I-TASSER results

I-TASSER results for job id Rv0008c

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

Input Sequence in FASTA format

>protein (145 residues)
MSEQVETRLTPRERLTRGLAYSAVGPVDVTRGLLELGVGLGLQSARSTAAGLRRRYREGR
LAREVAAAQETLAQELTAAQDVVANLPQALQDARTQRRSKHHLWIFAGIAAAILAGGAVA
FSIVRRSSRPEPSPRPPSVEVQPRS

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MSEQVETRLTPRERLTRGLAYSAVGPVDVTRGLLELGVGLGLQSARSTAAGLRRRYREGRLAREVAAAQETLAQELTAAQDVVANLPQALQDARTQRRSKHHLWIFAGIAAAILAGGAVAFSIVRRSSRPEPSPRPPSVEVQPRS
Prediction	CCCCCCCCCCCHHHHHHCCHHHCCCCEEHHHCHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEEEEHHHHHHHHCCEEEEEEEHCCCCCCCCCCCCCCCCCCCC
Conf.Score	9865445788588887654444457634445445544455456778999999999999778899999999999999999999998689998565655678874576466777764657999999868999999999988899899
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MSEQVETRLTPRERLTRGLAYSAVGPVDVTRGLLELGVGLGLQSARSTAAGLRRRYREGRLAREVAAAQETLAQELTAAQDVVANLPQALQDARTQRRSKHHLWIFAGIAAAILAGGAVAFSIVRRSSRPEPSPRPPSVEVQPRS
Prediction	8665464413445313431432122313014223443242224324432540353146443365244345413541430451044035205624666546431100011211231233110101335466636534462546468
	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

CCCCCCCCCCCHHHHHHCCHHHCCCCEEHHHCHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEEEEHHHHHHHHCCEEEEEEEHCCCCCCCCCCCCCCCCCCCC
MSEQVETRLTPRERLTRGLAYSAVGPVDVTRGLLELGVGLGLQSARSTAAGLRRRYREGRLAREVAAAQETLAQELTAAQDVVANLPQALQDARTQRRSKHHLWIFAGIAAAILAGGAVAFSIVRRSSRPEPSPRPPSVEVQPRS

5cwqA1

0.20

0.15

0.77

0.78

MUSTER

------------EELERESEEAERRLQEARKRSEEARERGDLKELAEALIEEARAVQELARVACERGNSEEAERASEKAQRVLEEARKVSEEAREQGDDEVLALALIAIALAVLALAEVA---CRGN------------------

5cwqA1

0.19

0.15

0.78

0.59

dPPAS

------------EELERESEEAERRLQEARKRSEEARERGDLKELAEALIEEARAVQELARVACERGNSEEAERASEKAQRVLEEARKVSEEAREQGDDEVLALALIAIALAVLALAEVA--CCRGN------------------

4kk2A1

0.18

0.14

0.76

0.52

wdPPAS

LIHDPLFEFDDRQWVERMIDYTVPG----VRGYSVVDSYQLLKGEELT-------DDEIFLSSALGWCIEWLQAYFLVLDDIMDE---------SHTRRGQPCWMIAANDGILLR--NHVPRILKKHFRGKP-------------

5cwqA1

0.20

0.15

0.77

0.70

wMUSTER

------------EELERESEEAERRLQEARKRSEEARERGDLKELAEALIEEARAVQELARVACERGNSEEAERASEKAQRVLEEARKVSEEAREQGDDEVLALALIAIALAVLALAEVA----RGN------------------

4hdtA2

0.25

0.21

0.86

0.63

wPPAS

M---PEVGFIPTYLLSR-A----PG----KLGLHAALTGAPASPLAEQRSWIDECYTGDTVADIIAALRAHDAPAAGEAADLIAT-PIALSVTLESVRRAAKLQSLERVSCASLKSGIRAQLV-------NPKWRPATLEVTEAD

5cwqA1

0.19

0.15

0.78

0.65

dPPAS2

------------EELERESEEAERRLQEARKRSEEARERGDLKELAEALIEEARAVQELARVACERGNSEEAERASEKAQRVLEEARKVSEEAREQGDDEVLALALIAIALAVLALAEVA--CCRGN------------------

5cwqA1

0.19

0.15

0.78

0.69

PPAS

------------EELERESEEAERRLQEARKRSEEARERGDLKELAEALIEEARAVQELARVACERGNSEEAERASEKAQRVLEEARKVSEEAREQGDDEVLALALIAIALAVLALAEVA--CCRGN------------------

