I-TASSER results

I-TASSER results for job id Rv0395

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

Input Sequence in FASTA format

>protein (134 residues)
MDWMPLGDYETFRHWSGKPRAWGPQESGWRAWFGGKIVDGLCEVLDEHLAVRRRGVPAAI
GCVPWLSSEAVAETLLALSVFCVVIDKGTSFPSRLRNPDKGFPNVALLRLRDMAPSEHGS
RCSSARGRLCLSMS

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MDWMPLGDYETFRHWSGKPRAWGPQESGWRAWFGGKIVDGLCEVLDEHLAVRRRGVPAAIGCVPWLSSEAVAETLLALSVFCVVIDKGTSFPSRLRNPDKGFPNVALLRLRDMAPSEHGSRCSSARGRLCLSMS
Prediction	CCCCCCCCHHHHHHHCCCCCCCCCCCCCEEEEHCCEEHHHHHHHHHHHHHHHCCCCCCEEHCCCCCCCHHHHHHHHHCCEEEEEEHCCCCCHHHCCCCCCCCCCEEEEEHHHCCCCCCCCCCCCCCCEEEEHCC
Conf.Score	99877786788887679999988877765899855435579999999875443687644545566666799999987574689997886675665787778997456663546876677655554554665579
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MDWMPLGDYETFRHWSGKPRAWGPQESGWRAWFGGKIVDGLCEVLDEHLAVRRRGVPAAIGCVPWLSSEAVAETLLALSVFCVVIDKGTSFPSRLRNPDKGFPNVALLRLRDMAPSEHGSRCSSARGRLCLSMS
Prediction	76444344263046146434323355432312233421430041046424344552320100121137440141134132000002544423640554653233111230362245643541453423113438
	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

CCCCCCCCHHHHHHHCCCCCCCCCCCCCEEEEHCCEEHHHHHHHHHHHHHHHCCCCCCEEHCCCCCCCHHHHHHHHHCCEEEEEEHCCCCCHHHCCCCCCCCCCEEEEEHHHCCCCCCCCCCCCCCCEEEEHCC
MDWMPLGDYETFRHWSGKPRAWGPQESGWRAWFGGKIVDGLCEVLDEHLAVRRRGVPAAIGCVPWLSSEAVAETLLALSVFCVVIDKGTSFPSRLRNPDKGFPNVALLRLRDMAPSEHGSRCSSARGRLCLSMS

4h04A3

0.13

0.94

0.67

MUSTER

-TPVDAGDIPQLKSISKGPWELITTPDGMKDTVSGKCLA-LFTGSKHLDVVTQVGARPELRVSVGQDQRNTANERNT-QKWQIRADKDGKY--TISP---ALTQQRLAIATGNEQNIDLETHRPAAGTVAQFVS

4xrbA1

0.12

0.10

0.89

0.63

dPPAS

SSVHYLTDGELPQLYDYPDGTWISSLDGGATVDGTSGAMAGPGDRFVFNLLRELADVRRILT---EGGPTLLGTFVERDELCLTIAPYVVGGLARRIVTGPGQVLTRMRCAHVLTDDSGYKT------------

2yv3A1

0.23

0.18

0.78

0.60

wdPPAS

MRVAVVG-REILKVLEARNFPLSPRSAGVRLAFRGEEI--PVEPLPEG----PLPVDLVLASAG--ISRAKALVWAE----ALVVDNSSAW--RYE------PWVPLV-----VPEVNREKIFQHRG---IIAN

1ujbA

0.20

0.18

0.88

0.62

wMUSTER

SDSRPLTTCDESRLMANWLKGQKVEIE--RVLVSPFLAEQTLEEVGDCL-----NLPSSAEVLPELTVGLVSAYLQALTASVLVISHLGYLVAELGETPPMFTTSAIASV-TL--DESG------NGTFNWQMS

2o3dA

0.28

0.20

0.71

0.56

wPPAS

--MAPRGRY------GPPSR-----RSENRVVVSGSGWQDLKDHMREAGDV------ADVGTVEFVRKEDMTYAVRKLD--------NTKFRSHGE--------TAYIRVKVDGPRSPSSR-SRSRSR---SLE

