I-TASSER results

I-TASSER results for job id Rv2696c

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

Input Sequence in FASTA format

>protein (259 residues)
MAFGRRTGKDGGKRKAGHAPVQPADEHVRPEDTVVASAAAASGVEDQEELQGPFDIDDFD
DPSVAVLARLDLGSVLIPMPAAGQVQVELTESGVPSAVWVITPNGRYSIAAYAAPKTGGL
WREVAGELADSLRKDSAKVSIKDGPWGREVIGIAAGVVRFIGVDGYRWMIRCVVNGPQET
VDALTEEAREALADTVVRRGDTPLPVRTPLPVHLPEPMAAQLREAAAAQADTQRQAAAGV
ARRGAQGSAMQQLRSTTGG

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 \| \| \| \| \| \| \| \| \| \| \| \| MAFGRRTGKDGGKRKAGHAPVQPADEHVRPEDTVVASAAAASGVEDQEELQGPFDIDDFDDPSVAVLARLDLGSVLIPMPAAGQVQVELTESGVPSAVWVITPNGRYSIAAYAAPKTGGLWREVAGELADSLRKDSAKVSIKDGPWGREVIGIAAGVVRFIGVDGYRWMIRCVVNGPQETVDALTEEAREALADTVVRRGDTPLPVRTPLPVHLPEPMAAQLREAAAAQADTQRQAAAGVARRGAQGSAMQQLRSTTGG
Prediction	CCCCCCCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEHCCEEEHCCCCCEEEEEEHCCCCCEEEEEEEHCCCEEEEEEEEHCCCCCCHHHHHHHHHHHHHHHCCCEEEEHCCCCCEEEEHCCCEEEEEHCCCCCEEEEEEEHCCCCCCHHHHHHHHHHHHHCEEHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHCC
Conf.Score	9988767776545545667777777777777777777877777788888999999766888876556775556578768899589999889998789999979958999998757899967899999999999979958998689966799986976999965788547999997688789899999999997455657999999988766779978888888777766556788888988888898778898876579
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 \| \| \| \| \| \| \| \| \| \| \| \| MAFGRRTGKDGGKRKAGHAPVQPADEHVRPEDTVVASAAAASGVEDQEELQGPFDIDDFDDPSVAVLARLDLGSVLIPMPAAGQVQVELTESGVPSAVWVITPNGRYSIAAYAAPKTGGLWREVAGELADSLRKDSAKVSIKDGPWGREVIGIAAGVVRFIGVDGYRWMIRCVVNGPQETVDALTEEAREALADTVVRRGDTPLPVRTPLPVHLPEPMAAQLREAAAAQADTQRQAAAGVARRGAQGSAMQQLRSTTGG
Prediction	6532324565656654555655555564556664555555555466565541112254163574443310100002013274140203237733020010115602010101001346420540153025204756151534614202002434632000000132100000001034433660152035002400032374122244202041275136535744554585665655544644462531342274568
	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                 220                 240

                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCCCCCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEHCCEEEHCCCCCEEEEEEHCCCCCEEEEEEEHCCCEEEEEEEEHCCCCCCHHHHHHHHHHHHHHHCCCEEEEHCCCCCEEEEHCCCEEEEEHCCCCCEEEEEEEHCCCCCCHHHHHHHHHHHHHCEEHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHCC
MAFGRRTGKDGGKRKAGHAPVQPADEHVRPEDTVVASAAAASGVEDQEELQGPFDIDDFDDPSVAVLARLDLGSVLIPMPAAGQVQVELTESGVPSAVWVITPNGRYSIAAYAAPKTGGLWREVAGELADSLRKDSAKVSIKDGPWGREVIGIAAGVVRFIGVDGYRWMIRCVVNGPQETVDALTEEAREALADTVVRRGDTPLPVRTPLPVHLPEPMAAQLREAAAAQADTQRQAAAGVARRGAQGSAMQQLRSTTGG

4cwuT

0.17

0.05

0.28

1.20

dPPAS2

-------APGLGVQTVDVQETQTSPVASAVADAAVQAVAAAASKTSTEVQTDPWMFRVSAPRRPRGSRKYGAASALLPE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

2rrlA

0.12

0.07

0.59

1.01

dPPAS2

-------HMASDDRATGPALTPLVVAAAATSAKVEVDSPPAPVTHGAAMPTLSSATAQPLPVASAPVLSAPLGSVMLFTRQGQSAQLRLHPEEGQVHISLKLDDNQAQLQMVSPSHVRAALEAALPMLRTQLAESGGQSSISSESFGQQQSSSQQQSSR----------------------------------------------------------------------------------------------------

4pwoA

0.13

0.11

0.84

0.66

MUSTER

TATDLPPGFSGKAGSVNATPGTKGLDGPTPLADGSFDATIFGPAKELKSADDILNVHRRNAKDPFAVGAVD-APLVI-SNQTETLMEEYVSKGLVRIEWNDLPHALAAAKAGRAAAAQGKFDEFRKALFEASRNVSGHPNNT--------LKDFERFARNAGVKDM--RFSREAQD-STYDEVLAKAADYAHGLAFVVGT-------QYISGAQPEEFIKVIESELKKSPTFSTPSSH---------------------

