I-TASSER results

I-TASSER results for job id Rv3657c

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

Input Sequence in FASTA format

>protein (191 residues)
MALWLGAGPSVVRARAGRPPRAHRPHQGLLLGRTDVADPLAVAASLDVLAVCLAAGMAVS
TAAAATAAVAPPRLARVLRRAADLLALGADPNIAWSRPPDLPPGTHDAQTDAVLRLARRS
AASGAALADGIVELAVQVRHDAAQAAAAAAERAGVLIAGPLGLCFLPAFLCVGIVPLVVG
LAGDVLQFGLV

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| MALWLGAGPSVVRARAGRPPRAHRPHQGLLLGRTDVADPLAVAASLDVLAVCLAAGMAVSTAAAATAAVAPPRLARVLRRAADLLALGADPNIAWSRPPDLPPGTHDAQTDAVLRLARRSAASGAALADGIVELAVQVRHDAAQAAAAAAERAGVLIAGPLGLCFLPAFLCVGIVPLVVGLAGDVLQFGLV
Prediction	CCEEHCCCCCCEEEHCCCCCCCCCCHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC
Conf.Score	96676688854444345666766545677766654555566779999999999969999999999999859779999999999999699999999999985567786789999999999999899799999999999999999999999999656899999999999999999999999999999756889
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| MALWLGAGPSVVRARAGRPPRAHRPHQGLLLGRTDVADPLAVAASLDVLAVCLAAGMAVSTAAAATAAVAPPRLARVLRRAADLLALGADPNIAWSRPPDLPPGTHDAQTDAVLRLARRSAASGAALADGIVELAVQVRHDAAQAAAAAAERAGVLIAGPLGLCFLPAFLCVGIVPLVVGLAGDVLQFGLV
Prediction	40000123332224314444444444553454646442213003001000000224131430042007415440040032004105343515401530472453452640320030033046341310520341055215523540463044031301322331333333233332222110331254436
	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

                   |                   |                   |                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCEEHCCCCCCEEEHCCCCCCCCCCHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC
MALWLGAGPSVVRARAGRPPRAHRPHQGLLLGRTDVADPLAVAASLDVLAVCLAAGMAVSTAAAATAAVAPPRLARVLRRAADLLALGADPNIAWSRPPDLPPGTHDAQTDAVLRLARRSAASGAALADGIVELAVQVRHDAAQAAAAAAERAGVLIAGPLGLCFLPAFLCVGIVPLVVGLAGDVLQFGLV

2vmbA

0.16

0.10

0.62

1.13

wPPAS

---------------------------GFAFKRGIS--TPDLALITRQLATLVQSGMPLEECLRAVAEQSEPRIRTMLVAVRAKVTEGYTLSDSLGD----YPHV-----ELFRSMVAAGEKSG-HLDSVLERLADYAENRQKMRSKLQQASENLYF----------------------------------

2vmbA

0.14

0.09

0.63

1.60

dPPAS2

-----------------------------GFAFKRGISTPDLALITRQLATLVQSGMPLEECLRAVAEQSEPRIRTMLVAVRAKVTEGYTLSDSLGDYPHVFD-------ELFRSMVAAGEKSG-HLDSVLERLADYAENRQKMRSKLQQASENLYF----------------------------------

2vmbA

0.16

0.10

0.63

1.06

PPAS

---------------------------GFAFKRGIS--TPDLALITRQLATLVQSGMPLEECLRAVAEQSEPRIRTMLVAVRAKVTEGYTLSDSLGDYPHVFD-------ELFRSMVAAGEKSG-HLDSVLERLADYAENRQKMRSKLQQASENLYF----------------------------------

2vmbA

0.16

0.10

0.63

1.29

Env-PPAS

---------------------------GFAFKRGIS--TPDLALITRQLATLVQSGMPLEECLRAVAEQSEPRIRTMLVAVRAKVTEGYTLSDSLGDYPHVFD-------ELFRSMVAAGEKSG-HLDSVLERLADYAENRQKMRSKLQQASENLYF----------------------------------

4yxxA

0.14

0.97

1.40

dPPAS2

VSLEQALKILKVAAELGTTVEEAVKRALKLKTKLGVS----LEQALKILEVAAELGTTVEEAVKRALKLKGVSLEQALKILEVAAKLGTTVEEAVKRALKLKTKLGVS-LEQALKILKVAAELGTTVEEAVKRALKLKTKLVSLEQALKILEVAAELVEEAVKRALKLKTKLGVLEQALKILEVAAKLGTT

4ke2A

0.18

0.16

0.91

1.30

dPPAS2

------------------MNIDPAARAAAAAAASKAAVTAADAAAAAATIAASAASVAAATAADDAAASIATAAAAAMAAKDTAAAAASAAAAAVASAAKALETINVKAAYAAATTANTAAAAAAATATTAAAAAAAKATIDNAAAAKAAAVATAVSDAAATAATAAAVAAATLEAAAAKAAATAVSAAAA