4e3eA1

0.17

0.99

0.80

Env-PPAS

-SAKTNPGNF-FEDFRLGQTIVHATPRTITEGDVALYTSLGSSTPFAQSLGLERAPIDSLLVFHIVFGKTVPDISLNAIAGGRFGAVSKVIGLRQNKDGKTGVVYVHSVGVEVVLEYIRWVVRKRDPNAPAPETLPDSVPVTPYT

5cwmA1

0.14

0.11

0.79

0.76

MUSTER

---------DPEDELKR-VEKLVKEAEELLRQAKEKGSEEDLEKALRTAEEAAREAKKVLEQAEKEGDPEVALRAVELVVRVAELLLRIAKESGSEEALER----ALRVAEEAARLAKRVLELAEKQG-----------------

5cwpA1

0.16

0.12

0.77

0.54

dPPAS

--------MSSDEEEARELIERAK---EAAERAQEAAERTGDPRVRELARELKRLAQEAAEEVKRDPSSSDVNEALKLIVEAIEAAVRALEAAERTGDPEVRELARELVRLAVEAAEEVQRNP----------------------

(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=-2.82

Estimated TM-score = 0.39±0.13

Estimated RMSD = 11.1±4.6Å

Download Model 2

C-score=-3.10

Download Model 3

C-score=-5.00

Download Model 4

C-score=-5.00

Download Model 5

C-score=-4.91

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	5cwqA	0.785	2.57	0.118	0.897
2	5cwmA	0.688	2.90	0.097	0.841
3	1w99A	0.678	3.34	0.069	0.890
4	4d8mA	0.661	3.18	0.091	0.841
5	2c9kA	0.650	3.53	0.090	0.876
6	3eb7A1	0.646	2.86	0.075	0.828
7	1ciyA	0.644	3.19	0.077	0.841
8	4w8jA	0.643	3.34	0.077	0.848
9	1dlcA	0.641	3.26	0.056	0.841
10	1ji6A	0.639	3.39	0.077	0.841

(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	0.10	6	3p1oA	III	Rep, Mult	54,57,58,61,64,114,117,118
2	0.05	3	3cu8A	III	Rep, Mult	47,51,54,55,60,64,114,115,143
3	0.05	3	3qvdA	FE	Rep, Mult	22,25,55
4	0.05	3	2wh0C	III	Rep, Mult	30,31,81,85,88,89
5	0.05	3	5fvkA	III	Rep, Mult	19,20,23,24,27,31,34,37,49,62,63,66,68,70,71,74,78,82,85
6	0.03	2	1yklG	DHB	Rep, Mult	25,26
7	0.03	2	1qjbB	III	Rep, Mult	23,30,31,76,80,83
8	0.03	2	1qjaA	III	Rep, Mult	50,51,54,57,58,104,107,111,114,115
9	0.02	1	3l26B	MG	Rep, Mult	136,137
10	0.02	1	1ysaC	NUC	Rep, Mult	46,47,50,53,57
11	0.02	1	3u7qB	IMD	Rep, Mult	75,78
12	0.02	1	2nofA	NUC	Rep, Mult	31,41,56,57
13	0.02	1	3bz1Z	CLA	Rep, Mult	83,87
14	0.02	1	1fp4B	CA	Rep, Mult	57,58
15	0.02	1	3j000	PEV	Rep, Mult	15,17,26

