I-TASSER results

I-TASSER results for job id Rv0426c

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

Input Sequence in FASTA format

>protein (147 residues)
MSVVGGTVRTVGRTVSGAATATTAAAGAVGGAAVSGIVGGVTGAAKGIQKGLSSGSKSTA
AAALAIGAIGVAGLVDWPILLAVGGGALLLRKLNRTPEVAAPPVKAKLAPVPDKPAAAKE
APAKASKTTARKTSGRRAGTAELRSTN

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MSVVGGTVRTVGRTVSGAATATTAAAGAVGGAAVSGIVGGVTGAAKGIQKGLSSGSKSTAAAALAIGAIGVAGLVDWPILLAVGGGALLLRKLNRTPEVAAPPVKAKLAPVPDKPAAAKEAPAKASKTTARKTSGRRAGTAELRSTN
Prediction	CCCCCHHHHHHHHHHCCCCEEEEHCCCCCCCCCCCCEEEEEHCHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHCCCCCEEEEHCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Conf.Score	986556776787765677478764455555444466565554478999999886787658999999877665444443456546656778876678888999876677889999875568887778887778776544555445689
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MSVVGGTVRTVGRTVSGAATATTAAAGAVGGAAVSGIVGGVTGAAKGIQKGLSSGSKSTAAAALAIGAIGVAGLVDWPILLAVGGGALLLRKLNRTPEVAAPPVKAKLAPVPDKPAAAKEAPAKASKTTARKTSGRRAGTAELRSTN
Prediction	643444314323532544353444333322333331122204221510351274344322111222233212221412010113312110331454675444644452543566555575445545556455444444445635758
	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

CCCCCHHHHHHHHHHCCCCEEEEHCCCCCCCCCCCCEEEEEHCHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHCCCCCEEEEHCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
MSVVGGTVRTVGRTVSGAATATTAAAGAVGGAAVSGIVGGVTGAAKGIQKGLSSGSKSTAAAALAIGAIGVAGLVDWPILLAVGGGALLLRKLNRTPEVAAPPVKAKLAPVPDKPAAAKEAPAKASKTTARKTSGRRAGTAELRSTN

4ke2A

0.25

0.24

0.99

0.76

MUSTER

MNIDPAARAAAAAAASKAATAADAAAAAATIAASAASVAAATAADDAAASIATINAASAAAKSIAAAAAMAAKDAASAAAAAVASAAKALETIN-VKAAYAAATTANTAAAAAAATATTAAAAAAAKATIDNAAAAKAAAVATAVSD

1xq8A

0.12

0.11

0.88

0.72

dPPAS

KEGVVAAAEKTKQGVAEAAGKTKEGVLYVGSKTKEGVVHGVATVAEKTKEQVTNVGGAVVTGVTAVAQKTVEGA-----------GSIAAATGFVKKDQLGKNEEGAPQEGILEDMPVDPDNEAYEMPSEEGYQDYEPEA-------

1xq8A

0.21

0.18

0.84

0.71

wdPPAS

MDVVVAAAEKTKQGVAEAAGKTKEGVLYVGSKTKEGVVHGVATVAEKTKEQVTNVGGAVVTGVTAVAQKTVEGA----IAAATG------DQLGKNEEGAPQEGILEDMPVDPDNEAYEMPSEEGYQDYEPEA--------------

2mu3A

0.18

1.00

0.75

wMUSTER

FGATGGLISRVANALANTSTLRTVLASSVVQRAAQSLASGVDGLARFAVQAVSRGSDTSAYAQAFSSALFNAGVLNASNIDTLGSLSALLNGVSQGLGINVDSGSTSSSSASYSQASASSTSGAGYTGPSGPSTGPSGYPGPLGGGA

2cp6A

0.26

0.22

0.83

0.76

wPPAS

TPPISNLTKTASESISNLSEAGSIKKGEIG---V--VGGTKAGV---VR-G------ETD------FAKGECG-VELP---AVAGGLFAVHKVTKIGFPSTTPAKAKANAVRRVMATTSASLKRSPSSVASSVSSRPSRTGLLTETS

1xq8A

0.21

0.18

0.88

0.78

dPPAS2

MDVVVAAAEKTKQGVAEAAGKTKEGVLYVGSKTKEGVVHGVATVAEKTKEQVTNVGGAVVTGVTAVAQKTVEGAGS--IAAATG---FVKKDQLGKNEEGAPQEGILEDMPVDPDNEAYEMPSEEGYQDYEPEA-------------

