I-TASSER results

I-TASSER results for job id Rv1944c

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

Input Sequence in FASTA format

>protein (196 residues)
MISDTEDFAHGDKAAPPRLRASYAACGGDAAGCWTMSDNGASRVPPVDETPAAESAEPIT
AVSLAWLPAGDYERALDLWPDFAGSDLVTGPDGPVAHPLYCRRMQQKLVEFAEAGFPGLA
VAAIRVAPFAAWCAEQGQEPDSPEARAEYAAYLTAHGDHDVMAWPPGRNQQCWCGSGHKY
KKCCAAASFIDTEPAP

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| MISDTEDFAHGDKAAPPRLRASYAACGGDAAGCWTMSDNGASRVPPVDETPAAESAEPITAVSLAWLPAGDYERALDLWPDFAGSDLVTGPDGPVAHPLYCRRMQQKLVEFAEAGFPGLAVAAIRVAPFAAWCAEQGQEPDSPEARAEYAAYLTAHGDHDVMAWPPGRNQQCWCGSGHKYKKCCAAASFIDTEPAP
Prediction	CCCCCHHHCCCCCCCCCHHHHHHHHCCCCCCCCEHCCCCCHHHCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCHHHHEHCCCCCHHHHHHHHCCCCCCCHHHCCHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCCCC
Conf.Score	9887555456787888555667776467766654557777455676545555556665577888876688999999999998764556777788886899999999999998765444434334454566666545678888566445554444457877778999889999999996555545775545788899
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| MISDTEDFAHGDKAAPPRLRASYAACGGDAAGCWTMSDNGASRVPPVDETPAAESAEPITAVSLAWLPAGDYERALDLWPDFAGSDLVTGPDGPVAHPLYCRRMQQKLVEFAEAGFPGLAVAAIRVAPFAAWCAEQGQEPDSPEARAEYAAYLTAHGDHDVMAWPPGRNQQCWCGSGHKYKKCCAAASFIDTEPAP
Prediction	7354365134356333441434233133412101223453256344565464454444031101211346314402530451345442444743252633145045424524554343233143425424433456545354462345224423454564346443656440202455515612314433646658
	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

CCCCCHHHCCCCCCCCCHHHHHHHHCCCCCCCCEHCCCCCHHHCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCHHHHEHCCCCCHHHHHHHHCCCCCCCHHHCCHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCCCC
MISDTEDFAHGDKAAPPRLRASYAACGGDAAGCWTMSDNGASRVPPVDETPAAESAEPITAVSLAWLPAGDYERALDLWPDFAGSDLVTGPDGPVAHPLYCRRMQQKLVEFAEAGFPGLAVAAIRVAPFAAWCAEQGQEPDSPEARAEYAAYLTAHGDHDVMAWPPGRNQQCWCGSGHKYKKCCAAASFIDTEPAP

4uosA

0.09

0.08

0.94

0.97

MUSTER

--GDNEEVKKMLEKMIEEIKKMLEKAIKKVKEMLEKMIKEIKKMLENGEDSEKILKKKEMAEKILKMVIELAEKILKKAKEMAEKILKKVKELGVDNEEVKKMLEKMIEEIKKMLEKAIKKVKEMLEKMIKEIKKMLENGEDSEKILKKAKEMAEKILKMVIELAEKI---------KKAKEMAEKILKKVKELGV

3dinA2

0.08

0.05

0.64

0.85

dPPAS

IFEDSTRVEEFCSGKNWDIESLKNSLSFFPAGLFDLDEKQLWEEYQRKKQEIGEDYRKVIRFLMLRIIDDHWRRYLEEVEHVKEAVQLRSYGQKDPIVEFKKETYYMFDEMMRRINDTIANYVLRV----------------------------------------------------------------------

3dinA2

0.10

0.06

0.60

1.79

wdPPAS

CSGKNWDI--------ESLKNSLSFFPADLDEKQFSSSELWEEYQRKKQEIG-EDYRKVIRFLMLRIIDDHWRRYLEEVEHVKEAVQLRSYGQKDPIVEFKKETYYMFDEMMRRINDTIANYVLRV----------------------------------------------------------------------

