I-TASSER results

I-TASSER results for job id Rv3241c

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

Input Sequence in FASTA format

>protein (214 residues)
MDSGQVLAEPKSNAEIVFKGRNVEIPDHFRIYVSQKLARLERFDRTIYLFDVELDHERNR
RQRKSCQRVEITARGRGPVVRGEACADSFYAALESAVVKLESRLRRGKDRRKVHYGDKTP
VSLAEATAVVPAPENGFNTRPAEAHDHDGAVVEREPGRIVRTKEHPAKPMSVDDALYQME
LVGHDFFLFYDKDTERPSVVYRRHAYDYGLIRLA

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| MDSGQVLAEPKSNAEIVFKGRNVEIPDHFRIYVSQKLARLERFDRTIYLFDVELDHERNRRQRKSCQRVEITARGRGPVVRGEACADSFYAALESAVVKLESRLRRGKDRRKVHYGDKTPVSLAEATAVVPAPENGFNTRPAEAHDHDGAVVEREPGRIVRTKEHPAKPMSVDDALYQMELVGHDFFLFYDKDTERPSVVYRRHAYDYGLIRLA
Prediction	CCCCCCCCCCCCCEEEEEEEEHCCCCHHHHHHHHHHHHHHHHHCCCCEEEEEEEEEHCCCCCCCCEEEEEEEEHCCCCEEEEEEHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEHCCCCCCHHHHHHHHHHCCCCEEEEEHCCCCCEEEEEHCCCCCEEEEHCC
Conf.Score	9887666777876699999986568899999999999999997789769999999956877788758999999959958999986798999999999999999999999999876567776644444556666566666666666666667777888689987556899999999999985799689998689998899999689987788779
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| MDSGQVLAEPKSNAEIVFKGRNVEIPDHFRIYVSQKLARLERFDRTIYLFDVELDHERNRRQRKSCQRVEITARGRGPVVRGEACADSFYAALESAVVKLESRLRRGKDRRKVHYGDKTPVSLAEATAVVPAPENGFNTRPAEAHDHDGAVVEREPGRIVRTKEHPAKPMSVDDALYQMELVGHDFFLFYDKDTERPSVVYRRHAYDYGLIRLA
Prediction	5754543755454040303045161364025105620530451265224040203134356466421202010417534030354263013003300520452045235434544456454535434533444554455444545446553476553421434426154032430143064372401002147474100001067350000248
	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

                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCCCCCCCCCCCEEEEEEEEHCCCCHHHHHHHHHHHHHHHHHCCCCEEEEEEEEEHCCCCCCCCEEEEEEEEHCCCCEEEEEEHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEHCCCCCCHHHHHHHHHHCCCCEEEEEHCCCCCEEEEEHCCCCCEEEEHCC
MDSGQVLAEPKSNAEIVFKGRNVEIPDHFRIYVSQKLARLERFDRTIYLFDVELDHERNRRQRKSCQRVEITARGRGPVVRGEACADSFYAALESAVVKLESRLRRGKDRRKVHYGDKTPVSLAEATAVVPAPENGFNTRPAEAHDHDGAVVEREPGRIVRTKEHPAKPMSVDDALYQMELVGHDFFLFYDKDTERPSVVYRRHAYDYGLIRLA

1n3gA

0.18

0.09

0.53

1.78

MUSTER

-------------MTMNITSKQMEITPAIRQHVADRLAKLEKWQTHLINPHIILSKEPQ------GFVADATINTPNGVLVASGKHEDMYTAINELINKLERQLNKLQHKGEARRAATSVKD----ANFVEEVEEE------------------------------------------------------------------------------

1n3gA

0.17

0.09

0.53

2.71

dPPAS

-------------MTMNITSKQMEITPAIRQHVADRLAKLEKWQTHLINPHIILSKEPQ------GFVADATINTPNGVLVASGKHEDMYTAINELINKLERQLNKLQHKGEARRAATSVKDANFVEEVEEE----------------------------------------------------------------------------------

1n3gA

0.17

0.09

0.53

3.89

wdPPAS

-------------MTMNITSKQMEITPAIRQHVADRLAKLEKWQTHLINPHIILSKEPQ------GFVADATINTPNGVLVASGKHEDMYTAINELINKLERQLNKLQHKGEARRAATSVKDANFVEEVEEE----------------------------------------------------------------------------------

1n3gA

0.17

0.09

0.53

2.27

wMUSTER

-------------MTMNITSKQMEITPAIRQHVADRLAKLEKWQTHLINPHIILSKEPQ------GFVADATINTPNGVLVASGKHEDMYTAINELINKLERQLNKLQHKGEARRAATSVKDANFVEEVEEE----------------------------------------------------------------------------------

1n3gA

0.18

0.09

0.53

3.40

wPPAS

-------------MTMNITSKQMEITPAIRQHVADRLAKLEKWQTHLINPHIILSKEPQ------GFVADATINTPNGVLVASGKHEDMYTAINELINKLERQLNKLQHKGEARRAATSVKDA---NFVEEVEEE-------------------------------------------------------------------------------

