I-TASSER results

I-TASSER results for job id Rv0398c

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

Input Sequence in FASTA format

>protein (213 residues)
MGVIARVVGVAACGLSLAVLAAAPTAGAEPTGALPPMTSSGSGPVIGDGDAALRQRISQQ
LFSFGDPTVQEVDGSDAAQFITAAAAVADRDVASVFLPLQRVLGCQQNTAGSGAGFGARA
YRRTDGQWGGAMLVVAKSTVSDVDALKACVKSGWRKATAGTPTSMCNNGWTYPPFADTRR
GEEGYFVLLAGTASDFCSAPNANYRTTASSWPG

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| MGVIARVVGVAACGLSLAVLAAAPTAGAEPTGALPPMTSSGSGPVIGDGDAALRQRISQQLFSFGDPTVQEVDGSDAAQFITAAAAVADRDVASVFLPLQRVLGCQQNTAGSGAGFGARAYRRTDGQWGGAMLVVAKSTVSDVDALKACVKSGWRKATAGTPTSMCNNGWTYPPFADTRRGEEGYFVLLAGTASDFCSAPNANYRTTASSWPG
Prediction	CCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCEEHCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEHCCCCCCEEEEEEEHCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEHCCHHHHHCCCCCHHHCCCCCCCC
Conf.Score	985466688999999888644788667788877888888899875578866778899998876589875556756789999998756776666788898888865679999888876445664589887589999855789878899998867654467887765568888898877777885799999756576654567645457778999
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| MGVIARVVGVAACGLSLAVLAAAPTAGAEPTGALPPMTSSGSGPVIGDGDAALRQRISQQLFSFGDPTVQEVDGSDAAQFITAAAAVADRDVASVFLPLQRVLGCQQNTAGSGAGFGARAYRRTDGQWGGAMLVVAKSTVSDVDALKACVKSGWRKATAGTPTSMCNNGWTYPPFADTRRGEEGYFVLLAGTASDFCSAPNANYRTTASSWPG
Prediction	641132013101001011212333434443514133136444220012345333540243024244441552545401410332342435402311320330040353644544412241133553421100000033324416202200444144344444421144213324446445354100000012134104424561454366258
	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                 180                 200

                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCEEHCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEHCCCCCCEEEEEEEHCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEHCCHHHHHCCCCCHHHCCCCCCCC
MGVIARVVGVAACGLSLAVLAAAPTAGAEPTGALPPMTSSGSGPVIGDGDAALRQRISQQLFSFGDPTVQEVDGSDAAQFITAAAAVADRDVASVFLPLQRVLGCQQNTAGSGAGFGARAYRRTDGQWGGAMLVVAKSTVSDVDALKACVKSGWRKATAGTPTSMCNNGWTYPPFADTRRGEEGYFVLLAGTASDFCSAPNANYRTTASSWPG

4ke2A

0.19

0.18

0.92

0.67

MUSTER

MNIDPAARAAAAAAASKAAVTAADAAAAAATIA----ASAASVAAATAADDAAASIATINAAS---AAAKSIAAAAAMAAKDTAAAAASAAAAAVASAAKALETINVKAAYAAATTANTAAAAAAATATTAAAAAAAKATIDNAAAAKAAAVATAVSDAAATAATAAAVAAATLEAAAAKAAA--------TAVSAAAAAAAAAIAFAAA-P-

2mu3A

0.14

0.12

0.87

0.61

dPPAS

GASAGLISRVANALANTSTLRTVLRTGVSQASSVVQRAAQSLASTLGVDGNNLARFAVQAVSRLPAGSDTSAYAQAFSSALFNAGVLNASNIDTLGSRVLSALLNGVSSAAQGLGINV------DSG----------SVQSDISSSSSFLSTSSSSASYSQASASSTSGAGYTGPSGPSTGPSGYPGPLGGGAPFGQSGFGG-----------

