I-TASSER results

I-TASSER results for job id Rv0787A

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

Input Sequence in FASTA format

>protein (79 residues)
MARVVVHVMPKAEILDPQGQAIVGALGRLGHLGISDVRQGKRFELEVDDTVDDTTLAEIA
ESLLANTVIEDWTISRDPQ

Predicted Secondary Structure

Sequence	20 40 60 \| \| \| MARVVVHVMPKAEILDPQGQAIVGALGRLGHLGISDVRQGKRFELEVDDTVDDTTLAEIAESLLANTVIEDWTISRDPQ
Prediction	CCEEEEEEEHCCCCCCHHHHHHHHHHHHHCCCCCCCEEEEEEEEEEHCCCCHHHHHHHHHHHHCCCCCCEEEEEEEHCC
Conf.Score	9689999995999999689999999999799886545677899999879988999999999977887757899999769
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 \| \| \| MARVVVHVMPKAEILDPQGQAIVGALGRLGHLGISDVRQGKRFELEVDDTVDDTTLAEIAESLLANTVIEDWTISRDPQ
Prediction	7540404032374243332510451077141740551321330203155754563045107512223332415253468
	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

                   |                   |                   |

Sec.Str
Seq

CCEEEEEEEHCCCCCCHHHHHHHHHHHHHCCCCCCCEEEEEEEEEEHCCCCHHHHHHHHHHHHCCCCCCEEEEEEEHCC
MARVVVHVMPKAEILDPQGQAIVGALGRLGHLGISDVRQGKRFELEVDDTVDDTTLAEIAESLLANTVIEDWTISRDPQ

1twjA

0.41

0.99

3.91

MUSTER

MYKVKVYVSLKESVLDPQGSAVQHALHSMTYNEVQDVRIGKYMELTIEKSDLDVLVKEMCEKLLANTVIEDYRYEVEE-

2yx5A

0.28

1.00

8.38

dPPAS

MYKATVIIKLKKGVLNPEGRTIQRALNFLGFNNVKEVQTYKMIDIIMEENKVKEEVEEMCKKLLANPVIHDYEIKVEKI

1twjA

0.41

0.99

6.30

wdPPAS

MYKVKVYVSLKESVLDPQGSAVQHALHSMTYNEVQDVRIGKYMELTIEKSDLDVLVKEMCEKLLANTVIEDYRYEVEE-

1twjA

0.40

0.39

0.97

4.18

wMUSTER

-YKVKVYVSLKESVLDPQGSAVQHALHSMTYNEVQDVRIGKYMELTIEKSDLDVLVKEMCEKLLANTVIEDYRYEVEE-

1twjA

0.41

0.99

4.52

wPPAS

MYKVKVYVSLKESVLDPQGSAVQHALHSMTYNEVQDVRIGKYMELTIEKSDLDVLVKEMCEKLLANTVIEDYRYEVEE-

1twjA

0.41

0.99

10.47

dPPAS2

MYKVKVYVSLKESVLDPQGSAVQHALHSMTYNEVQDVRIGKYMELTIEKSDLDVLVKEMCEKLLANTVIEDYRYEVEE-

1twjA

0.41

0.99

4.71

PPAS

MYKVKVYVSLKESVLDPQGSAVQHALHSMTYNEVQDVRIGKYMELTIEKSDLDVLVKEMCEKLLANTVIEDYRYEVEE-

1twjA

0.41

0.99

5.35

Env-PPAS

MYKVKVYVSLKESVLDPQGSAVQHALHSMTYNEVQDVRIGKYMELTIEKRDLDVLVKEMCEKLLANTVIEDYRYEVEE-

2yx5A

0.28

1.00

3.83

MUSTER

MYKATVIIKLKKGVLNPEGRTIQRALNFLGFNNVKEVQTYKMIDIIMEENKVKEEVEEMCKKLLANPVIHDYEIKVEKE

1twjA

0.41

0.99

8.31

dPPAS

MYKVKVYVSLKESVLDPQGSAVQHALHSMTYNEVQDVRIGKYMELTIEKSDLDVLVKEMCEKLLANTVIEDYRYEVEE-

(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 1 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=1.86

Estimated TM-score = 0.98±0.05

Estimated RMSD = 0.5±0.5Å

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	1twjA	0.924	1.06	0.410	0.987
2	2yx5A	0.899	1.20	0.278	1.000
3	1vq3C	0.840	1.48	0.247	0.975
4	2zw2A	0.837	1.47	0.218	0.987
5	2cuwA	0.810	1.42	0.307	0.949
6	1gtdB	0.786	1.53	0.253	0.937
7	1t3tA1	0.760	2.11	0.143	0.924
8	1zq1C3	0.605	3.02	0.041	0.911
9	4wj3B	0.605	3.25	0.080	0.924
10	2d6fD3	0.593	3.12	0.053	0.924

(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	0.17	9	3c62B	CA	Rep, Mult	16,18
2	0.07	4	2nr9A	PA6	Rep, Mult	22,26
3	0.06	3	1b4bA	ARG	Rep, Mult	40,48,49,50
4	0.04	2	3lufA	MG	Rep, Mult	16,71,73
5	0.04	2	3px0A	DCP	Rep, Mult	19,20,21,22,23
6	0.04	2	1lshB	UPL	Rep, Mult	4,45
7	0.02	1	3h0rE	ATP	Rep, Mult	5,6,7,42
8	0.02	1	3uomA	CA	Rep, Mult	46,67
9	0.02	1	3h0rT	ADP	Rep, Mult	5,7,39,40,42
10	0.02	1	1pvyA	CA	Rep, Mult	61,66
11	0.02	1	3kc2B	MG	Rep, Mult	13,14,18

