I-TASSER results

I-TASSER results for job id Rv0335c

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

Input Sequence in FASTA format

>protein (171 residues)
MRSMGFLHRACRAPSSLPAPLMARPGRSVLARPAATPPGPLCATTRPRPPQGNQPPASRI
SNFPPKRHKTRVLAAAEDEVSAAVAALISAHGRRHHSLNNQAAAFHGQFAQNLNVGAGSC
ASAETTADAPTQALLGPADRQRRQRRAVRQWLVRWAAHPGRATRGFHNHRQ

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MRSMGFLHRACRAPSSLPAPLMARPGRSVLARPAATPPGPLCATTRPRPPQGNQPPASRISNFPPKRHKTRVLAAAEDEVSAAVAALISAHGRRHHSLNNQAAAFHGQFAQNLNVGAGSCASAETTADAPTQALLGPADRQRRQRRAVRQWLVRWAAHPGRATRGFHNHRQ
Prediction	CCCCCCHHHHHCCCCCCCCCCCCCCCCEEEEEEEHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Conf.Score	987654455545677777766667776566777765757899999888888788999998876454555543577665899999999999999999999999999999999999989999999999999999997756677677888777777788898888888888899
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MRSMGFLHRACRAPSSLPAPLMARPGRSVLARPAATPPGPLCATTRPRPPQGNQPPASRISNFPPKRHKTRVLAAAEDEVSAAVAALISAHGRRHHSLNNQAAAFHGQFAQNLNVGAGSCASAETTADAPTQALLGPADRQRRQRRAVRQWLVRWAAHPGRATRGFHNHRQ
Prediction	755343134314444424433444543330022133343312201330342244333343223333332131332342200200031023204302200330231042014103432321120132122213312332434454343344324223443544542346468
	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

CCCCCCHHHHHCCCCCCCCCCCCCCCCEEEEEEEHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
MRSMGFLHRACRAPSSLPAPLMARPGRSVLARPAATPPGPLCATTRPRPPQGNQPPASRISNFPPKRHKTRVLAAAEDEVSAAVAALISAHGRRHHSLNNQAAAFHGQFAQNLNVGAGSCASAETTADAPTQALLGPADRQRRQRRAVRQWLVRWAAHPGRATRGFHNHRQ

2g38C

0.22

0.10

0.44

1.68

wdPPAS

-------------------------------------PEALTVAATEVRRIRDRAIQSDAQVAPMTTA---VRPPAADLVSEKAATFLVEYARKYRQTIAAAAVVLEEFAHALTTG-------------------------------------------------------

2g38C

0.22

0.10

0.44

1.52

wPPAS

-------------------------------------PEALTVAATEVRRIRDRAIQSDAQVAPMTTA---VRPPAADLVSEKAATFLVEYARKYRQTIAAAAVVLEEFAHALTTG-------------------------------------------------------

2g38C

0.22

0.10

0.44

1.48

dPPAS2

-------------------------------------PEALTVAATEVRRIRDRAIQSDAQVAPMTTA---VRPPAADLVSEKAATFLVEYARKYRQTIAAAAVVLEEFAHALTTG-------------------------------------------------------

4ke2A

0.16

0.12

0.71

1.06

dPPAS2

DTAAAAASAAAAAVASAAKALETINV------------KAAYAAATTANTAAAAAAATATTAAAAAAAKATIDNAAAAKAAAVATAVSDAAATAATAAAVAAATLEAAAAKAAATAVSAAAAAAAAAIAFAAAP-------------------------------------

4ke2A

0.13

1.00

0.84

MUSTER

MNIDPAARAAAAAAASKAAVTAADAAAAAATIAASAASVAAATAADDAAASIATINAASAAAKSIAAAAAMAAKDTAAAAASAAAAAVASAAKALETINVKAAYAAATTANTAAAAAAATATTAAAAAAAKATIDNAAAAKAAAVDAAATAATAAAVAAATLEAAAAKAAA

2g38C

0.22

0.10

0.44

0.76

dPPAS

-------------------------------------PEALTVAATEVRRIRDRAIQSDAQVAPMTTA---VRPPAADLVSEKAATFLVEYARKYRQTIAAAAVVLEEFAHALTTG-------------------------------------------------------

1wa8A

0.09

0.05

0.58

0.71

wdPPAS

-------------------------------AEMKTDAATLAQEAGNFERISGDLKTQIDQVESTAGSLQGQWRGA-------AGTAAQAAVVRFQEAANKQKQELDEISTNIRQAGVQYSRADEEQQQALSSQMGF----------------------------------

2g38C

0.21

0.09

0.44

0.78

wMUSTER

--------------------------------------EALTVAATEVRRIRDRAIQSDAQVAPMTTA---VRPPAADLVSEKAATFLVEYARKYRQTIAAAAVVLEEFAHALTTG-------------------------------------------------------