2i9wA

0.15

0.12

0.79

1.05

wMUSTER

FSIQT----INPALNAVSTPLLYQDC-------------QPYHDGLYNQAIRADTAEHLRTRYSAFVLVK--PEYIVKTPAQQDLLD-------------IKAIENWAKETDWAGLEVVAHTPKLSKRHAQVEFKTPDGLQAHHELSTFVKIKNKANSDDPTVSSVTQKQPCICGSGEKFKRCCGYI---------

3dinA2

0.10

0.06

0.63

2.23

wPPAS

IFED-STRVEEFCSG-ESLKNSLSFFPADLDEKQFSSSELWEEYQRKKQEIG-EDYRKVIRFLMLRIIDDHWRRYLEEVEHVKEAVQLRSYGQKDPIVEFKKETYYMFDEMMRRINDTIANYVLRV----------------------------------------------------------------------

3dl8A2

0.07

0.04

0.58

1.88

dPPAS2

LDEGALEKSDIFGKEPDEMLELIMDRI-------------ITKYNEKEEQFGKEQMREFEKVIVLRAVDSKWMDHIDAMDQLRQGIHLRAYAQTNPLREYQMEGFAMFEHMIESIEDEVAKFVMKA----------------------------------------------------------------------

3dinA2

0.10

0.06

0.63

1.56

PPAS

IFED-STRVEEFCSG-ESLKNSLSFFPADLDEKQFSSSELWEEYQRKKQEIG-EDYRKVIRFLMLRIIDDHWRRYLEEVEHVKEAVQLRSYGQKDPIVEFKKETYYMFDEMMRRINDTIANYVLRV----------------------------------------------------------------------

3dinA2

0.10

0.06

0.64

1.91

Env-PPAS

IFEDVSTRVEEFCSGKESLKNSLSFFPADLDEKQFSSSEELHDYQRKKQEIG-EDYRKVIRFLMLRIIDDHWRRYLEEVEHVKEAVQLRSYGQKDPIVEFKKETYYMFDEMMRRINDTIANYVLRV----------------------------------------------------------------------

4ke2A

0.19

0.18

0.98

0.90

MUSTER

MNIDAAAAAAASKAAVTAADAAAAAATIAASAASVAAATAADDAAASIATINAASAAAKSIAAAAAMAAKDTAAAAASAAAAAVASAAKALETINVKAAYAAATTANTAAAAAAATATTAAAAAAAKATIDNAAAAKAAAVATAVSDAAATAATAAAVAAATLEAAAAKAA----ATAVSAAAAAAAAAIAFAAAP

3dl8A2

0.07

0.04

0.58

0.81

dPPAS

LDEGALEKSDIFGKEPDEMLELIMDRI-------------ITKYNEKEEQFGKEQMREFEKVIVLRAVDSKWMDHIDAMDQLRQGIHLRAYAQTNPLREYQMEGFAMFEHMIESIEDEVAKFVMKA----------------------------------------------------------------------

(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=-3.22

Estimated TM-score = 0.35±0.12

Estimated RMSD = 12.8±4.2Å

Download Model 2

C-score=-3.34

Download Model 3

C-score=-3.73

Download Model 4

C-score=-3.41

Download Model 5

C-score=-3.74

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	4mt1A	0.499	5.15	0.059	0.806
2	3ba6A	0.486	5.30	0.055	0.816
3	3jd8A3	0.484	4.71	0.036	0.719
4	3gvdI	0.483	4.68	0.091	0.709
5	2e4xB	0.477	5.06	0.054	0.791
6	2y8nA	0.477	5.64	0.073	0.867
7	3mc4A	0.476	4.54	0.091	0.689
8	4av3A	0.475	4.97	0.033	0.755
9	3pflA	0.473	5.32	0.071	0.801
10	3dl8A	0.473	4.03	0.057	0.622