1n3gA

0.17

0.09

0.53

7.40

dPPAS2

-------------MTMNITSKQMEITPAIRQHVADRLAKLEKWQTHLINPHIILSKEPQ------GFVADATINTPNGVLVASGKHEDMYTAINELINKLERQLNKLQHKGEARRAATSVKDANFVEEVEEE----------------------------------------------------------------------------------

1n3gA

0.17

0.09

0.53

2.74

PPAS

-------------MTMNITSKQMEITPAIRQHVADRLAKLEKWQTHLINPHIILSKEPQ------GFVADATINTPNGVLVASGKHEDMYTAINELINKLERQLNKLQHKGEARRAATSVKDANFVEEVEEE----------------------------------------------------------------------------------

1n3gA

0.17

0.09

0.53

3.04

Env-PPAS

-------------MTMNITSKQMEITPAIRQHVADRLAKLEKWQTHLINPHIILSKEPQ------GFVADATINTPNGVLVASGKHEDMYTAINELINKLERQLNKLQHKGEARRAATSVKDANFVEEVEEE----------------------------------------------------------------------------------

1imuA

0.18

0.09

0.50

1.66

MUSTER

-------------MTLNITSKQMDITPAIREHLEERLAKLGKWQTQLISPHFVLNKVPN------GFSVEASIGTPLGNLLASATSDDMYKAINEVEEKLERQLNKLQHKSESRRADERLKDSFEN----------------------------------------------------------------------------------------

2rqlA

0.29

0.13

0.44

2.52

dPPAS

-------------MQLNITGNNVEITEALREFVTAKFAKLEQYFDRINQVYVVLKVEKVT------HTSDATLHVNGGEIHASAEGQDMYAAIDGLIDKLARQLTKHKDKLKQH----------------------------------------------------------------------------------------------------

(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=-2.76

Estimated TM-score = 0.40±0.13

Estimated RMSD = 11.9±4.4Å

Download Model 2

C-score=-2.70

Download Model 3

C-score=-2.86

Download Model 4

C-score=-3.11

Download Model 5

C-score=-3.20

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	1n3gA	0.480	1.89	0.168	0.528
2	1cruB	0.458	5.74	0.005	0.794
3	2y8nA	0.438	5.79	0.039	0.766
4	1yiqA1	0.437	5.82	0.026	0.766
5	4cvbA	0.435	5.50	0.032	0.743
6	5i2aA	0.432	5.89	0.061	0.766
7	1e5mA	0.430	5.39	0.037	0.720
8	5fauA	0.429	6.06	0.051	0.785
9	1vl4A	0.428	5.20	0.034	0.668
10	4uhwA	0.428	5.57	0.044	0.729

(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	0.15	4	3v2eY	NUC	Rep, Mult	17,18,19,20,22,30,36,39,43,46,48,49,53,58,65,72,74,76,81,82,83,91,94,99,102,103,105,106,108,109,110,112
2	0.11	3	3v28X	NUC	Rep, Mult	19,42,43,57,58,81,82,83,99,103,108,109,110,111,112,127
3	0.04	1	4x23P	III	Rep, Mult	98,101
4	0.04	1	4fylA	3CO	Rep, Mult	70,81,83
5	0.04	1	1c9uB	CA	Rep, Mult	175,177,186,203
6	0.04	1	4s1yA	CPT	Rep, Mult	99,204
7	0.04	1	1jb0M	CLA	Rep, Mult	92,96
8	0.04	1	4fylA	3CO	Rep, Mult	55,70