5cwqA1

0.16

0.09

0.59

1.20

dPPAS2

---------------------------------------------------------------------------EELERESEEAER--RLQEARKRSEEARERGDLKELAEALIEEARAVQELARVACERGNSEEAERASEKAQRVLEEARKVSEEAREQGDDEVLALALIAIALAVLALAEVACCRGN-

4tqlA1

0.03

0.79

1.09

dPPAS2

----------------------------------YKQMVQELEKARDRMEKLYKE---MVELIQKAIELMR-KIFQEVKQEVEKAIE-EKLLEKLKQIMQEAKQKMEKLLKQLKEEMKKMKEKMEKLLKEMKQRMEEVKKKMDDELLEKIKKNIDDLKKIAEDLIKKAEENIKEAKKIAEQLVKRAKQ-LI

4yxxA

0.16

0.97

MUSTER

VSLEQALKILKVAAELGTTVEEAVKRALKLKTKLGVS----LEQALKILEVAAELGTTVEEAVKRALKLKGVSLEQALKILEVAAKLGTTVEEAVKRALKLKTKLGVS-LEQALKILKVAAELGTTVEEAVKRALKLKTKLSLEQALKILEVAAVEEAVKRALKLKTKLGVSLEQALKILEVAAKLGTTVE

4ke2A

0.18

0.96

0.90

dPPAS

-------MNIDPAARAAAAAAASKAAVTAADAAAAAATIAASAASVAAATAADDAAASIATINAASAAAKSIAAAAAMAAKDTAAAAASAAAAAVASAAKALETINVKAAYAAATTANTAAAAAAATATTAAAAAAAKATIDNAAAAKAAAVATAVSDAAATAATAAAVAAATLEAAAAKAAATAVSAAAA

(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=-1.93

Estimated TM-score = 0.48±0.15

Estimated RMSD = 9.5±4.6Å

Download Model 2

C-score=-4.29

Download Model 3

C-score=-3.17

Download Model 4

C-score=-4.48

Download Model 5

C-score=-3.89

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	2vmbA	0.537	2.02	0.133	0.597
2	3j9tQ	0.537	4.59	0.074	0.811
3	5doqA	0.535	4.69	0.073	0.843
4	5doqB	0.531	4.50	0.055	0.827
5	3rkoN	0.520	4.71	0.065	0.822
6	3rkoM	0.520	4.88	0.106	0.848
7	4f4cA4	0.511	4.50	0.061	0.791
8	4he8M	0.510	4.97	0.065	0.833
9	3ihyC	0.504	5.07	0.076	0.817
10	2yevA	0.504	5.19	0.052	0.833

(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	0.06	3	3rdhA	3RD	Rep, Mult	7,46,47,113,116
2	0.06	3	3prqZ	CLA	Rep, Mult	172,175,176
3	0.06	3	4xk8L	CLA	Rep, Mult	46,142
4	0.04	2	3dtuC	DMU	Rep, Mult	78,81,82,85
5	0.04	2	3qqvA	MG	Rep, Mult	47,52,181
6	0.04	2	2e75G	OPC	Rep, Mult	127,131
7	0.02	1	2i5wA	CA	Rep, Mult	164,166,172
8	0.02	1	3omiC	TRD	Rep, Mult	72,75,79
9	0.02	1	4evbA	ZN	Rep, Mult	133,137
10	0.02	1	2np5C	NDS	Rep, Mult	121,122,124,128
11	0.02	1	5d6kA	97M	Rep, Mult	47,48,54,128,132
12	0.02	1	3fyeC	TRD	Rep, Mult	46,110,118
13	0.02	1	1c6mA	KR	Rep, Mult	62,63,85,121
14	0.02	1	4eiyA	CLR	Rep, Mult	163,166,167,174,181,182,188
15	0.02	1	2hk6A	FE	Rep, Mult	140,144
16	0.02	1	3dtuC	DXC	Rep, Mult	63,66,67,70,75,78
17	0.02	1	4uk1E	MG	Rep, Mult	136,139

	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	3g0sA	0.479	5.30	0.035	0.822	4.2.1.52	NA
2	0.060	1f7bA	0.481	5.24	0.098	0.806	4.1.3.3	81
3	0.060	2weiA	0.379	5.69	0.069	0.681	2.7.1.17	84
4	0.060	2pcqA	0.485	4.98	0.083	0.780	4.2.1.52	NA
5	0.060	1i09A	0.483	5.06	0.078	0.785	2.7.11.26,2.7.1.37	47
6	0.060	2x6fA	0.486	5.09	0.048	0.791	2.7.1.137,2.7.1.153,2.7.1.154	88
7	0.060	1occA	0.495	5.35	0.047	0.838	1.9.3.1	NA
8	0.060	1xkyA	0.482	5.26	0.072	0.801	4.2.1.52	NA
9	0.060	1xl9A	0.487	5.13	0.067	0.796	4.2.1.52	NA
10	0.060	1qleA	0.385	5.85	0.091	0.707	1.9.3.1	NA
11	0.060	1u59A	0.442	4.86	0.075	0.696	2.7.10.2,2.7.1.112	47
12	0.060	2vc6A	0.480	5.06	0.080	0.791	4.2.1.52	139
13	0.060	3eb2B	0.489	4.81	0.053	0.791	4.2.1.52	NA
14	0.060	1iduA	0.482	4.61	0.081	0.702	1.11.1.10	NA
15	0.060	3hngA	0.428	4.74	0.060	0.644	2.7.10.1	47,50
16	0.060	1y6bA	0.439	4.78	0.072	0.665	2.7.10.1,2.7.1.112	54
17	0.060	3bi8A	0.488	5.14	0.049	0.806	4.2.1.52	NA
18	0.060	2fp0B	0.484	4.91	0.087	0.744	3.2.1.143	50,186
19	0.060	3ihyC	0.504	5.07	0.076	0.817	2.7.1.137	35,69,140