3la9A

0.15

0.14

0.91

0.90

PPAS

ISSITTNTTNLGNSTAGGGATYDPATGAISAPSYNANGTTATNTSVGAAIDNINANGIKYFHANSTDP-DSVATGT----VAIGPNA--------NVDYSSGATTSAAVPVASAFGGFAGSAPIGVFSVGAPGAERQAGRISAASTN

2jy9A

0.15

0.14

0.93

1.02

Env-PPAS

MIAISRTV-----SIADNEEITAIRAQGAGGQHVNKTSSAIH-----LRFDIRASGLPEYYKQRLLTASHHLISDDGVIIIKAQEREAAIARLVAVIKELTAEQKSRRATRPTRASKERRLSSKAQKSSVKALRGKVRRPLDLEHHH

4wj1A

0.14

0.13

0.93

0.72

MUSTER

LQYELPGLERKAHECESTRPEGPGDATKPDELATTASVYSKLASAAKLKATFAAGDRERIAAAIRAAAGAYQKI-----------EEQKAAELSRQNGSDAPPPAAEAVVPDSGIPGPLAIPSEYPSAAAAADEDWEAAARIIHSGD

3la9A

0.14

0.95

0.66

dPPAS

ITTNTTNLGNSTAAALGGGATYDPATGAISAPSYNGTTATNTSVGAAIDNINANGIKYFHA-----NSTDPDSVATGTNSVAIGPNAVANV--DYSVAIGSGATTSAAVPVASAFGGFAGSAPIGVFSVGAPGAERQAGRISAASTD

(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=-4.22

Estimated TM-score = 0.27±0.08

Estimated RMSD = 14.8±3.6Å

Download Model 2

C-score=-4.29

Download Model 3

C-score=-4.64

Download Model 4

C-score=-4.64

Download Model 5

C-score=-4.69

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	2d05A	0.473	4.75	0.041	0.803
2	1chkA	0.463	4.86	0.076	0.803
3	4ilyB	0.459	4.64	0.091	0.789
4	4oltA	0.457	5.07	0.066	0.823
5	2epoA	0.454	4.21	0.054	0.728
6	2j8sA3	0.440	4.76	0.081	0.755
7	5aexA	0.440	4.79	0.079	0.748
8	2b2jA	0.438	4.90	0.094	0.755
9	3rkoL	0.437	4.73	0.062	0.742
10	3g5sA1	0.435	5.03	0.092	0.769

(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	0.08	4	1zj9A	SF4	Rep, Mult	21,22,23,25,28,40,41,42,43,44
2	0.06	3	2a68P	MG	Rep, Mult	66,70,71
3	0.04	2	4qvpK	MG	Rep, Mult	48,52
4	0.04	2	5tw7E	MG	Rep, Mult	69,72,75
5	0.04	2	1y1aA	CA	Rep, Mult	52,53,56,58
6	0.04	2	2wscK	UUU	Rep, Mult	35,61,65
7	0.02	1	1aqlA	TCH	Rep, Mult	28,30,40,42
8	0.02	1	1dlqB	LIO	Rep, Mult	34,37
9	0.02	1	2o012	CLA	Rep, Mult	73,111
10	0.02	1	2o01H	CLA	Rep, Mult	85,89
11	0.02	1	3arcx	CLA	Rep, Mult	51,52,55
12	0.02	1	1xk0A	NO	Rep, Mult	68,72
13	0.02	1	3aodA	MIY	Rep, Mult	57,60,65
14	0.02	1	3rv5B	DXC	Rep, Mult	46,50
15	0.02	1	1zyrN	STD	Rep, Mult	60,63,64,68
16	0.02	1	3et2A	1BO	Rep, Mult	22,61

	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	3cmmC	0.421	5.45	0.055	0.809	6.3.2.19	68
2	0.060	3hdeA	0.417	4.69	0.098	0.694	3.2.1.17	NA
3	0.060	1zy9A	0.423	5.16	0.080	0.762	3.2.1.22	NA
4	0.060	1wmwA	0.408	5.08	0.078	0.721	2.5.1.-	NA
5	0.060	2pm8A	0.410	5.49	0.044	0.796	3.1.1.8	NA
6	0.060	2hgsA	0.423	5.27	0.061	0.789	6.3.2.3	NA
7	0.060	1c7jA	0.371	5.41	0.039	0.708	3.1.1.-	NA
8	0.060	1zj9B	0.420	5.28	0.061	0.789	1.8.7.1	64
9	0.060	3c8zB	0.422	5.13	0.086	0.762	6.1.1.16	NA
10	0.060	3kalA	0.424	5.40	0.008	0.789	6.3.2.3	NA
11	0.060	1gaxA	0.411	5.36	0.030	0.755	6.1.1.9	36
12	0.060	2wghB	0.413	4.32	0.059	0.673	1.17.4.1	NA
13	0.060	2o7qA	0.415	5.04	0.052	0.762	4.2.1.10,1.1.1.25	NA
14	0.060	1oqzB	0.420	5.06	0.022	0.742	3.5.1.93	83
15	0.060	1br2A	0.411	5.21	0.063	0.742	3.6.1.32	NA
16	0.060	1iduA	0.403	5.23	0.080	0.721	1.11.1.10	NA
17	0.060	1zj8A	0.416	5.26	0.071	0.769	1.8.7.1	NA
18	0.060	2veoB	0.440	4.90	0.040	0.775	3.1.1.3	93
19	0.060	2anxA	0.403	4.80	0.066	0.687	3.2.1.17	60,62,82,88

