AASSGGISTNARMLIQFGFIERLAVAGDRRTYFRLRPNAFAAGERERIRAMAELQDLADV
GLRALGDAPPQRSRRLREMRDLLAYMENVVSDALGRYSQRTGEDD

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MSVNDGVDQMGAEPDIMEFVEQMGGYFESRSLTRLAGRLLGWLLVCDPERQSSEELATALAASSGGISTNARMLIQFGFIERLAVAGDRRTYFRLRPNAFAAGERERIRAMAELQDLADVGLRALGDAPPQRSRRLREMRDLLAYMENVVSDALGRYSQRTGEDD
Prediction	CCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCEEEEHCCCCCEEEEEHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
Conf.Score	998777545676599999999999999998998688999999998389999999999998898888999999999989979996799757899977888999999999999999999999999858999999999999999999999999999999999998759
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MSVNDGVDQMGAEPDIMEFVEQMGGYFESRSLTRLAGRLLGWLLVCDPERQSSEELATALAASSGGISTNARMLIQFGFIERLAVAGDRRTYFRLRPNAFAAGERERIRAMAELQDLADVGLRALGDAPPQRSRRLREMRDLLAYMENVVSDALGRYSQRTGEDD
Prediction	664566465463673144004300420463513311011100000045641215301731733423024104303734104434557424420413641034115432631551251045017425775652452053025004203610450153047347888
	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

CCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCEEEEHCCCCCEEEEEHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
MSVNDGVDQMGAEPDIMEFVEQMGGYFESRSLTRLAGRLLGWLLVCDPERQSSEELATALAASSGGISTNARMLIQFGFIERLAVAGDRRTYFRLRPNAFAAGERERIRAMAELQDLADVGLRALGDAPPQRSRRLREMRDLLAYMENVVSDALGRYSQRTGEDD

4nb5A

1.00

0.88

2.33

MUSTER

--------------DIMEFVEQMGGYFESRSLTRLAGRLLGWLLVCDPERQSSEELATALAASSGGISTNARMLIQFGFIERLAVAGDRRTYFRLRPNAFAAGERERIRAMAELQDLADVGLRALGDAPPQRSRRLREMRDLLAYMENVVSDALGRYSQ------

4nb5A

1.00

0.88

2.61

dPPAS

--------------DIMEFVEQMGGYFESRSLTRLAGRLLGWLLVCDPERQSSEELATALAASSGGISTNARMLIQFGFIERLAVAGDRRTYFRLRPNAFAAGERERIRAMAELQDLADVGLRALGDAPPQRSRRLREMRDLLAYMENVVSDALGRYSQ------

4nb5A

1.00

0.88

3.09

wdPPAS

--------------DIMEFVEQMGGYFESRSLTRLAGRLLGWLLVCDPERQSSEELATALAASSGGISTNARMLIQFGFIERLAVAGDRRTYFRLRPNAFAAGERERIRAMAELQDLADVGLRALGDAPPQRSRRLREMRDLLAYMENVVSDALGRYSQ------

4nb5A

1.00

0.88

2.75

wMUSTER

--------------DIMEFVEQMGGYFESRSLTRLAGRLLGWLLVCDPERQSSEELATALAASSGGISTNARMLIQFGFIERLAVAGDRRTYFRLRPNAFAAGERERIRAMAELQDLADVGLRALGDAPPQRSRRLREMRDLLAYMENVVSDALGRYSQ------

4nb5A

1.00

0.88

3.39

wPPAS

--------------DIMEFVEQMGGYFESRSLTRLAGRLLGWLLVCDPERQSSEELATALAASSGGISTNARMLIQFGFIERLAVAGDRRTYFRLRPNAFAAGERERIRAMAELQDLADVGLRALGDAPPQRSRRLREMRDLLAYMENVVSDALGRYSQ------

4nb5A

1.00

0.88

5.30

dPPAS2

--------------DIMEFVEQMGGYFESRSLTRLAGRLLGWLLVCDPERQSSEELATALAASSGGISTNARMLIQFGFIERLAVAGDRRTYFRLRPNAFAAGERERIRAMAELQDLADVGLRALGDAPPQRSRRLREMRDLLAYMENVVSDALGRYSQ------