2mxxA

0.10

0.08

0.86

0.68

wPPAS

MATDAA-----NNDGAYYLQTQFTNADKV---------EYLAQHDGEIRAEAAADPAVVAAKAALDA-----VEGGSHNYGEVKAAYEAAFNNAFNAVRNKYVQRFQAYNNATEQEGKTY-TPEQANARYLKR----VGAANNQNPAAEDGATTPASKEEAKKSELPKHHH

2nd4A

0.12

0.11

0.93

0.90

dPPAS2

-----------GENPSASNQLIQKKYVSW-RDAADEANTQVAAHEAEIKEETLRQPGVVAAQQALDKANAIVGHDHEQAVKRAQEDYNTAYNEAYNTVRNRYIQVLQQKYIEAAKAQGNYRTNEQRIADDIKAQTGKDVKDENGNYVVKDEKGNVVATVDKDGKTVKADAK

(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=-3.44

Estimated TM-score = 0.33±0.11

Estimated RMSD = 13.1±4.2Å

Download Model 2

C-score=-3.95

Download Model 3

C-score=-4.25

Download Model 4

C-score=-4.40

Download Model 5

C-score=-4.13

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	4a01A	0.566	4.58	0.067	0.877
2	5j65A	0.552	3.85	0.079	0.766
3	1ciiA	0.545	4.62	0.050	0.830
4	1sumB	0.540	4.20	0.027	0.772
5	2d4yA	0.537	3.97	0.053	0.778
6	3pe0A	0.536	4.33	0.054	0.807
7	4k1pA	0.535	3.95	0.048	0.772
8	3r6nA	0.532	4.41	0.026	0.813
9	4q25A	0.532	4.55	0.059	0.795
10	2lemA	0.532	4.45	0.076	0.795

(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	0.09	3	4ayxA	GLY	Rep, Mult	48,105
2	0.06	2	2j9tA	BO3	Rep, Mult	66,67,70,87,88,91
3	0.06	2	2a01A	AC9	Rep, Mult	97,98,101,102
4	0.06	2	2ll8A	PNS	Rep, Mult	78,81
5	0.06	2	2ff4B	III	Rep, Mult	71,86,87,88,89,91
6	0.06	2	2rd9A	IMD	Rep, Mult	91,95
7	0.03	1	3zvwC	MG	Rep, Mult	111,116
8	0.03	1	3k2sA	CLR	Rep, Mult	75,81,85,88,89
9	0.03	1	1cc1L	SF4	Rep, Mult	145,150
10	0.03	1	3ggzB	III	Rep, Mult	64,67,68,100