	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	0.066	1wcrA	0.480	2.34	0.077	0.572	2.7.1.69	NA
2	0.060	2f6dA	0.552	3.65	0.043	0.765	3.2.1.3	33,44,86
3	0.060	1qleA	0.499	4.61	0.042	0.835	1.9.3.1	NA
4	0.060	1jk0A	0.558	4.09	0.071	0.814	1.17.4.1	NA
5	0.060	2eabA	0.589	3.92	0.043	0.855	3.2.1.63	NA
6	0.060	2vn4A	0.553	4.19	0.107	0.862	3.2.1.3	NA
7	0.060	1uzrB	0.574	3.81	0.066	0.821	1.17.4.1	NA
8	0.060	1hzfA	0.551	3.56	0.051	0.759	3.4.21.43	NA
9	0.060	1smsA	0.551	3.84	0.043	0.786	1.17.4.1	NA
10	0.060	1h0nA	0.569	3.76	0.037	0.793	1.17.4.1	NA
11	0.060	2bq1I	0.573	3.75	0.066	0.821	1.17.4.1	NA
12	0.060	1i1iP	0.569	4.23	0.050	0.883	3.4.24.16	NA
13	0.060	1ut9A	0.557	3.78	0.067	0.821	3.2.1.4	NA
14	0.060	1biqB	0.568	3.75	0.070	0.793	1.17.4.1	NA
15	0.060	1gaiA	0.563	4.46	0.101	0.890	3.2.1.3	NA
16	0.060	1rw9A	0.543	4.50	0.101	0.869	4.2.2.5	NA
17	0.060	1j0mA	0.542	4.33	0.083	0.835	4.2.2.12	23
18	0.060	3e04D	0.553	3.22	0.055	0.710	4.2.1.2	83
19	0.060	1g87B	0.567	3.81	0.029	0.841	3.2.1.4	NA
20	0.060	3gtdA	0.544	3.43	0.048	0.710	4.2.1.2	100

(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	0.10	0.694	3.11	0.08	0.90	4moaA	GO:0005102 GO:0006952 GO:0009405 GO:0030435
1	0.09	0.641	3.26	0.06	0.84	1dlcA	GO:0005102 GO:0006952 GO:0009405 GO:0030435
2	0.09	0.644	3.19	0.08	0.84	1ciyA	GO:0005102 GO:0006952 GO:0009405 GO:0030435
3	0.09	0.643	3.34	0.08	0.85	4w8jA	GO:0005102 GO:0006952 GO:0009405 GO:0030435
4	0.07	0.639	3.39	0.08	0.84	1ji6A	GO:0005102 GO:0006952 GO:0009405 GO:0030435
5	0.07	0.612	3.23	0.09	0.81	1i5pA	GO:0005102 GO:0006952 GO:0009405 GO:0030435
6	0.07	0.546	3.04	0.07	0.72	3eb7A	GO:0005102 GO:0006952 GO:0009405 GO:0030435
7	0.07	0.661	3.18	0.09	0.84	4d8mA	GO:0009405 GO:0030435
8	0.07	0.650	3.53	0.09	0.88	2c9kA	GO:0005102 GO:0006952 GO:0009405 GO:0030435
9	0.07	0.504	3.29	0.06	0.67	3ck6E	GO:0005886 GO:0016020 GO:0016021 GO:0030001 GO:0046873 GO:0055085
10	0.06	0.488	4.43	0.08	0.75	4uvkA	GO:0000755 GO:0003682 GO:0005634 GO:0005829 GO:0006473 GO:0007064 GO:0009847 GO:0031505 GO:0031618 GO:0031934 GO:0034990 GO:1990707
11	0.06	0.403	5.20	0.06	0.71	3pa8A	GO:0009405 GO:0016740 GO:0016757
12	0.06	0.425	3.15	0.03	0.54	2y4uA	GO:0004860 GO:0005737 GO:0005783 GO:0005788 GO:0005790 GO:0005829 GO:0006417 GO:0006986 GO:0016020 GO:0019901 GO:0031205 GO:0036494 GO:0036498 GO:0043066 GO:0051087 GO:0051603 GO:0051607 GO:0051787 GO:0070062 GO:0070417 GO:1903561 GO:1903912 GO:1904030
13	0.06	0.306	6.07	0.09	0.65	1gnzA	GO:0030246 GO:0046872
14	0.06	0.380	4.78	0.02	0.61	1v6yA	GO:0000272 GO:0004553 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0031176
15	0.06	0.381	4.70	0.06	0.62	3t2dA	GO:0046872
16	0.06	0.372	4.67	0.02	0.61	1isvA	GO:0000272 GO:0004553 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0031176
17	0.06	0.358	4.45	0.02	0.53	4k3vB	GO:0006810 GO:0007155 GO:0030001 GO:0046872
18	0.06	0.363	4.76	0.06	0.63	1ig0B	GO:0000166 GO:0004788 GO:0005524 GO:0009229 GO:0016301 GO:0016310 GO:0016740 GO:0030975

Consensus prediction of GO terms

Molecular Function	GO:0005102
GO-Score	0.37
Biological Processes	GO:0006952	GO:0030435	GO:0009405
GO-Score	0.37	0.37	0.37
Cellular Component
GO-Score

(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.