4nb5A

1.00

0.88

2.99

PPAS

--------------DIMEFVEQMGGYFESRSLTRLAGRLLGWLLVCDPERQSSEELATALAASSGGISTNARMLIQFGFIERLAVAGDRRTYFRLRPNAFAAGERERIRAMAELQDLADVGLRALGDAPPQRSRRLREMRDLLAYMENVVSDALGRYSQ------

4nb5A

1.00

0.88

4.05

Env-PPAS

--------------DIMEFVEQMGGYFESRSLTRLAGRLLGWLLVCDPERQSSEELATALAASSGGISTNARMLIQFGFIERLAVAGDRRTYFRLRPNAFAAGERERIRAMAELQDLADVGLRALGDAPPQRSRRLREMRDLLAYMENVVSDALGRYSQ------

5jbrA

0.20

0.18

0.88

1.86

MUSTER

-----------NAVTEEQLTFSQAGDLATWQLPRTTGRTYGYLLLQS-EATSFQEIGADLGLSPGAVSTSVRELVAWGLARTIPQPGSRRLLVEAAGG-FEQLLAASHERSRAFIRTLRSGQALA--DDDRVATRLVDLTDLFEAYVEAGEQLRRRHEAGG----

5jbrA

0.20

0.18

0.88

2.11

dPPAS

-----------NAVTEEQLTFSQAGDLATWQLPRTTGRTYGYLLLQS-EATSFQEIGADLGLSPGAVSTSVRELVAWGLARTIPQPGSRRLLVEAAGG-FEQLLAASHERSRAFIRTLRSGQALA--DDDRVATRLVDLTDLFEAYVEAGEQLRRRHEAGG----

(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=0.37

Estimated TM-score = 0.76±0.10

Estimated RMSD = 4.2±2.8Å

Download Model 2

C-score=-1.91

Download Model 3

C-score=-1.73

Download Model 4

C-score=-2.52

Download Model 5

C-score=-2.42

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	4nb5A	0.865	0.61	1.000	0.879
2	1ku9A	0.672	2.70	0.136	0.849
3	5jbrA	0.639	2.98	0.203	0.836
4	2wauA	0.584	4.30	0.042	0.867
5	4gf2A1	0.576	4.29	0.062	0.867
6	2w6dA	0.576	4.43	0.064	0.842
7	2c6jA	0.567	4.26	0.057	0.842
8	2xu0A	0.566	4.26	0.074	0.849
9	3rrcA	0.556	4.05	0.030	0.800
10	1zrlA1	0.554	4.36	0.043	0.824

(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	0.14	5	3q5fA	NUC	Rep, Mult	17,52,53,54,64,65,68,82,90,91,92
2	0.08	2	4nb5B	2JT	Rep, Mult	30,77,79,103,104,106,107
3	0.06	2	2rakA	PIB	Rep, Mult	38,39,40,49,56
4	0.06	2	2w6dB	CPL	Rep, Mult	20,21,23,24,25,40,41,43
5	0.06	2	3bpxB	SAL	Rep, Mult	35,39,60,66,67,70
6	0.06	2	3q5fA	NUC	Rep, Mult	20,33,35,62,63,65,66,69,88,89,90
7	0.03	1	4nb5A	2JT	Rep, Mult	77,106,107,109,110,113
8	0.03	1	2wbiB	FAD	Rep, Mult	30,73,74,78
9	0.03	1	3rkoL	LFA	Rep, Mult	24,27,28,70

	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	3ihyC	0.492	5.26	0.076	0.867	2.7.1.137	80
2	0.060	1yisA	0.463	4.86	0.058	0.758	4.3.2.2	NA
3	0.060	1khvB	0.470	4.14	0.038	0.697	2.7.7.48	64
4	0.060	2ebaA	0.475	4.54	0.044	0.685	1.3.99.7	NA
5	0.060	2iukB	0.454	4.67	0.056	0.733	1.13.11.12	41
6	0.060	3ilwA	0.467	4.14	0.080	0.642	5.99.1.3	NA
7	0.060	1no3A	0.463	5.31	0.047	0.836	1.13.11.12	NA
8	0.060	1rx0A	0.471	4.71	0.070	0.721	1.3.99.-	NA
9	0.060	1qd1B	0.406	5.50	0.035	0.746	2.1.2.5,4.3.1.4	NA
10	0.060	2o6yA	0.480	5.25	0.092	0.806	4.3.1.-	NA
11	0.060	2e9fB	0.464	3.64	0.063	0.600	4.3.2.1	NA
12	0.060	2p0mA	0.468	5.32	0.083	0.830	1.13.11.33	NA
13	0.060	3djlA	0.469	4.30	0.039	0.667	1.3.99.-	NA
14	0.060	3czoB	0.470	5.39	0.084	0.842	4.3.1.3	NA
15	0.060	1jqiA	0.474	4.59	0.071	0.709	1.3.99.2	NA
16	0.060	2x38A	0.507	5.28	0.141	0.867	2.7.1.153	NA
17	0.060	3d9dA	0.474	4.98	0.051	0.727	1.7.3.1	NA
18	0.060	3kb9A	0.470	4.87	0.060	0.770	4.2.3.37	70,81
19	0.060	3mddA	0.473	4.60	0.036	0.709	1.3.99.3	119