4rwzA1

0.20

0.11

0.57

0.70

dPPAS2

----------------------------MIVQLGKASVTWTRADLEAKLA-GHARVLIDVGTGD--GRFVYRSAGAHPDTYCIGVD---PAGERMRKPARGRPNALFVVA------------------------

4xrbA1

0.15

0.13

0.88

0.66

PPAS

SSVHYLTD-GELPQLYDYPGTW--SLDGGATVDGTSGAMAGPGDRFVFNLLRELADVRRILT-PTLLGTFVERDV--LDELCLTIAPYVVGGLARRIVTGPGQVLTRMRCAHVLTDDSGYR---VKT-------

1tlgA

0.18

0.14

0.78

0.66

Env-PPAS

-------DYEIL--FSDETMNY--ADA-GTYSRGMALMRDSTMVKAILAFTEVKGHDYWVG----ADN------LQDGAYNFLWND-GVSLPTDSDLWSPNEPSVQIWS-------KYNLGCGGARRVICEKEL

4kngE

0.16

0.96

0.67

MUSTER

LKMDPTGKLNL--TLEGVFAGVAEITPAEGKLMQSH-PLYLCN--ASDDDNLEPGFISIVKLEPCLSLASKARMAGERGASAVLFDEDRAAAEQLQQPLGLTWPVVLIWGNDAEK-EFVYKNQKAHVRIELKEP

4rwzA1

0.13

0.07

0.59

0.62

dPPAS

----------------------------MIVQLGKASVT---WTRADLEAKLAGHARVLIDVGTGDGRFVYRSAGAHPDTYCIGVDREVSWRASRKPARGGRPNALFVVA------------------------

(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=-4.15

Estimated TM-score = 0.27±0.08

Estimated RMSD = 14.3±3.8Å

Download Model 2

C-score=-4.42

Download Model 3

C-score=-4.92

Download Model 4

C-score=-4.97

Download Model 5

C-score=-4.96

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	3skvA	0.559	4.17	0.074	0.881
2	2hbxA	0.559	4.82	0.069	0.955
3	3j9qA	0.557	4.59	0.063	0.925
4	3qr3A	0.553	4.58	0.068	0.910
5	1e51A	0.549	3.71	0.084	0.806
6	4hjwA	0.547	4.42	0.076	0.895
7	1b4eA	0.547	3.75	0.084	0.813
8	3ij6A	0.547	4.49	0.070	0.895
9	5d8wA	0.546	4.47	0.060	0.888
10	5thkA	0.545	4.44	0.076	0.881

(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	0.10	5	5dknA	B7I	Rep, Mult	44,48
2	0.08	4	1b5dA	DCM	Rep, Mult	52,53
3	0.06	3	1it7B	MG	Rep, Mult	53,54,56,78,79
4	0.06	3	3ktiG	III	Rep, Mult	46,50,74,77
5	0.04	2	4a8qC	ATP	Rep, Mult	18,20,86
6	0.02	1	3v2dF	MG	Rep, Mult	20,21
7	0.02	1	1cq1B	CA	Rep, Mult	17,19
8	0.02	1	2eulA	ZN	Rep, Mult	39,43
9	0.02	1	2yyeA	CO	Rep, Mult	38,39
10	0.02	1	3ij6B	NA	Rep, Mult	41,42,46,47,75
11	0.02	1	4qvpK	MG	Rep, Mult	71,75
12	0.02	1	3bvcA	CA	Rep, Mult	8,10

