I-TASSER results

I-TASSER results for job id Rv1499

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

Input Sequence in FASTA format

>protein (132 residues)
MPSGEPSTAGHFEHLPRGSFGRILSVLNAAADHHPRELLVVGIATFDQKRPAVGVDEHDP
GGAATPAVVINYESRSSAGGTIGHSTTSQVACCLYQQPKRPALRPTKAAATTAATTWIER
VQNRRGRHSALV

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MPSGEPSTAGHFEHLPRGSFGRILSVLNAAADHHPRELLVVGIATFDQKRPAVGVDEHDPGGAATPAVVINYESRSSAGGTIGHSTTSQVACCLYQQPKRPALRPTKAAATTAATTWIERVQNRRGRHSALV
Prediction	CCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCEEEEEEEEHCCCCCCCCCCCCCCCCCCCCCEEEEEHCCCCCCCCCCCCCCCCCEEEEEHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCC
Conf.Score	999998877654457887566789988887656888579988754567888767778898877787789875566778875556777635776545899888764455666677899999998765544579
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MPSGEPSTAGHFEHLPRGSFGRILSVLNAAADHHPRELLVVGIATFDQKRPAVGVDEHDPGGAATPAVVINYESRSSAGGTIGHSTTSQVACCLYQQPKRPALRPTKAAATTAATTWIERVQNRRGRHSALV
Prediction	756454633431441353312301410432364323300000013145633334246344433323111031444543323234433430000015437433244353344431331153047454544337
	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

                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCEEEEEEEEHCCCCCCCCCCCCCCCCCCCCCEEEEEHCCCCCCCCCCCCCCCCCEEEEEHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCC
MPSGEPSTAGHFEHLPRGSFGRILSVLNAAADHHPRELLVVGIATFDQKRPAVGVDEHDPGGAATPAVVINYESRSSAGGTIGHSTTSQVACCLYQQPKRPALRPTKAAATTAATTWIERVQNRRGRHSALV

4ienA

0.17

0.16

0.95

0.72

MUSTER

LPSHELIMSELMMTAFSGNGGELLLLLDQVA-YSGNYCVTLSVDKVLFKEPIIGDL-----GRTSMEIGIRVEAQNIRTGEIRHTNSCYFTMVAVKDGKPPPLEILTDRQRCRYEKAKKRRDISLQASEDMS

4ienA

0.20

0.19

0.93

0.57

dPPAS

LPSHEPDTANFSGNV---HGGELLLLLDQVAYYSGNYCVTLSVDKVLFKEPI------HIGDLVTFYAAVNYTGRTSRTGEIRHTNSCYFTMVAVKDGKPPPLEILTDRQRCRYEKAKKRRDISLQASEDMS

4ienA

0.20

0.18

0.92

0.60

wdPPAS

LPSHEPDTANFSGNV---HGGELLLLLDQVA-YSGNYCVTLSVDKVLFKEPIIGV------GRTSMEIGIRVEAQNIRTGEIRHTNSCYFTMVAVKDGK-PPLEILTDRQRCRYEKAKKRRDISLQASEDMS

4ienA

0.19

0.17

0.93

0.77

wMUSTER

LPSHEPDTANFSGNV---HGGELLLLLDQVA-YSGNYCVTLSVDKVLFKEPIIGDL-----GRTSMEIGIRVEAQNIRTGEIRHTNSCYFTMVAVKDGKPPPLEILTDRQRCRYEKAKKRRDISLQASEDMS

4kt3B

0.24

0.19

0.78

0.48

wPPAS

--SLQPA------RIKDS--G--LT--REQA----EQVLRVAL--YQLQRPGVFIDQDENGKPPHPDFSLGYND-PKAGATVSLNTGDEINSC-----KRAELRALQRRVARTGKSLADEKSQREG---GCE

4ienA

0.20

0.19

0.93

0.56

dPPAS2

LPSHEPDTANFSGNV---HGGELLLLLDQVAYYSGNYCVTLSVDKVLFKEPI------HIGDLVTFYAAVNYTGRTSRTGEIRHTNSCYFTMVAVKDGKPPPLEILTDRQRCRYEKAKKRRDISLQASEDMS

1ouqA1

0.21

0.17

0.79

0.57

PPAS

LPA--PVDATSDEVRKN--LMDMFRDRQAFSEH--WKMLLSVCRSWLNNRKWF------P---AEPEDVRDYRGLAVK--TIQQGQLNM----LHRRSGLP--RPSDSNAVSLVMRRIRKENVDAGE-----

