I-TASSER results

I-TASSER results for job id Rv0679c

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

Input Sequence in FASTA format

>protein (165 residues)
MVEKPLRADRATHSRLATFALALAAAALPLAGCSSTANPPAATTTPATATTTTATSGPTA
APTVTTGESTTASIQIGDMLTYGSIGTTATLDCADGKSLNVAGSDNTLTVNGTCETVTVG
GANNKIAFDRIDERLVVVGLDNTVTYKNGDPTIDNLGAGNRINKE

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MVEKPLRADRATHSRLATFALALAAAALPLAGCSSTANPPAATTTPATATTTTATSGPTAAPTVTTGESTTASIQIGDMLTYGSIGTTATLDCADGKSLNVAGSDNTLTVNGTCETVTVGGANNKIAFDRIDERLVVVGLDNTVTYKNGDPTIDNLGAGNRINKE
Prediction	CCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEHCCCEEEEHCCCCCEEEEEHCCCEEEEEEEEEEEEEEHCCCEEEEEEHCCEEEEEHCCCEEEHCCCCCEEHCCCCCCEEEHC
Conf.Score	988776555445554578889988888754566677888888888888888888888888887677888877677888679998585899987999879999758789999887589998568689997666779999858589977999756647898678859
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MVEKPLRADRATHSRLATFALALAAAALPLAGCSSTANPPAATTTPATATTTTATSGPTAAPTVTTGESTTASIQIGDMLTYGSIGTTATLDCADGKSLNVAGSDNTLTVNGTCETVTVGGANNKIAFDRIDERLVVVGLDNTVTYKNGDPTIDNLGAGNRINKE
Prediction	746442534432443011002132332231222333454544444443444444544444444444455553536444423133344544141654430303144130203040440203236140204403540303134120214535140353346243558
	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

CCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEHCCCEEEEHCCCCCEEEEEHCCCEEEEEEEEEEEEEEHCCCEEEEEEHCCEEEEEHCCCEEEHCCCCCEEHCCCCCCEEEHC
MVEKPLRADRATHSRLATFALALAAAALPLAGCSSTANPPAATTTPATATTTTATSGPTAAPTVTTGESTTASIQIGDMLTYGSIGTTATLDCADGKSLNVAGSDNTLTVNGTCETVTVGGANNKIAFDRIDERLVVVGLDNTVTYKNGDPTIDNLGAGNRINKE

1go7P

0.15

0.96

0.97

wMUSTER

WGENETGADYNGHYGGAPMIDDIAAIQRLYGANMTTRTGD----SVYGFNSNTDRDFYTATDSSKALIFSVWDAGGTDTFDFSGYSNNQRINLNEGSFSDVGGLKGNVSIAHGVTIENAIGGNDILVGNSADNILQGGAGNDVLYGGAGADTLY-GGAGRTFV-S

3ljyA2

0.15

0.12

0.77

0.97

wPPAS

-VNSPLTGDE---------------TVIKANANSLV-------------QLKETVTVGKLDLNVSGSANVVNHLEADKECDIDGSG---SITIKKGNDYSIVSSG-DIHLAVPQLSCKVTGNGLEVHATDN--KANVVGKG-NIRYK-GPTAVQQIGKG-TVEEK

3wprA

0.18

0.17

0.95

1.02

dPPAS2

IENEIARIKKLIKAVGNQVVTTQTTLVNSLGG-NAKVNADGTITGPTYNVAQGNQTNVGDALTALDNAINTAATTSKSTVSNGQNIVVSKSKNADGSDNYEVSTAKDLTVD------SVKAGDTVLNNAGITIGNNAVVLNNTGLTISGGPSVTLAGIDAG-NKT

3jx8A2

0.28

0.20

0.73

0.96

wPPAS

-ISKPVNR-------------------EINAGSGNV-------------ELRGPVKGYKLECNAGSGNIIAKDIQ-LDNLSCASSG---EIE--IGTSFNVAGSG-EIKCQARKAECNIASSGESVYATQI--DANIVG-SGEIHYK-GDPEISKIGSG-SINKV

4uicA

0.15

0.99

0.86

MUSTER

VNQYVSKVTDAFKAELQKAAQDAKAAYEAALTPKVESVSAIDSTSFKVTFTKPVDKATAIPKNFSITLKGTETKLYPKSVEVSESGLTATVTLYDGKTYTVVTSGLKDT-EFETSTNEFTYNKPVPASITFNFNKLPEDSAVDVTVKDAAGNVIKSGFELEFTSS

2kb4A

0.13

0.10

0.79

0.74

dPPAS

-----------------------------MSDNNGTPEPQVETTSVFRADLLKEMESSTGTAPASTGAENLPAGGPNAGARFLLDQPTTTAGRHPESDIFLDDVTVEFRINEGEFEVVDVGSLNGTYVNREPRNAQVMQTGDEIQIGKFRLVFLAGPAE------