4pscA

0.15

0.12

0.81

0.58

wdPPAS

DTITAACDLISDGEDAAASLFGISETENDGDVTV--LFARGTC---GNVGVLVGPWFFDSLQT-GSRTVKGVP---PASVQDFLSGSVQNGINMANQIKSVLQSC------PNTKLVLGGY--------GSMVVASNLDAATMSKISAVVLFGDPYYGKPVANFDCHDG-GGDIILLPH---LTY----ADTAAAFVVPVSHH----------

2ayxA

0.17

0.13

0.77

0.60

wMUSTER

VHSVAAPHELPALLARIYLIEMESDDPANALPSTDKAVSDNDDMLVVDDHPINRRLLADQLGSLGYQCKTANDGVDALNVLSKNH--IDIVLSD----------VNPNMDGYRL---TQRIR----QLGLTLPVIGVTANALAEEKQRCLESG-----------M--DSCSKPVTLDV----------IKQTLTLYAER--VRKSRDS-----

4pscA

0.24

0.18

0.75

0.60

wPPAS

LSELAKVITAACDLISDGEDAAASLFGISETEN-GDVT--GTCP--GNVGVLVGPWFFDSLQT-GSRTVKGVP---PASVQDFLSGSVQNGINMANQIKSVLQSC-PNTGGS--------------Q--GSMVVAASNLDAAMSKISAVV----PYYGKPVANFDCHDG---N------GGDLTY----ADTAAAFVVPVSHH----------

4pscA

0.12

0.10

0.87

0.62

dPPAS2

DTITAACDLISDGEDAAASLFGISETENDGDVTVLFARGTCDPGNVGVLVGPWFFDSLQTALGSRTLGVKGVPY--PASVQDFLSGSVQNGINMANQIKSVLQSC------PNTKLVLGGYSQ------GSMVVASNLDAATMSKISAVVLFGDPYYGKPVANFDCHDGQGGDIILLPHLT----YAEDADTAAAFVVPLVSHH---------

4pscA

0.15

0.13

0.83

0.73

PPAS

DTITAACDLISDGEDAAASLFGISETENDP----GDVTTCDPGNVGVLVGPWFFDSLQTALGS-RTLGVKGVP---PASVQDFLSGSVQNGINMANQIKSVLQSC-------NTKLVLGGY--------GSMVVASNLDAATMSKISAVVLFGDPYYGKPVANFDCHDGQGGDIILLPHLT---YAE--ADTAAAFVVPLVSHH---------

4mvfA1

0.14

0.05

0.38

0.70

Env-PPAS

-------------------------------------------------------------------------------LILCHSG----KLEDKYI-IDEKL-------GQGT-YGCKGIDKVTNQL-YAIKEEKKDRLKNINRFFQEIEI------------MLDH----PNTYEN---DNYIYLIME-----LC----------------

2mu3A

0.18

0.15

0.85

0.64

MUSTER

AGLISRVANALANTSTLRTVLRTGVSQQIASSVVQRAAQSLASTL-GVDGNNLARFAVQAVSRLP----AGSDTSAYAQAFSSALFNAGVLNASNIDTLGSRVLSANGVSSAAQGLGINV----DSG----------SVQSDISSSSSFLSTSSSSASYSQASASSTSGAGYTGPSGPSTGPSGY------------GPLGGGAPFGQSGFGG

4pscA

0.12

0.11

0.89

0.56

dPPAS

DTITAACDLISDGEDAAASLFGISETENDGDVTVLFARGTCDPGNVGVLVGPWFFDSLQTALGSRTLGVKGVPY--PASVQDFLSGSVQNGINMANQIKSVLQSC------PNTKLVLGGYSQ------GSMVVASNLDAATMSKISAVVLFGDPYYGKPVANFDCHDGDNICQGGDIILLPHLTYAEDADTAAAFVVPLVSHH---------