(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	0.68	0.873	1.22	0.99	0.90	4nb5B	GO:0003677 GO:0006351 GO:0006355
1	0.31	0.691	2.95	0.13	0.90	1ku9A	GO:0003677 GO:0003700 GO:0006351 GO:0006355
2	0.19	0.401	2.70	0.13	0.48	3bpxA	GO:0003677 GO:0003700 GO:0006351 GO:0006355
3	0.11	0.398	3.28	0.10	0.48	2nyxB	GO:0003677 GO:0003700 GO:0005886 GO:0006351 GO:0006355 GO:0044212
4	0.07	0.584	4.30	0.04	0.87	2wauA	GO:0004872 GO:0009405 GO:0016021 GO:0016337 GO:0020002 GO:0020013 GO:0020030 GO:0020033 GO:0020035 GO:0046789 GO:0050839
5	0.07	0.548	4.34	0.03	0.84	2y8dA	GO:0004872 GO:0009405 GO:0016021
6	0.07	0.567	4.26	0.06	0.84	2c6jA	GO:0004872 GO:0009405 GO:0016020 GO:0016021
7	0.07	0.533	4.51	0.04	0.84	4gf2A	GO:0004872 GO:0009405 GO:0016020 GO:0016021
8	0.07	0.511	4.91	0.06	0.81	4p1tA	GO:0004872 GO:0009405 GO:0016021
9	0.07	0.562	4.34	0.06	0.82	4nuuB	GO:0004872 GO:0009405 GO:0016020 GO:0016021
10	0.07	0.559	4.43	0.02	0.84	3vuvA	GO:0004872 GO:0009405 GO:0009986 GO:0016020 GO:0016021 GO:0042493 GO:0046812 GO:0046872
11	0.07	0.518	4.32	0.05	0.80	1zroA	GO:0004872 GO:0009405 GO:0016021
12	0.07	0.473	4.37	0.03	0.72	5f3jA	GO:0004872 GO:0009405 GO:0016020 GO:0016021
13	0.07	0.515	4.22	0.06	0.79	4k2uA	GO:0004872 GO:0008201 GO:0009405 GO:0016020 GO:0016021 GO:0020009 GO:0030260 GO:0046789
14	0.07	0.511	4.69	0.06	0.85	3cpzA	GO:0004872 GO:0009405 GO:0016021
15	0.07	0.486	4.47	0.06	0.75	2yk0A	GO:0004872 GO:0009405 GO:0016020 GO:0016021 GO:0046872
16	0.06	0.378	4.98	0.08	0.65	2y75E	GO:0003677 GO:0006351 GO:0006355 GO:0042802
17	0.06	0.323	6.09	0.07	0.67	3qiaA	GO:0000166 GO:0004518 GO:0004519 GO:0005524 GO:0006314 GO:0006754 GO:0006810 GO:0006811 GO:0015991 GO:0015992 GO:0016539 GO:0016787 GO:0016820 GO:0033178 GO:0046034 GO:0090305
18	0.06	0.388	3.35	0.06	0.49	5cyvB	GO:0003677 GO:0003700 GO:0006351 GO:0006355

Consensus prediction of GO terms

Molecular Function	GO:0003677	GO:0003700
GO-Score	0.84	0.50
Biological Processes	GO:0006355
GO-Score	0.84
Cellular Component	GO:0005886	GO:0020002	GO:0016021	GO:0020030
GO-Score	0.11	0.07	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.