3jx8A2

0.15

0.12

0.79

0.89

wdPPAS

-ISKPVNR-------------------EINAGSGNVE----LRGPVKGYKLECNAGSGNIIAKDIQLDNLSCSLASSGEIEVIGTVDRASFNVAGSGEIKAFD------CQARKAECNIASSGESVYATQI--DANIVG-SGEIHYK-GDPEISKSIGSGSINKV

1aklA

0.11

0.10

0.97

0.93

wMUSTER

MSYWETGQDFKGAYSSAPLLDDIAAIQKLYGANLTTRTGDTVYGFNSNTERDFYSATSSSSKLVFS----VWDAGGNDTLDFSGFSQNQKINLNEKALSDVGGLKGNVSIAAGVTVENAIGGSDLLIGNDVANVLKGGAGNDILYGGLGADQLW-GGAGATFVGD

3petA2

0.21

0.13

0.63

0.91

wPPAS

-IENGLTTDNL----------------IESKGVGNV----------------------------------DIQSLTCQLNVQSGVG-DVKLE---GTALHSKGVGN-IELRANAVEASSQGVGDTCNATES--DAAVRGVGS-IKYK-GSPTIKSKGVGT-IKNI

2kb4A

0.17

0.12

0.68

0.97

dPPAS2

---------------------------------MSDNNGTPEPQVETTSVFRADLLKEMESSTGTAPASTGAENLPAGSALLVVKRGP-----NAGARFLLDQP-----------TTTAGHPESDIFL----DDVTVSRRHAEFRINEGEFEVVDVGSLNYVNRE

(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=-1.76

Estimated TM-score = 0.50±0.15

Estimated RMSD = 8.8±4.6Å

Download Model 2

C-score=-4.41

Download Model 3

C-score=-4.19

Download Model 4

C-score=-5.00

Download Model 5

C-score=-4.69

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	1go7P	0.730	3.25	0.112	0.970
2	1srpA	0.729	3.22	0.126	0.964
3	1omjA	0.728	3.27	0.094	0.970
4	1aklA	0.727	3.29	0.087	0.970
5	3vstA	0.528	4.72	0.076	0.849
6	1ogmX	0.521	4.57	0.029	0.800
7	1qcxA	0.519	4.52	0.034	0.806
8	1vblA	0.517	4.91	0.076	0.836
9	3gqnA1	0.514	4.55	0.085	0.794
10	2vdcA	0.513	4.51	0.116	0.830

(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	0.04	2	2vdcA	F3S	Rep, Mult	93,99,114,117,129,130
2	0.04	2	3jcuA	CLA	Rep, Mult	23,117
3	0.04	2	3sucA	ATP	Rep, Mult	92,114,115,133,134,135,136
4	0.04	2	2iq7A	UUU	Rep, Mult	124,128,143,145,160
5	0.04	2	2chrA	MN	Rep, Mult	92,127,147,148
6	0.04	2	4l6vK	CLA	Rep, Mult	16,17,20
7	0.04	2	1izlD	PHO	Rep, Mult	20,21,24,25
8	0.02	1	3t6vB	CBS	Rep, Mult	55,150,152,157
9	0.02	1	4u6sA	FMT	Rep, Mult	88,124,141,143,160
10	0.02	1	3i8wA	CB5	Rep, Mult	119,120,126,151,153
11	0.02	1	3ufnB	ROC	Rep, Mult	103,105
12	0.02	1	2qciB	065	Rep, Mult	92,103,104,105,106,120,121,122,153
13	0.02	1	2v8vD	URP	Rep, Mult	121,160
14	0.02	1	1dk5A	SO4	Rep, Mult	13,104,105,106
15	0.02	1	1rq9A	DMQ	Rep, Mult	155,157
16	0.02	1	1fbmD	RTL	Rep, Mult	16,23
17	0.02	1	2upjB	U02	Rep, Mult	92,94,95,96,120,121,151,153
18	0.02	1	1yfqA	CA	Rep, Mult	111,112

	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	1ru4A	0.492	4.55	0.074	0.746	4.2.2.2	NA
2	0.060	3eqoA	0.515	4.93	0.067	0.867	3.2.1.58	NA
3	0.060	1airA	0.498	4.62	0.065	0.770	4.2.2.2	78
4	0.060	1go7P	0.730	3.25	0.112	0.970	3.4.24.-	4
5	0.060	2pecA	0.510	4.65	0.058	0.751	4.2.2.2	122
6	0.060	1ogoX	0.491	4.59	0.043	0.782	3.2.1.11	123
7	0.060	1dceA	0.475	4.51	0.054	0.751	2.5.1.60	NA
8	0.060	1aklA	0.727	3.29	0.087	0.970	3.4.24.40	NA
9	0.060	1idjA	0.467	4.59	0.047	0.721	4.2.2.10	92
10	0.060	2qx3A	0.505	4.68	0.050	0.764	4.2.2.2	92
11	0.060	1pclA	0.477	4.53	0.045	0.751	4.2.2.2	161
12	0.060	3dsxA	0.387	3.99	0.049	0.570	2.5.1.60	NA
13	0.060	1llwA	0.475	5.41	0.097	0.873	1.4.7.1	NA
14	0.060	2vncB	0.332	5.97	0.041	0.661	3.2.1.-	75
15	0.060	1xg2A	0.491	5.29	0.067	0.836	3.1.1.11	NA
16	0.060	2wanA	0.501	4.81	0.075	0.830	3.2.1.41	NA
17	0.060	1omjA	0.728	3.27	0.094	0.970	3.4.24.40	NA
18	0.060	1kcdA	0.476	4.51	0.073	0.721	3.2.1.15	92
19	0.060	1oocB	0.477	4.93	0.071	0.782	4.2.2.2	124,144,164