	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	1dgjA	0.411	6.11	0.022	0.752	1.2.-.-	39
2	0.060	3h8eA	0.414	5.46	0.101	0.682	3.4.11.1	NA
3	0.060	3fk5A	0.414	5.81	0.051	0.710	2.3.1.41	NA
4	0.060	1afwB	0.409	5.45	0.067	0.687	2.3.1.16	NA
5	0.060	2gp6A	0.411	5.37	0.078	0.692	2.3.1.41	168
6	0.060	1b3nA	0.421	5.37	0.059	0.706	2.3.1.179,2.3.1.41	NA
7	0.060	1jroB	0.424	5.58	0.040	0.715	1.1.1.204	NA
8	0.060	2pflA	0.422	5.80	0.053	0.743	2.3.1.54	170,195,200
9	0.060	2gqdA	0.425	5.54	0.063	0.729	2.3.1.179	28
10	0.060	2hb6B	0.378	5.45	0.061	0.640	3.4.11.1	76
11	0.060	2ac1A	0.409	5.12	0.016	0.664	3.2.1.26	44
12	0.060	1g72A	0.405	5.18	0.048	0.659	1.1.99.8	5
13	0.060	1c9uB	0.460	5.52	0.011	0.780	1.1.5.2,1.1.99.17	NA
14	0.060	1m21A	0.407	5.71	0.064	0.710	3.5.1.-	NA
15	0.060	1tqyA	0.423	5.57	0.063	0.729	2.3.1.41	NA
16	0.060	2ix4A	0.375	6.01	0.049	0.664	2.3.1.41	NA
17	0.060	2p0uA	0.410	5.89	0.066	0.720	2.3.1.74	107
18	0.060	2aeyA	0.409	5.55	0.017	0.692	3.2.1.80	NA
19	0.060	1kitA	0.410	5.70	0.064	0.710	3.2.1.18	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	0.25	0.401	1.61	0.29	0.43	4heiA	GO:0044238
1	0.20	0.371	2.09	0.36	0.42	2ywqC	GO:0044238
2	0.18	0.393	1.76	0.22	0.43	3tqmC	GO:0044238
3	0.17	0.480	1.89	0.17	0.53	1n3gA	GO:0003723 GO:0005829 GO:0006417 GO:0009409 GO:0019843 GO:0022627 GO:0043024 GO:0044238 GO:0045900 GO:0045947
4	0.16	0.387	2.20	0.28	0.44	2rqlA	GO:0005829 GO:0006417 GO:0017148 GO:0043022 GO:0043024 GO:0044238
5	0.09	0.413	2.08	0.16	0.46	1imuA	GO:0006417 GO:0044238
6	0.08	0.397	5.91	0.06	0.70	3a9gA	GO:0003824 GO:0005975 GO:0016901 GO:0046872 GO:0048038 GO:0055114
7	0.07	0.422	5.70	0.05	0.73	1cm5A	GO:0003824 GO:0005737 GO:0005829 GO:0005975 GO:0006006 GO:0006567 GO:0008152 GO:0008861 GO:0016020 GO:0016740 GO:0016746
8	0.06	0.410	5.88	0.03	0.72	2g8sA	GO:0003824 GO:0005509 GO:0005975 GO:0016491 GO:0016901 GO:0030288 GO:0046872 GO:0048038 GO:0055114 GO:0070968
9	0.06	0.460	5.52	0.01	0.78	1c9uB	GO:0003824 GO:0005975 GO:0008876 GO:0016491 GO:0016901 GO:0046872 GO:0048038 GO:0055114
10	0.06	0.341	5.69	0.03	0.58	3ho5B	GO:0003824 GO:0005576 GO:0005737 GO:0005886 GO:0005887 GO:0005975 GO:0007165 GO:0007224 GO:0007405 GO:0008270 GO:0009887 GO:0009953 GO:0009968 GO:0009986 GO:0016020 GO:0016901 GO:0040036 GO:0045879 GO:0046872 GO:0048038 GO:0048705 GO:0055114 GO:0060170 GO:0060441 GO:0097108
11	0.06	0.367	5.54	0.06	0.63	2wftB	GO:0003824 GO:0005576 GO:0005737 GO:0005886 GO:0005887 GO:0005975 GO:0007165 GO:0007224 GO:0007405 GO:0008270 GO:0009887 GO:0009953 GO:0009968 GO:0009986 GO:0016020 GO:0016901 GO:0040036 GO:0045879 GO:0046872 GO:0048038 GO:0048705 GO:0055114 GO:0060170 GO:0060441 GO:0097108
12	0.06	0.441	6.02	0.04	0.78	5bweA	GO:0003824 GO:0008152
13	0.06	0.337	5.67	0.04	0.58	2ismB	GO:0003824 GO:0005975 GO:0016901 GO:0046872 GO:0048038 GO:0055114
14	0.06	0.369	5.60	0.04	0.64	2wg4B	GO:0003824 GO:0005576 GO:0005737 GO:0005886 GO:0005887 GO:0005975 GO:0007165 GO:0007224 GO:0007405 GO:0008270 GO:0009887 GO:0009953 GO:0009968 GO:0009986 GO:0016020 GO:0016901 GO:0040036 GO:0045879 GO:0046872 GO:0048038 GO:0048705 GO:0055114 GO:0060170 GO:0060441 GO:0097108
15	0.06	0.398	5.82	0.05	0.70	3dasA	GO:0003824 GO:0005975 GO:0016901 GO:0046872 GO:0048038 GO:0055114
16	0.06	0.334	6.02	0.05	0.59	3cb2A	GO:0000086 GO:0000166 GO:0000212 GO:0000226 GO:0000242 GO:0000794 GO:0000930 GO:0003924 GO:0005200 GO:0005525 GO:0005737 GO:0005813 GO:0005814 GO:0005815 GO:0005827 GO:0005829 GO:0005856 GO:0005874 GO:0005876 GO:0005881 GO:0005929 GO:0007017 GO:0007020 GO:0031122 GO:0031252 GO:0031513 GO:0036064 GO:0045177 GO:0055037
17	0.06	0.336	5.92	0.03	0.60	2qc5A	GO:0000287 GO:0016835 GO:0017001 GO:0046677
18	0.06	0.419	6.10	0.07	0.76	2f3oA	GO:0003824 GO:0008152 GO:0016829

Consensus prediction of GO terms

Molecular Function	GO:0003723	GO:0043024
GO-Score	0.35	0.31
Biological Processes	GO:0017148	GO:0006446	GO:0006950	GO:0006448	GO:0009266
GO-Score	0.35	0.35	0.35	0.35	0.35
Cellular Component	GO:0015935	GO:0022626
GO-Score	0.35	0.35

(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.