5gaoE

0.17

0.15

0.89

0.84

dPPAS

AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA----AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA-----------AAAAAAA-------------AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAARAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA

2hyxA1

0.14

0.09

0.66

0.74

wdPPAS

--------------GAMEIREQLNLGGIVNAQNAQLSNCSDGAAQLESCGTAP----DLKGIT-----------GWLNTPGNKPIDLK---RGKVVLIDFWYKDSGLAVIGVHTPEYA--FEKVPGNVAKGAANLGISALDNNY-YR---NRYWP-AEYLIDATG---TVRHIKFGEG-DYNVTETLVRQLLNDA----VKLPQPSSTTTPDLTPRA------------------------------------------

4pwoA

0.14

0.11

0.83

0.65

wMUSTER

TATDLPPGFSGKAGSVNATPGTKGLDGPTPLADGSFDATIFGPAKELKSADDILNVHRRNAKDPFAVGAVD-APLVI------TLMEEYVSKGLVRIEWNDLPHALAAAKAGRAAAAQGKFDEFRKALFEASRNVSGHPNNTL----KDFERFARN----AGVDMER--FSREAQDSTYDEAKAADYAHGLVSGTFVVGT-------QYISGAQPEEFIKVIESELKKSPTFSTPSSH---------------------

2hyxA1

0.17

0.11

0.68

0.72

wPPAS

---GREQLNLGGIVNAQNAQLSNCSDGAAQLESCGTAPDLKGITGWLNTPGNPIDLKS--------RGKIDFAY--IPHVV--GWYQAYKDSG-------------LAVIGVHTPEYA--FEKVPGNVAKGAANLGISALDNNYAYRNR----WP-AEYLIDATG---TVRHIKFGE-GDYNVTETLVRQLLNDA---GVKLPQPSSTTTPDLTPRA------------------------------------------

4behB

0.16

0.03

0.20

1.01

dPPAS2

VPAG----GAVAVSAAPGSAAPAAGSAPAAAEEKKDEKKEESEESDDDMGFGLFD------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

5gaoE

0.16

0.15

0.97

0.77

PPAS

AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA--------AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAARAAAAAAAAAA

2j3tD

0.13

0.10

0.79

0.62

Env-PPAS

-----------------------AIFSVYVVNKAGGLIYQLDSYEAEKTFSYPLDLLLKLHDERGQRDGIRVGHAVL-AINGMDVNGRYTADGKEVLEYLGNPANYPVSIRFGRPRLTSNEKLMLASMFHSLFAIGSQLSPEQGSSGIEMLETDTFKLHCYQTLTGIKFVVLADPRQAGI-DSLLRKIYEIYSDFAL---KNPFYSLE-MPIR-CELFDQNLKLALEVAEKAGTF------------------------

(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=-3.18

Estimated TM-score = 0.36±0.12

Estimated RMSD = 13.5±4.0Å

Download Model 2

C-score=-4.33

Download Model 3

C-score=-5.00

Download Model 4

C-score=-4.70

Download Model 5

C-score=-4.97

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	4pwoA	0.780	2.14	0.117	0.857
2	3f4tA	0.515	3.67	0.047	0.652
3	3ghaA	0.506	3.13	0.087	0.610
4	4xvwA	0.484	3.25	0.056	0.595
5	4gxzA	0.481	3.24	0.082	0.591
6	4z7xA	0.480	3.88	0.055	0.633
7	2remC	0.472	3.87	0.094	0.614
8	3gykA	0.471	3.21	0.147	0.579
9	4k2dA	0.471	3.96	0.087	0.622
10	4n30A	0.471	3.42	0.072	0.583

(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	3a68A	CA	Rep, Mult	187,190
2	0.06	3	2ushA	WO4	Rep, Mult	167,171,199
3	0.04	2	2bsqH	NUC	Rep, Mult	197,199
4	0.04	2	3eu4A	CA	Rep, Mult	65,101,113,187
5	0.02	1	2x7qA	CA	Rep, Mult	147,149
6	0.02	1	2ya0A	NA	Rep, Mult	19,72,93,94
7	0.02	1	1ti1A	D12	Rep, Mult	77,82,211,218
8	0.02	1	2i89B	MG	Rep, Mult	161,162
9	0.02	1	5esrA	MG	Rep, Mult	18,223
10	0.02	1	1r4wC	GSH	Rep, Mult	113,114,115,161,163,164
11	0.02	1	2uwfA	CA	Rep, Mult	71,149
12	0.02	1	1yklG	DHB	Rep, Mult	52,53
13	0.02	1	2d32D	CYS	Rep, Mult	83,128,129,132
14	0.02	1	4dw5A	BMA	Rep, Mult	216,217
15	0.02	1	2gxsB	CA	Rep, Mult	119,123
16	0.02	1	3dksC	III	Rep, Mult	79,80,100,101,196
17	0.02	1	2y8nA	SF4	Rep, Mult	168,171
18	0.02	1	1n24B	MG	Rep, Mult	194,208
19	0.02	1	2d32B	MG	Rep, Mult	45,53,56
20	0.02	1	2d32A	CYS	Rep, Mult	104,187,189,192