(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	0.574	3.53	0.11	0.72	3jc8Ca	GO:0016020 GO:0016021
1	0.07	0.537	2.02	0.13	0.60	2vmbA	GO:0005886 GO:0006810 GO:0008565 GO:0009306 GO:0015031 GO:0015627 GO:0015628 GO:0016020 GO:0016021
2	0.07	0.538	2.15	0.13	0.60	2vmaA	GO:0005886 GO:0006810 GO:0008565 GO:0009306 GO:0015031 GO:0015627 GO:0015628 GO:0016020 GO:0016021
3	0.07	0.531	4.50	0.06	0.83	5doqB	GO:0016020 GO:0016021 GO:0055114
4	0.07	0.537	4.59	0.07	0.81	3j9tQ	GO:0000220 GO:0000329 GO:0005773 GO:0005774 GO:0006810 GO:0006811 GO:0007034 GO:0007035 GO:0015078 GO:0015991 GO:0015992 GO:0016020 GO:0033179 GO:0046961
5	0.07	0.535	4.69	0.07	0.84	5doqA	GO:0016020 GO:0016021
6	0.07	0.479	5.11	0.12	0.80	4he8I	GO:0005886 GO:0006810 GO:0008137 GO:0016020 GO:0016021 GO:0016491 GO:0042773 GO:0048038 GO:0050136 GO:0055114
7	0.07	0.477	1.85	0.16	0.53	2whnA	GO:0005886 GO:0006810 GO:0009306 GO:0016020 GO:0016021
8	0.06	0.510	4.97	0.07	0.83	4he8G	GO:0005886 GO:0008137 GO:0016020 GO:0016021 GO:0016491 GO:0042773 GO:0048038 GO:0055114
9	0.06	0.383	5.96	0.06	0.72	3k6sC	GO:0004872 GO:0005886 GO:0007155 GO:0007229 GO:0008305 GO:0009887 GO:0009986 GO:0016020 GO:0016021 GO:0030198 GO:0034113 GO:0046872 GO:0050900 GO:1903955
10	0.06	0.346	6.19	0.04	0.68	4nenA	GO:0004872 GO:0005886 GO:0007155 GO:0007229 GO:0008305 GO:0009887 GO:0009986 GO:0016020 GO:0016021 GO:0030198 GO:0034113 GO:0046872 GO:0050900 GO:1903955
11	0.06	0.381	5.28	0.06	0.66	4jcmA	GO:0003824 GO:0005975 GO:0016740 GO:0030246 GO:0043169 GO:0046872 GO:2001070
12	0.06	0.375	5.08	0.03	0.61	3mcaA	GO:0000166 GO:0002181 GO:0002182 GO:0003746 GO:0003924 GO:0005525 GO:0005622 GO:0005737 GO:0005829 GO:0006412 GO:0006414 GO:0006417 GO:0032790
13	0.06	0.424	5.35	0.06	0.73	1nfgA	GO:0005737 GO:0016787 GO:0016810 GO:0046872
14	0.06	0.359	5.41	0.09	0.59	2q5lA	GO:0000287 GO:0003824 GO:0009851 GO:0016829 GO:0016831 GO:0030976 GO:0046872 GO:0047434
15	0.06	0.339	6.06	0.06	0.64	4nehA	GO:0004872 GO:0005886 GO:0007155 GO:0007229 GO:0008305 GO:0009887 GO:0009986 GO:0016020 GO:0016021 GO:0030198 GO:0034113 GO:0046872 GO:0050900 GO:1903955
16	0.06	0.498	5.20	0.07	0.82	4he8F	GO:0005886 GO:0008137 GO:0016020 GO:0016021 GO:0016491 GO:0042773 GO:0048038 GO:0055114
17	0.06	0.322	5.21	0.08	0.54	2ex5A	GO:0003677 GO:0004518 GO:0004519 GO:0006314 GO:0009507 GO:0009536 GO:0016787 GO:0046872 GO:0090305
18	0.06	0.343	5.37	0.04	0.60	3ed5A	GO:0008152 GO:0016787

Consensus prediction of GO terms

Molecular Function	GO:0008565	GO:0046961
GO-Score	0.13	0.07
Biological Processes	GO:0051234
GO-Score	0.37
Cellular Component	GO:0031224
GO-Score	0.38

(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.