(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	0.18	10	2ysaA	ZN	Rep, Mult	172,174,178,183
2	0.04	2	4tt0A	IOD	Rep, Mult	74,75,78
3	0.04	2	3u32N	DCW	Rep, Mult	109,116
4	0.04	2	3ar3A	PTY	Rep, Mult	65,68,72,76,195
5	0.02	1	4g28B	0W8	Rep, Mult	87,88
6	0.02	1	3zjsA	AZI	Rep, Mult	66,126,184
7	0.02	1	2agvA	PTY	Rep, Mult	78,82,85,86
8	0.02	1	3ar4A	PTY	Rep, Mult	62,69,73
9	0.02	1	3swfB	ZN	Rep, Mult	54,58
10	0.02	1	2q6qA	CO	Rep, Mult	73,77
11	0.02	1	2eauA	PTY	Rep, Mult	3,60,64,68
12	0.02	1	5d91A	8K6	Rep, Mult	72,73
13	0.02	1	1crxB	NUC	Rep, Mult	103,107
14	0.02	1	3ar3A	PTY	Rep, Mult	57,61,64,65
15	0.02	1	4yiyA	MG	Rep, Mult	176,177

	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	3b8cA	0.463	5.51	0.059	0.811	3.6.3.6	NA
2	0.060	1no3A	0.452	5.32	0.056	0.755	1.13.11.12	NA
3	0.060	3mc4A	0.476	4.54	0.091	0.689	2.3.1.30	NA
4	0.060	2qb0B	0.303	5.54	0.039	0.520	3.2.1.17	NA
5	0.060	1t3qB	0.460	5.46	0.043	0.791	1.3.99.17	NA
6	0.060	1h16A	0.476	5.34	0.071	0.806	2.3.1.54	NA
7	0.060	3n58A	0.440	5.36	0.042	0.730	3.3.1.1	157
8	0.060	1ssqD	0.485	4.65	0.050	0.709	2.3.1.30	NA
9	0.060	2iukA	0.440	5.98	0.033	0.816	1.13.11.12	NA
10	0.060	1vncA	0.460	5.34	0.070	0.750	1.11.1.10	106
11	0.060	3ixzA	0.468	5.55	0.045	0.796	3.6.3.10	NA
12	0.060	2d0tB	0.442	4.88	0.061	0.684	1.13.11.52	91
13	0.060	3b8eC	0.464	5.70	0.060	0.816	3.6.3.9	120
14	0.060	3b8eA	0.464	5.76	0.049	0.827	3.6.3.9	NA
15	0.060	3d64A	0.443	5.18	0.029	0.725	3.3.1.1	NA
16	0.060	3d64B	0.447	5.38	0.034	0.745	3.3.1.1	64,157
17	0.060	3b9jJ	0.326	5.79	0.044	0.587	1.17.1.4,1.17.3.2	NA
18	0.060	2e1qA	0.447	5.38	0.036	0.770	1.17.3.2,1.17.1.4	NA
19	0.060	3b8cB	0.473	5.47	0.076	0.821	3.6.3.6	169