(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	0.14	0.727	3.29	0.09	0.97	1aklA	GO:0001869 GO:0004222 GO:0005509 GO:0005576 GO:0005615 GO:0006508 GO:0008233 GO:0008237 GO:0008270 GO:0009405 GO:0010765 GO:0016787 GO:0045959 GO:0046872
1	0.13	0.730	3.25	0.11	0.97	1go7P	GO:0004222 GO:0005509 GO:0005576 GO:0005615 GO:0006508 GO:0008233 GO:0008237 GO:0008270 GO:0016787 GO:0031012 GO:0046872
2	0.13	0.728	3.27	0.09	0.97	1omjA	GO:0004222 GO:0005509 GO:0005615 GO:0006508 GO:0008237 GO:0008270 GO:0016787 GO:0046872
3	0.12	0.730	3.21	0.13	0.96	1af0A	GO:0004222 GO:0005509 GO:0005576 GO:0005615 GO:0006508 GO:0008233 GO:0008237 GO:0008270 GO:0009405 GO:0016787 GO:0031012 GO:0046872
4	0.10	0.686	3.45	0.10	0.93	3hdaP	GO:0004222 GO:0005509 GO:0005576 GO:0005615 GO:0006508 GO:0008233 GO:0008237 GO:0008270 GO:0016787 GO:0031012 GO:0046872
5	0.06	0.363	4.38	0.05	0.53	2ifyA	GO:0003824 GO:0004619 GO:0005737 GO:0006007 GO:0006096 GO:0008152 GO:0016853 GO:0030145 GO:0030435 GO:0043937 GO:0046537 GO:0046872
6	0.06	0.334	5.26	0.05	0.59	2agmA	GO:0005576 GO:0005615 GO:0016853 GO:0042121
7	0.06	0.407	5.64	0.07	0.73	2quaA	GO:0004806 GO:0016787 GO:0046872
8	0.06	0.440	5.20	0.05	0.73	3a6zC	GO:0005509 GO:0046872
9	0.06	0.344	3.05	0.11	0.44	2ml3A	GO:0005509 GO:0005576 GO:0005615 GO:0016853 GO:0042121
10	0.06	0.330	5.06	0.02	0.56	3k7nA	GO:0004222 GO:0005576 GO:0006508 GO:0008233 GO:0008237 GO:0008270 GO:0016787 GO:0046872
11	0.06	0.377	4.66	0.04	0.59	5cvwA	GO:0000166 GO:0004016 GO:0005509 GO:0005516 GO:0005524 GO:0005576 GO:0006171 GO:0008294 GO:0009405 GO:0016829 GO:0019835 GO:0044179
12	0.06	0.313	5.25	0.04	0.54	1r54A	GO:0004222 GO:0006508 GO:0008233 GO:0008237 GO:0008270 GO:0016020 GO:0016021 GO:0016787 GO:0046872
13	0.06	0.319	5.17	0.07	0.55	4j4mB	GO:0004222 GO:0006508 GO:0008237 GO:0046872
14	0.06	0.284	6.03	0.06	0.54	1su3B	GO:0004175 GO:0004222 GO:0004252 GO:0005509 GO:0005576 GO:0005578 GO:0006508 GO:0008233 GO:0008237 GO:0008270 GO:0016032 GO:0016787 GO:0022617 GO:0030574 GO:0031012 GO:0032461 GO:0044267 GO:0046872 GO:0050900
15	0.06	0.328	5.30	0.03	0.58	3gboA	GO:0004222 GO:0005576 GO:0006508 GO:0008233 GO:0008237 GO:0016787 GO:0046872
16	0.06	0.333	5.41	0.04	0.60	2rjqA	GO:0004222 GO:0005178 GO:0005576 GO:0005578 GO:0005615 GO:0005788 GO:0006508 GO:0008201 GO:0008233 GO:0008237 GO:0008270 GO:0016787 GO:0022617 GO:0031012 GO:0036066 GO:0042742 GO:0046872 GO:0050840
17	0.06	0.320	5.49	0.05	0.58	1wniA	GO:0004222 GO:0005576 GO:0006508 GO:0008233 GO:0008237 GO:0016787 GO:0046872
18	0.06	0.276	5.47	0.05	0.51	2r5oA	GO:0000166 GO:0005524 GO:0016887

Consensus prediction of GO terms

Molecular Function	GO:0004222	GO:0005509	GO:0008270
GO-Score	0.49	0.49	0.49
Biological Processes	GO:0051704	GO:0006508
GO-Score	0.50	0.49
Cellular Component	GO:0005615	GO:0031012
GO-Score	0.49	0.32

(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.