(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	0.459	4.64	0.09	0.79	4ilyB	GO:0005576 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0016977
1	0.06	0.322	5.49	0.02	0.62	2w8dB	GO:0003824 GO:0005576 GO:0005886 GO:0008152 GO:0008484 GO:0016020 GO:0016021 GO:0016740 GO:0046872 GO:0070395 GO:0071555
2	0.06	0.353	5.39	0.08	0.67	3tqlA	GO:0003333 GO:0004970 GO:0006865 GO:0015424 GO:0016020 GO:0035235 GO:0042626 GO:0055085
3	0.06	0.327	5.27	0.04	0.62	2epoB	GO:0004553 GO:0004563 GO:0005975 GO:0008152 GO:0016787 GO:0016798
4	0.06	0.369	5.20	0.10	0.67	3nwoA	GO:0006508 GO:0008233 GO:0016787
5	0.06	0.452	4.27	0.04	0.74	5a6kA	GO:0004553 GO:0005975 GO:0016787
6	0.06	0.458	4.20	0.04	0.73	5a6aB	GO:0004553 GO:0005975 GO:0016787
7	0.06	0.454	4.21	0.05	0.73	2epoA	GO:0004553 GO:0004563 GO:0005975 GO:0008152 GO:0016787 GO:0016798
8	0.06	0.303	5.70	0.06	0.60	3d43B	GO:0004252 GO:0006508 GO:0008233 GO:0008236 GO:0016787 GO:0046872
9	0.06	0.315	5.08	0.04	0.58	2p0wA	GO:0000784 GO:0000790 GO:0004402 GO:0005634 GO:0005654 GO:0005737 GO:0006323 GO:0006335 GO:0006336 GO:0006348 GO:0006475 GO:0007584 GO:0010485 GO:0016363 GO:0016568 GO:0016573 GO:0016740 GO:0016746 GO:0042393 GO:0043231 GO:0043234 GO:0043967
10	0.06	0.298	5.28	0.05	0.53	2qibA	GO:0003677 GO:0003700 GO:0006351 GO:0006355
11	0.06	0.463	4.86	0.08	0.80	1chkA	GO:0005576 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0016977
12	0.06	0.318	5.37	0.02	0.60	4mlvA	GO:0004418 GO:0006779 GO:0006782 GO:0016740 GO:0018160 GO:0033014
13	0.06	0.341	5.15	0.04	0.60	4e1yA	GO:0016829 GO:0042597
14	0.06	0.334	5.43	0.07	0.61	4rkcA	GO:0003824 GO:0006520 GO:0008483 GO:0008793 GO:0009058 GO:0016740 GO:0030170 GO:0080130
15	0.06	0.342	4.50	0.04	0.56	3gn8A
16	0.06	0.456	4.82	0.06	0.81	4oltB	GO:0005576 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0016977
17	0.06	0.290	5.15	0.04	0.51	3j9wAI	GO:0000462 GO:0003735 GO:0005840 GO:0006412 GO:0022627 GO:0030529
18	0.06	0.304	4.75	0.06	0.52	1cbiA	GO:0001972 GO:0005215 GO:0005501 GO:0005737 GO:0005829 GO:0006810 GO:0008289 GO:0016918 GO:0019841 GO:0034653

Consensus prediction of GO terms

Molecular Function	GO:0016977	GO:0008484	GO:0016740	GO:0004563	GO:0004970	GO:0046872	GO:0015424	GO:0008233
GO-Score	0.07	0.06	0.06	0.06	0.06	0.06	0.06	0.06
Biological Processes	GO:0005975	GO:0006865	GO:0071555	GO:0006508	GO:0035235	GO:0070395	GO:0003333
GO-Score	0.12	0.06	0.06	0.06	0.06	0.06	0.06
Cellular Component	GO:0005576	GO:0016021	GO:0005886
GO-Score	0.13	0.06	0.06

(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.