(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	0.20	0.464	5.76	0.05	0.83	3b8eA	GO:0000166 GO:0002028 GO:0005391 GO:0005524 GO:0005886 GO:0005890 GO:0006810 GO:0006811 GO:0006813 GO:0006814 GO:0006883 GO:0010107 GO:0010248 GO:0015991 GO:0016020 GO:0016021 GO:0016787 GO:0030007 GO:0030955 GO:0031402 GO:0036376 GO:0042383 GO:0043231 GO:0046872 GO:0051117 GO:0086009 GO:0090662 GO:1990573
1	0.07	0.472	5.50	0.03	0.82	3w5bA	GO:0000166 GO:0005388 GO:0005509 GO:0005524 GO:0005783 GO:0005789 GO:0005793 GO:0006810 GO:0006811 GO:0006816 GO:0006942 GO:0016020 GO:0016021 GO:0016529 GO:0016787 GO:0031448 GO:0031673 GO:0031674 GO:0033017 GO:0045988 GO:0046872 GO:0048471 GO:0070588
2	0.07	0.463	4.71	0.05	0.70	3a3yA	GO:0000166 GO:0005391 GO:0005524 GO:0006810 GO:0006811 GO:0006813 GO:0006814 GO:0010248 GO:0016020 GO:0016021 GO:0016787 GO:0046872 GO:0090662
3	0.07	0.468	5.55	0.04	0.80	3ixzA	GO:0000166 GO:0000287 GO:0005391 GO:0005524 GO:0005886 GO:0005887 GO:0006810 GO:0006811 GO:0006813 GO:0006814 GO:0006883 GO:0008900 GO:0010107 GO:0010248 GO:0015991 GO:0015992 GO:0016020 GO:0016021 GO:0016787 GO:0030007 GO:0036376 GO:0043231 GO:0046872
4	0.07	0.419	5.85	0.06	0.73	4k0eC	GO:0005215 GO:0006810 GO:0006812 GO:0008324 GO:0016020 GO:0016021 GO:0098655
5	0.07	0.420	5.86	0.06	0.76	3nogA	GO:0005215 GO:0005886 GO:0005887 GO:0006810 GO:0006855 GO:0015238 GO:0015307 GO:0016020 GO:0016021 GO:0042493 GO:0042802 GO:0046618
6	0.07	0.463	5.51	0.06	0.81	3b8cA	GO:0000166 GO:0000287 GO:0005524 GO:0005886 GO:0005887 GO:0006754 GO:0006810 GO:0006811 GO:0008553 GO:0015991 GO:0015992 GO:0016020 GO:0016021 GO:0016787 GO:0016887 GO:0046872 GO:0051453
7	0.07	0.445	5.67	0.06	0.78	4k0eB	GO:0005215 GO:0006810 GO:0006812 GO:0008324 GO:0016020 GO:0016021 GO:0098655
8	0.07	0.407	5.64	0.07	0.71	1mhsA	GO:0000166 GO:0005524 GO:0005886 GO:0005887 GO:0006754 GO:0006810 GO:0006811 GO:0008553 GO:0015992 GO:0016020 GO:0016021 GO:0016787 GO:0016887 GO:0043231 GO:0046872 GO:0051453 GO:1902600
9	0.07	0.464	5.21	0.08	0.76	3w9iF	GO:0005215 GO:0005886 GO:0006810 GO:0006855 GO:0015238 GO:0016020 GO:0016021 GO:0046677
10	0.06	0.499	5.15	0.06	0.81	4mt1A	GO:0005215 GO:0006810 GO:0016020 GO:0016021
11	0.06	0.403	4.82	0.05	0.60	2v50D	GO:0005215 GO:0005886 GO:0006810 GO:0006855 GO:0015238 GO:0016020 GO:0016021 GO:0046677
12	0.06	0.419	5.89	0.06	0.77	3d9bA	GO:0005215 GO:0005886 GO:0005887 GO:0006810 GO:0006855 GO:0015238 GO:0015307 GO:0016020 GO:0016021 GO:0042493 GO:0042802 GO:0046618
13	0.06	0.394	5.19	0.05	0.63	4k0eA	GO:0005215 GO:0006810 GO:0006812 GO:0008324 GO:0016020 GO:0016021 GO:0098655
14	0.06	0.421	5.13	0.05	0.70	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
15	0.06	0.443	5.31	0.06	0.76	4bbjA	GO:0000166 GO:0005886 GO:0006812 GO:0016020 GO:0016021 GO:0016787 GO:0019829 GO:0046872 GO:0098655
16	0.06	0.350	5.67	0.04	0.63	1nrwA	GO:0005737 GO:0016311 GO:0016787 GO:0016791 GO:0044283 GO:0046872
17	0.06	0.326	4.79	0.05	0.52	1u3iA	GO:0004364 GO:0016740
18	0.06	0.417	5.80	0.07	0.76	4umvA	GO:0000166 GO:0005886 GO:0006812 GO:0016020 GO:0016021 GO:0016787 GO:0019829 GO:0030001 GO:0046872 GO:0098655

Consensus prediction of GO terms

Molecular Function	GO:0019899	GO:0031420	GO:0005524	GO:0005391
GO-Score	0.41	0.41	0.35	0.31
Biological Processes	GO:0055078	GO:0071805	GO:0071436	GO:0006875	GO:0015988	GO:0030004	GO:0055075	GO:0010959	GO:0042391	GO:0098739	GO:0010248
GO-Score	0.51	0.51	0.51	0.51	0.51	0.51	0.51	0.41	0.41	0.41	0.31
Cellular Component	GO:0043229	GO:0043227	GO:0090533	GO:0098797	GO:0005887
GO-Score	0.51	0.51	0.41	0.41	0.41

(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.