	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	1qleA	0.455	5.38	0.057	0.801	1.9.3.1	NA
2	0.060	3hq2B	0.481	5.28	0.057	0.830	3.4.24.-	NA
3	0.060	2fenD	0.461	4.48	0.024	0.672	5.5.1.2	NA
4	0.060	2esdA	0.466	5.19	0.028	0.760	1.2.1.9	18
5	0.060	3k2wB	0.460	5.39	0.068	0.772	1.2.1.8	NA
6	0.060	1cc1L	0.486	4.18	0.065	0.702	1.12.99.6	NA
7	0.060	1m56A	0.465	4.86	0.051	0.737	1.9.3.1	NA
8	0.060	1w07B	0.477	4.24	0.035	0.714	1.3.3.6	NA
9	0.060	2epoA	0.505	4.28	0.075	0.719	3.2.1.52	NA
10	0.060	1jswB	0.464	4.35	0.030	0.637	4.3.1.1	NA
11	0.060	1y5nC	0.457	4.58	0.063	0.690	1.7.99.4	109
12	0.060	1j38A	0.461	5.16	0.027	0.789	3.4.15.1	91,95
13	0.060	1y791	0.500	5.13	0.032	0.836	3.4.15.5	NA
14	0.060	2fonB	0.475	4.51	0.053	0.708	1.3.3.6	NA
15	0.060	2e9fB	0.466	4.18	0.025	0.637	4.3.2.1	NA
16	0.060	3kb9A	0.461	3.95	0.042	0.614	4.2.3.37	113,118
17	0.060	2d4eC	0.461	5.43	0.061	0.778	1.2.1.60	NA
18	0.060	1fftA	0.468	5.35	0.019	0.807	1.10.3.-	NA
19	0.060	1occA	0.460	5.38	0.058	0.801	1.9.3.1	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	0.08	0.524	4.09	0.07	0.76	2i0mA	GO:0005737 GO:0006810 GO:0006817 GO:0030643 GO:0042803 GO:0045936 GO:2000186
1	0.07	0.532	4.55	0.06	0.80	4q25A	GO:0005315 GO:0005436 GO:0005737 GO:0005886 GO:0006810 GO:0006817 GO:0006935 GO:0015321 GO:0030643 GO:0035435 GO:0035725 GO:0042803 GO:0044341 GO:0045936 GO:0050922 GO:0050928 GO:0055085 GO:0060326 GO:2000186
2	0.07	0.532	4.62	0.04	0.81	1t72A	GO:0005315 GO:0005436 GO:0005737 GO:0005886 GO:0006810 GO:0006817 GO:0010629 GO:0015321 GO:0030643 GO:0035435 GO:0035725 GO:0042803 GO:0044341 GO:0045936 GO:0055085 GO:2000186
3	0.07	0.540	4.20	0.03	0.77	1sumB	GO:0005315 GO:0005436 GO:0005737 GO:0005886 GO:0006810 GO:0006817 GO:0015321 GO:0030643 GO:0035435 GO:0035725 GO:0042803 GO:0044341 GO:0045936 GO:0055085 GO:2000186
4	0.07	0.554	4.67	0.08	0.88	4av6A	GO:0000287 GO:0004427 GO:0005509 GO:0005886 GO:0005887 GO:0006810 GO:0006811 GO:0006814 GO:0009678 GO:0015081 GO:0015992 GO:0016020 GO:0016021 GO:0016787 GO:0030955 GO:0035725 GO:0042803 GO:0046872
5	0.07	0.545	4.62	0.05	0.83	1ciiA	GO:0005886 GO:0016020 GO:0016021 GO:0019835 GO:0042742 GO:0050829
6	0.06	0.566	4.58	0.07	0.88	4a01A	GO:0004427 GO:0005773 GO:0005774 GO:0006810 GO:0006811 GO:0009678 GO:0015992 GO:0016020 GO:0016021 GO:0016787 GO:0046872 GO:0055085
7	0.06	0.553	4.49	0.04	0.85	4av3B	GO:0000287 GO:0004427 GO:0005509 GO:0005886 GO:0005887 GO:0006810 GO:0006811 GO:0006814 GO:0009678 GO:0015081 GO:0015992 GO:0016020 GO:0016021 GO:0016787 GO:0030955 GO:0035725 GO:0042803 GO:0046872
8	0.06	0.552	3.85	0.08	0.77	5j65A	GO:0030435
9	0.06	0.376	4.84	0.07	0.64	2ld6A	GO:0000155 GO:0000160 GO:0000166 GO:0004673 GO:0004871 GO:0005524 GO:0005737 GO:0006935 GO:0007165 GO:0016301 GO:0016310 GO:0016740 GO:0016772 GO:0018106 GO:0023014
10	0.06	0.477	4.24	0.04	0.71	1w07B	GO:0000062 GO:0001676 GO:0003995 GO:0003997 GO:0005777 GO:0005829 GO:0006629 GO:0006631 GO:0006635 GO:0008152 GO:0009055 GO:0009506 GO:0009611 GO:0009620 GO:0009695 GO:0016491 GO:0016627 GO:0033539 GO:0046686 GO:0050660 GO:0052890 GO:0055088 GO:0055114
11	0.06	0.326	5.88	0.04	0.64	1us2A	GO:0000272 GO:0004553 GO:0005975 GO:0008152 GO:0009279 GO:0016020 GO:0016787 GO:0016798 GO:0031176 GO:0045493
12	0.06	0.347	4.67	0.03	0.56	1a87A	GO:0005886 GO:0016020 GO:0016021 GO:0019835 GO:0042742 GO:0050829
13	0.06	0.344	5.45	0.09	0.64	3fewX	GO:0016020 GO:0016021 GO:0019835 GO:0050829
14	0.06	0.384	4.83	0.03	0.63	1colA	GO:0005886 GO:0016020 GO:0016021 GO:0019835 GO:0042742 GO:0050829
15	0.06	0.330	4.85	0.04	0.55	2i88A	GO:0005886 GO:0016020 GO:0016021 GO:0019835 GO:0042742 GO:0050829
16	0.06	0.324	5.60	0.07	0.58	2ad5B	GO:0000166 GO:0003883 GO:0005524 GO:0005829 GO:0006221 GO:0006241 GO:0006541 GO:0016874 GO:0042802 GO:0044210
17	0.06	0.402	3.63	0.06	0.54	2gyqA	GO:0046872
18	0.06	0.327	4.68	0.04	0.51	2wlkA	GO:0005242 GO:0005244 GO:0006810 GO:0006811 GO:0006813 GO:0016020 GO:0016021 GO:0034765 GO:0071805

Consensus prediction of GO terms

Molecular Function	GO:0046983	GO:0042802	GO:1901677	GO:0015081	GO:0015296	GO:0015114
GO-Score	0.59	0.59	0.37	0.37	0.37	0.37
Biological Processes	GO:1903796	GO:0055062	GO:0072502	GO:2000185	GO:0010563	GO:0019220	GO:0098662	GO:0006814
GO-Score	0.50	0.50	0.50	0.50	0.50	0.50	0.48	0.48
Cellular Component	GO:0044424	GO:0071944	GO:0016020
GO-Score	0.50	0.48	0.36

(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.