	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	2zjfA	0.374	6.23	0.077	0.649	3.3.2.3	190
2	0.060	1zjaA	0.383	6.10	0.077	0.645	5.4.99.11	NA
3	0.060	1ti6A	0.386	6.37	0.057	0.687	1.97.1.2	NA
4	0.060	1yq2A	0.373	6.42	0.044	0.664	3.2.1.23	123
5	0.060	1llwA	0.372	6.34	0.036	0.656	1.4.7.1	NA
6	0.060	2vtfA	0.394	6.32	0.056	0.691	3.2.1.96	93,95,120
7	0.060	2je8B	0.343	6.32	0.056	0.614	3.2.1.25	NA
8	0.060	2qnoA	0.325	6.22	0.020	0.575	3.2.1.4	NA
9	0.060	3l4uA	0.381	6.13	0.076	0.652	3.2.1.20,3.2.1.3	116
10	0.060	3fn9C	0.378	6.06	0.046	0.649	3.2.1.23	NA
11	0.060	3a1kA	0.316	6.73	0.045	0.591	3.5.1.4	92
12	0.060	1bf2A	0.401	5.70	0.048	0.652	3.2.1.68	NA
13	0.060	2wanA	0.396	5.88	0.048	0.656	3.2.1.41	194
14	0.060	2prmA	0.378	6.47	0.074	0.679	1.3.5.2	38
15	0.060	2jiiB	0.381	5.92	0.054	0.645	2.7.11.1	NA
16	0.060	1yzxB	0.441	3.44	0.080	0.544	2.5.1.18	NA
17	0.060	2zueA	0.375	5.82	0.048	0.629	6.1.1.19	NA
18	0.060	2b4kA	0.378	5.64	0.043	0.602	3.1.1.43	NA
19	0.060	1cygA	0.392	5.87	0.077	0.649	2.4.1.19	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	0.29	0.780	2.14	0.12	0.86	4pwoA	GO:0016020 GO:0016021
1	0.07	0.515	3.67	0.05	0.65	3f4tA	GO:0003756 GO:0019153 GO:0055114
2	0.07	0.506	3.14	0.09	0.61	3eu3A	GO:0016491 GO:0030420 GO:0055114
3	0.07	0.479	3.72	0.14	0.61	4ihuB	GO:0005618 GO:0005886 GO:0009986 GO:0016020 GO:0016021 GO:0040007
4	0.07	0.471	3.96	0.09	0.62	4k2dA	GO:0015035 GO:0042597 GO:0045454 GO:0055114
5	0.07	0.481	3.24	0.08	0.59	4gxzA	GO:0005623 GO:0015035 GO:0045454 GO:0055114
6	0.07	0.494	3.23	0.06	0.61	4xvwA	GO:0005623 GO:0045454
7	0.07	0.461	4.02	0.08	0.62	3h93A	GO:0015035 GO:0042597 GO:0045454 GO:0055114
8	0.07	0.472	3.87	0.09	0.61	2remC	GO:0042597 GO:0045454
9	0.07	0.451	4.51	0.09	0.64	3a3tA	GO:0005623 GO:0045454
10	0.07	0.466	4.06	0.07	0.62	3gmfA	GO:0016020 GO:0016021 GO:0016853
11	0.07	0.471	3.42	0.07	0.58	4n30A	GO:0016853
12	0.07	0.471	3.21	0.15	0.58	3gykA
13	0.06	0.423	3.39	0.09	0.53	3bciA	GO:0016853
14	0.06	0.430	4.14	0.09	0.58	3l9vA	GO:0015035 GO:0016853 GO:0042597 GO:0045454 GO:0055114
15	0.06	0.414	3.68	0.06	0.53	2h0hB	GO:0003756 GO:0015035 GO:0042597 GO:0055114
16	0.06	0.402	3.33	0.09	0.50	4xvwL	GO:0005623 GO:0045454
17	0.06	0.402	4.14	0.07	0.54	3hd5A	GO:0015035 GO:0042597 GO:0045454 GO:0055114
18	0.06	0.282	6.87	0.05	0.53	4werA	GO:0000166 GO:0003951 GO:0008152 GO:0016301 GO:0016310

Consensus prediction of GO terms

Molecular Function	GO:0015035	GO:0019153	GO:0003756
GO-Score	0.07	0.07	0.07
Biological Processes	GO:0044710
GO-Score	0.37
Cellular Component	GO:0016021
GO-Score	0.34

(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.