3hzsA1

0.22

0.18

0.83

0.69

Env-PPAS

----------NLYFQGHMDVDELRKIENVSADNMPEYVKGAFISMQD-ER----FYNHDLKGTTR-ALFSTISDRDVQGGTI----TQQVVKNYFYDNDR-SF--TRKVKELFVAHRVEKQYNKNEILSFYL

4kt3B

0.14

0.13

0.91

0.71

MUSTER

--SLQPARIKD-SGLTREQAEQVLRVALKHQDYQLQRVFIDGDLQDENGKPP-----H-PG---YYDFSLGYNDPKAGATEYGLSVSLNTGDTWEINSCKRLDGAELRALQRRVARTGKSLADEKSQREGLG

2v6gA1

0.17

0.14

0.82

0.55

dPPAS

-----SSVAG-----VTGIIGNSLAEILPLADTPGGPWKVYGVAR----RTRPAWHED----NPINYVQCDISDPDDSQAKLPLTDVTHVFYVTWANR------STEQENCEANSKMFRNVLDAVIPNCPNL

(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=-2.11

Estimated TM-score = 0.46±0.15

Estimated RMSD = 9.1±4.6Å

Download Model 2

C-score=-4.58

Download Model 3

C-score=-4.75

Download Model 4

C-score=-5.00

Download Model 5

C-score=-5.00

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	4ienA	0.786	2.80	0.124	0.977
2	4ncpA	0.733	3.02	0.102	0.962
3	3b7kA	0.728	3.04	0.078	0.955
4	1vpmA	0.720	3.20	0.167	0.955
5	2qq2C	0.720	3.34	0.070	0.970
6	1y7uA	0.699	3.27	0.159	0.955
7	4zv3A	0.687	3.35	0.096	0.924
8	2v1oA	0.678	3.25	0.099	0.909
9	1yliB	0.594	3.40	0.082	0.803
10	4hznA	0.590	4.31	0.081	0.932

(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	0.16	10	1q4sB	COA	Rep, Mult	39,41,42,43,91,93,94
2	0.13	8	1vpmB	COA	Rep, Mult	15,20,47,48,50,51,85
3	0.05	3	1wn3E	HXC	Rep, Mult	27,28,31,32,40,41,43,90,91,93
4	0.04	3	1ykpA	DHB	Rep, Mult	8,10,16
5	0.02	1	1yliA	COA	Rep, Mult	21,23,45,46,49,86
6	0.01	1	1vliA	ZN	Rep, Mult	58,84
7	0.01	1	3tuxA	MN	Rep, Mult	5,50
8	0.01	1	1ykpC	DHB	Rep, Mult	8,10,16,125
9	0.01	1	3dnuA	PO4	Rep, Mult	65,104,110,111
10	0.01	1	1mtlB	UUU	Rep, Mult	14,16,17
11	0.01	1	2f3xB	MLC	Rep, Mult	28,32,39,40
12	0.01	1	3f5oG	UUU	Rep, Mult	27,44,45,88,89,91
13	0.01	1	3iehA	ZN	Rep, Mult	11,13,84
14	0.01	1	2a19C	MG	Rep, Mult	47,59
15	0.01	1	3dr2B	CA	Rep, Mult	50,59