	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	1cg2A	0.541	2.87	0.077	0.785	3.4.17.11	16
2	0.060	1vgyA	0.531	3.05	0.104	0.797	3.5.1.18	21
3	0.060	3eoqB	0.490	3.21	0.097	0.747	3.4.24.56	NA
4	0.060	3dq0A	0.499	3.56	0.134	0.835	1.5.99.12	NA
5	0.060	1d8yA	0.548	3.55	0.027	0.911	2.7.7.7	18
6	0.060	1w6tB	0.491	3.71	0.061	0.823	4.2.1.11	NA
7	0.060	2qcuB	0.493	3.46	0.070	0.785	1.1.5.3	45
8	0.060	1diiA	0.475	3.94	0.069	0.848	1.17.99.1	NA
9	0.060	1t3tA	0.760	2.11	0.143	0.924	6.3.5.3	NA
10	0.060	1uhvB	0.524	3.25	0.015	0.772	3.2.1.37	9
11	0.060	1l3sA	0.576	3.64	0.077	0.899	2.7.7.7	18
12	0.060	3c46B	0.354	3.74	0.029	0.595	2.7.7.6	NA
13	0.060	2ptxA	0.506	3.42	0.141	0.785	4.2.1.11	11
14	0.060	2jguA	0.446	3.91	0.039	0.835	2.7.7.7	34
15	0.060	1tgoA	0.551	3.63	0.066	0.861	2.7.7.7	40
16	0.060	3ic1A	0.545	3.06	0.078	0.797	3.5.1.18	7
17	0.060	2qyvA	0.491	3.23	0.068	0.772	3.4.13.3	NA
18	0.060	2zviA	0.490	2.87	0.056	0.696	5.3.2.-	40
19	0.060	1iyxA	0.498	3.99	0.057	0.861	4.2.1.11	11

(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	0.62	0.904	1.13	0.41	0.99	1t4aA	GO:0000166 GO:0004642 GO:0005524 GO:0005737 GO:0006164 GO:0006189 GO:0016874
1	0.49	0.899	1.20	0.28	1.00	2yx5A	GO:0000166 GO:0004642 GO:0005524 GO:0005737 GO:0006164 GO:0006189 GO:0016874
2	0.46	0.833	1.41	0.30	0.97	2cuwA	GO:0000166 GO:0004642 GO:0005524 GO:0005737 GO:0006164 GO:0006189 GO:0016874
3	0.44	0.840	1.48	0.25	0.97	1vq3C	GO:0000166 GO:0004642 GO:0005524 GO:0005737 GO:0006164 GO:0006189 GO:0016874
4	0.43	0.837	1.47	0.22	0.99	2zw2A	GO:0000166 GO:0004642 GO:0005524 GO:0005737 GO:0006164 GO:0006189 GO:0016874
5	0.40	0.836	1.43	0.24	0.99	1gtdB	GO:0000166 GO:0004642 GO:0005524 GO:0005737 GO:0006164 GO:0006189 GO:0016874
6	0.07	0.477	2.37	0.11	0.67	4v6uBl	GO:0003723 GO:0003735 GO:0005840 GO:0006412 GO:0019843 GO:0030529 GO:0070180
7	0.07	0.357	4.26	0.07	0.71	4dmzB	GO:0016020 GO:0016021
8	0.07	0.364	3.79	0.09	0.66	4etxA	GO:0000166 GO:0016020 GO:0016021
9	0.06	0.343	4.64	0.11	0.72	2mp4A	GO:0003779 GO:0005622 GO:0005737 GO:0005865 GO:0009792 GO:0015629 GO:0030042 GO:0030240 GO:0030529 GO:0030838 GO:0040011 GO:0051014 GO:0051015 GO:0071689
10	0.06	0.384	3.09	0.00	0.56	2b3dA	GO:0005829 GO:0008753 GO:0050660 GO:0055114
11	0.06	0.335	4.21	0.08	0.66	4ociA	GO:0005509 GO:0046872
12	0.06	0.299	4.04	0.05	0.53	2ia9D	GO:0007049 GO:0030435 GO:0030436 GO:0051301
13	0.06	0.351	3.91	0.05	0.62	1td9D	GO:0005737 GO:0006085 GO:0008152 GO:0008959 GO:0016407 GO:0016740 GO:0016746
14	0.06	0.268	3.74	0.03	0.46	5fj4C	GO:0001682 GO:0003723 GO:0003735 GO:0004526 GO:0005622 GO:0005737 GO:0005840 GO:0006412 GO:0008033 GO:0019843 GO:0030529 GO:0042254 GO:0090501 GO:0090502
15	0.06	0.262	3.45	0.05	0.44	2fc3A	GO:0001682 GO:0003723 GO:0003735 GO:0004526 GO:0005622 GO:0005737 GO:0005840 GO:0006412 GO:0008033 GO:0019843 GO:0030529 GO:0042254 GO:0090501 GO:0090502

Consensus prediction of GO terms

Molecular Function	GO:0004642	GO:0005524
GO-Score	0.97	0.97
Biological Processes	GO:0006189
GO-Score	0.97
Cellular Component	GO:0005737
GO-Score	0.97

(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.