(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=-3.24

Estimated TM-score = 0.35±0.12

Estimated RMSD = 13.1±4.1Å

Download Model 2

C-score=-4.32

Download Model 3

C-score=-5.00

Download Model 4

C-score=-4.86

Download Model 5

C-score=-4.50

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	4pscA	0.727	2.87	0.114	0.869
2	4wy8A	0.629	4.31	0.063	0.883
3	3dcnA	0.623	3.17	0.152	0.775
4	1cusA	0.617	3.26	0.198	0.779
5	4n5iX	0.616	4.36	0.089	0.887
6	1lzkA	0.605	4.15	0.082	0.836
7	2c7bA	0.605	4.24	0.110	0.840
8	4oylA	0.604	3.27	0.154	0.761
9	3gbsA	0.604	3.28	0.160	0.761
10	1jkmB	0.603	4.20	0.108	0.855

(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	0.07	4	3dd5E	DEP	Rep, Mult	41,42,80,83,122,123,130
2	0.06	3	4pseA	C11	Rep, Mult	10,14,42,83,184
3	0.04	2	3aioC	MPD	Rep, Mult	13,14,51,53,186
4	0.04	2	2muwB	3LW	Rep, Mult	193,196
5	0.04	2	2cixA	MAN	Rep, Mult	192,201,202
6	0.04	2	1dxoA	DQN	Rep, Mult	154,191
7	0.02	1	1xzcA	PMB	Rep, Mult	98,102,144,146
8	0.02	1	2c1dA	ZN	Rep, Mult	73,76
9	0.02	1	3o72C	OXY	Rep, Mult	125,179
10	0.02	1	1xzbA	MAC	Rep, Mult	11,12,15,45
11	0.02	1	1izcA	MG	Rep, Mult	182,195
12	0.02	1	1x07A	MG	Rep, Mult	39,155
13	0.02	1	1yajB	SIA	Rep, Mult	23,24,46,47
14	0.02	1	2aj4A	MG	Rep, Mult	49,141
15	0.02	1	3dayA	UNX	Rep, Mult	52,187,188
16	0.02	1	3qebZ	MN	Rep, Mult	125,142,144,195
17	0.02	1	2hrrA	SIA	Rep, Mult	40,41,46,51,52
18	0.02	1	2hrqC	SUC	Rep, Mult	39,40,90,95

	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	0.073	3esbA	0.624	3.34	0.207	0.793	3.1.1.74	76
2	0.068	3dcnA	0.623	3.17	0.152	0.775	3.1.1.74	76
3	0.066	1bs9A	0.554	3.42	0.131	0.714	3.1.1.72	NA
4	0.066	2czqA	0.547	3.57	0.101	0.709	3.1.1.-	42,125
5	0.060	1cleA	0.526	5.29	0.085	0.836	3.1.1.3	NA
6	0.060	3gbsA	0.604	3.28	0.160	0.761	3.1.1.74	NA
7	0.060	1bu8A	0.537	4.23	0.041	0.765	3.1.1.3	NA
8	0.060	1gz7A	0.541	5.04	0.067	0.826	3.1.1.3	NA
9	0.060	2pvsB	0.540	4.01	0.046	0.756	3.1.1.3	NA
10	0.060	1hplA	0.539	4.17	0.056	0.761	3.1.1.3	146
11	0.060	3fakA	0.600	3.98	0.086	0.817	3.1.1.-	76
12	0.060	1e5tA	0.566	4.80	0.042	0.840	3.4.21.26	125
13	0.060	1ethA	0.549	3.98	0.051	0.761	3.1.1.3	NA
14	0.060	1lpsA	0.531	5.39	0.071	0.845	3.1.1.3	49
15	0.060	1gz7C	0.540	5.30	0.054	0.850	3.1.1.3	50,121,153
16	0.060	1qozA	0.559	3.36	0.138	0.714	3.1.1.72	NA
17	0.060	1r9mB	0.548	5.11	0.080	0.845	3.4.14.5	NA
18	0.060	3ga7A	0.580	4.20	0.089	0.812	3.1.1.-	NA
19	0.060	2c7bA	0.605	4.24	0.110	0.840	3.1.1.1	198
20	0.060	2veoB	0.481	4.78	0.036	0.747	3.1.1.3	NA
21	0.060	1orvA	0.523	4.96	0.074	0.798	3.4.14.5	NA
22	0.060	2gbcA	0.545	5.14	0.090	0.840	3.4.14.5,3.4.15.5	40
23	0.060	3g0bB	0.547	5.12	0.080	0.845	3.4.14.5	42,44