	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	0.174	2qq2C	0.720	3.34	0.070	0.970	3.1.2.2	18
2	0.076	1y7uA	0.699	3.27	0.159	0.955	3.1.2.20	24,31,88,90
3	0.060	2c2iA	0.454	3.61	0.101	0.667	4.2.1.17	NA
4	0.060	1mkaA	0.441	4.48	0.062	0.720	4.2.1.60	NA
5	0.060	3khpA	0.507	4.26	0.062	0.849	1.-.-.-	NA
6	0.060	3ir3A	0.487	3.08	0.056	0.651	4.2.1.-	NA
7	0.060	3khpC	0.460	3.41	0.101	0.659	1.-.-.-	54
8	0.060	1s9cG	0.528	3.87	0.064	0.795	4.2.1.107	NA
9	0.060	2v1oE	0.680	3.23	0.100	0.901	3.1.2.2	21,31
10	0.060	2x6fA	0.440	4.46	0.051	0.712	2.7.1.137,2.7.1.153,2.7.1.154	51
11	0.060	1tbuB	0.477	2.98	0.084	0.614	3.1.2.2	21,58,87
12	0.060	1z6bA	0.462	3.59	0.080	0.659	4.2.1.-	NA
13	0.060	2qvrA	0.436	4.68	0.094	0.742	3.1.3.11	40
14	0.060	1e9iD	0.437	4.65	0.052	0.773	4.2.1.11	NA
15	0.060	2gq1A	0.431	4.24	0.063	0.674	3.1.3.11	NA
16	0.060	1uofA	0.447	4.96	0.073	0.788	1.14.20.1	NA
17	0.060	2yu1A	0.439	4.78	0.049	0.735	1.14.11.27	NA
18	0.060	1ikpA	0.486	4.21	0.049	0.765	2.4.2.-	NA
19	0.060	2pffB	0.526	4.19	0.058	0.856	2.3.1.86	18,83
20	0.060	1pn4C	0.503	3.70	0.061	0.750	4.2.1.-	NA
21	0.060	1pn4D	0.531	3.96	0.065	0.811	4.2.1.-	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	0.28	0.726	3.14	0.17	0.96	3spsA	GO:0016787
1	0.27	0.786	2.80	0.12	0.98	4ienA	GO:0016787
2	0.23	0.579	3.64	0.09	0.80	2gvhB	GO:0016787
3	0.15	0.585	3.10	0.11	0.77	3d6lA	GO:0016787
4	0.14	0.727	3.12	0.09	0.95	4mocA	GO:0003986 GO:0005524 GO:0005737 GO:0005829 GO:0006084 GO:0006090 GO:0006629 GO:0006631 GO:0006637 GO:0008289 GO:0016787 GO:0035338 GO:0047617 GO:0052689
5	0.14	0.594	3.40	0.08	0.80	1yliB	GO:0016787
6	0.13	0.724	3.19	0.15	0.98	1y7uA	GO:0016787 GO:0046872 GO:0047617
7	0.13	0.730	3.12	0.08	0.96	4mobA	GO:0003986 GO:0005524 GO:0005737 GO:0005829 GO:0006084 GO:0006090 GO:0006629 GO:0006631 GO:0006637 GO:0008289 GO:0016787 GO:0035338 GO:0047617 GO:0052689
8	0.12	0.690	3.13	0.07	0.91	4zv3B	GO:0000062 GO:0005654 GO:0005737 GO:0005829 GO:0009062 GO:0015937 GO:0016290 GO:0016787 GO:0036042 GO:0036114 GO:0036116 GO:0042803 GO:0043005 GO:0044297 GO:0051792 GO:0052689 GO:0070062 GO:1900535
9	0.11	0.557	3.22	0.10	0.74	5dm5B	GO:0016787
10	0.08	0.541	3.67	0.08	0.76	4mtuA	GO:0016829 GO:0046872
11	0.07	0.514	3.14	0.08	0.67	2fs2B	GO:0010124 GO:0016289 GO:0016787 GO:0016790
12	0.06	0.375	5.65	0.03	0.77	2q3oB	GO:0003824 GO:0003959 GO:0005777 GO:0006629 GO:0006631 GO:0006633 GO:0009620 GO:0009695 GO:0010181 GO:0010193 GO:0016491 GO:0016629 GO:0031408 GO:0055114
13	0.06	0.308	5.33	0.06	0.59	1up6E	GO:0003824 GO:0004553 GO:0005975 GO:0008152 GO:0008706 GO:0016616 GO:0016787 GO:0016798 GO:0046872 GO:0055114
14	0.06	0.340	5.34	0.07	0.65	1qydA	GO:0009807 GO:0010283 GO:0010284 GO:0016491 GO:0055114 GO:1902123 GO:1902125 GO:1902128 GO:1902129 GO:1902132 GO:1902135
15	0.06	0.270	5.19	0.00	0.52	1yycA	GO:0005829 GO:0005886 GO:0009269 GO:0048046
16	0.06	0.328	4.89	0.01	0.57	2ld6A	GO:0000155 GO:0000160 GO:0000166 GO:0004673 GO:0004871 GO:0005524 GO:0005737 GO:0006935 GO:0007165 GO:0016301 GO:0016310 GO:0016740 GO:0016772 GO:0018106 GO:0023014
17	0.06	0.319	4.87	0.10	0.52	3l42A	GO:0003677 GO:0005634 GO:0005654 GO:0005737 GO:0006351 GO:0006355 GO:0008270 GO:0016568 GO:0043966 GO:0045893 GO:0046872 GO:0070776 GO:1901796
18	0.06	0.346	4.63	0.06	0.61	3kycB	GO:0000166 GO:0005524 GO:0005634 GO:0005654 GO:0005737 GO:0005829 GO:0008047 GO:0008134 GO:0008641 GO:0016874 GO:0016925 GO:0019948 GO:0031510 GO:0043085 GO:0046872 GO:0046982

Consensus prediction of GO terms

Molecular Function	GO:0016787
GO-Score	0.70
Biological Processes	GO:0006084	GO:0006631	GO:0035338	GO:0006090
GO-Score	0.14	0.14	0.14	0.14
Cellular Component	GO:0005829
GO-Score	0.14

(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.