(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	0.13	0.731	2.92	0.11	0.88	4psdA	GO:0005576 GO:0008152 GO:0016787 GO:0050525 GO:0052689
1	0.08	0.599	4.37	0.06	0.85	3qh4A	GO:0008152 GO:0016787
2	0.08	0.615	4.47	0.10	0.90	4n5hX	GO:0008152 GO:0016787
3	0.07	0.603	4.20	0.11	0.85	1jkmB	GO:0008152 GO:0016787
4	0.07	0.624	3.34	0.21	0.79	3esbA	GO:0005576 GO:0008152 GO:0016787 GO:0050525 GO:0052689
5	0.07	0.604	4.12	0.10	0.84	2c7bA	GO:0008152 GO:0016787 GO:0052689
6	0.07	0.632	3.35	0.16	0.81	5ajhA	GO:0005576 GO:0008152 GO:0016787 GO:0050525 GO:0052689
7	0.07	0.607	4.38	0.06	0.85	1lzkA	GO:0008152 GO:0016787
8	0.07	0.596	4.15	0.10	0.83	4v2iA	GO:0008152 GO:0016787 GO:0052689
9	0.07	0.604	3.28	0.16	0.76	3gbsA	GO:0005576 GO:0008152 GO:0016042 GO:0016787 GO:0050525 GO:0052689
10	0.07	0.603	4.21	0.09	0.85	4ou5A	GO:0008152 GO:0016787
11	0.07	0.618	3.26	0.14	0.78	4oyyC	GO:0005576 GO:0008152 GO:0016787 GO:0050525 GO:0052689
12	0.07	0.623	3.17	0.15	0.77	3dcnA	GO:0005576 GO:0008152 GO:0009405 GO:0016787 GO:0050525 GO:0052689
13	0.07	0.592	4.27	0.13	0.83	3aikA	GO:0008152 GO:0016787 GO:0042802 GO:0052689
14	0.07	0.596	4.57	0.10	0.87	4wy5A	GO:0008152 GO:0016787 GO:0052689
15	0.07	0.600	3.98	0.09	0.82	3fakA	GO:0008152 GO:0016787
16	0.07	0.536	4.96	0.08	0.85	2o7rA	GO:0008152 GO:0016787 GO:0052689
17	0.07	0.599	4.13	0.09	0.84	3zwqA	GO:0008152 GO:0016787
18	0.07	0.572	4.63	0.08	0.84	3wj2B	GO:0008152 GO:0016787 GO:0052689
19	0.07	0.597	4.40	0.13	0.85	4p9nA	GO:0008152 GO:0016787
20	0.07	0.554	3.42	0.13	0.71	1bs9A	GO:0000272 GO:0005576 GO:0005975 GO:0008152 GO:0016787 GO:0030245 GO:0045493 GO:0046555 GO:0052689
21	0.07	0.559	3.36	0.14	0.71	1qozA	GO:0000272 GO:0004553 GO:0005576 GO:0005975 GO:0008152 GO:0016787 GO:0030245 GO:0030248 GO:0045493 GO:0046555 GO:0052689

Consensus prediction of GO terms

Molecular Function	GO:0016788
GO-Score	0.37
Biological Processes	GO:0008152
GO-Score	0.36
Cellular Component	GO:0005576
GO-Score	0.19

(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.