	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	1e5jA	0.531	4.29	0.063	0.873	3.2.1.4	NA
2	0.060	1w0cA	0.531	4.47	0.023	0.881	1.5.1.33	NA
3	0.060	1bwpA	0.520	4.27	0.091	0.873	3.1.1.47	NA
4	0.060	2bfpD	0.532	4.46	0.023	0.881	1.5.1.33	NA
5	0.060	2qt3A	0.538	4.28	0.089	0.873	3.5.99.4	60
6	0.060	2gdzA	0.541	4.28	0.053	0.866	1.1.1.141	NA
7	0.060	3ekzA	0.534	4.31	0.061	0.866	4.1.2.13	NA
8	0.060	2wm1A	0.543	4.63	0.055	0.903	4.1.1.45	NA
9	0.060	1e51B	0.544	3.67	0.084	0.798	4.2.1.24	87
10	0.060	1g0cA	0.530	4.37	0.062	0.881	3.2.1.4	NA
11	0.060	2wghB	0.531	4.21	0.048	0.888	1.17.4.1	42,43,62
12	0.060	1k6wA	0.516	4.63	0.081	0.881	3.5.4.1	NA
13	0.060	2waaA	0.534	4.28	0.080	0.888	3.1.1.72	85
14	0.060	1h7rA	0.541	4.09	0.076	0.843	4.2.1.24	87
15	0.060	1kkoA	0.470	4.88	0.086	0.836	4.3.1.2	NA
16	0.060	2z1bD	0.539	4.09	0.085	0.821	4.2.1.24	87
17	0.060	7reqB	0.531	4.41	0.075	0.843	5.4.99.2	NA
18	0.060	1hxhA	0.531	4.32	0.053	0.866	1.1.1.51	NA
19	0.060	1e51A	0.549	3.71	0.084	0.806	4.2.1.24	36

(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	0.24	0.547	4.49	0.07	0.90	3ij6A	GO:0016787 GO:0046872
1	0.13	0.525	4.39	0.07	0.88	1egzA	GO:0000272 GO:0004553 GO:0005576 GO:0005975 GO:0008152 GO:0008810 GO:0016787 GO:0016798 GO:0030245 GO:0030246
2	0.07	0.544	4.44	0.08	0.89	4hjwC	GO:0001760 GO:0006568 GO:0016787 GO:0046872 GO:1904984
3	0.07	0.548	4.34	0.09	0.89	4qroA	GO:0016787 GO:0046872
4	0.07	0.540	4.49	0.06	0.89	4ofcA	GO:0001760 GO:0005829 GO:0006568 GO:0006569 GO:0008270 GO:0016787 GO:0016829 GO:0016831 GO:0046872 GO:0046874 GO:0051259 GO:0070062 GO:1904984 GO:1905004 GO:1905012
5	0.07	0.526	4.36	0.05	0.84	2e9lA	GO:0004348 GO:0004553 GO:0004565 GO:0005737 GO:0005829 GO:0005975 GO:0006687 GO:0008152 GO:0008422 GO:0016139 GO:0016787 GO:0016798 GO:0017042 GO:0046477 GO:0102483
6	0.07	0.523	4.34	0.06	0.87	1tvnA	GO:0004553 GO:0005509 GO:0005576 GO:0005975 GO:0007155 GO:0008152 GO:0008810 GO:0016787 GO:0016798 GO:0030246
7	0.07	0.525	4.39	0.07	0.84	3nurA	GO:0016787
8	0.07	0.516	4.27	0.07	0.84	4ee9A	GO:0004553 GO:0005975 GO:0008152 GO:0008810 GO:0016787 GO:0016798
9	0.07	0.529	4.38	0.11	0.88	5fipB	GO:0004553 GO:0005975 GO:0008152 GO:0008810 GO:0016020 GO:0016021 GO:0016787 GO:0016798 GO:0030245
10	0.07	0.499	4.36	0.08	0.83	5bywE	GO:0000272 GO:0004553 GO:0005975 GO:0008152 GO:0008810 GO:0016787 GO:0016798 GO:0030245
11	0.07	0.553	4.58	0.07	0.91	3qr3A	GO:0000272 GO:0004553 GO:0005576 GO:0005975 GO:0008152 GO:0008810 GO:0016787 GO:0016798 GO:0030245 GO:0030248
12	0.07	0.490	4.65	0.06	0.86	4im4A	GO:0000272 GO:0003824 GO:0004553 GO:0005576 GO:0005975 GO:0008152 GO:0008810 GO:0016787 GO:0016798 GO:0030245 GO:0030248 GO:0045493 GO:0046555 GO:0046872 GO:2000884
13	0.07	0.487	4.58	0.10	0.83	3amgB	GO:0004553 GO:0005576 GO:0005975 GO:0006073 GO:0008152 GO:0008422 GO:0009251 GO:0009986 GO:0016787 GO:0016798
14	0.07	0.524	4.76	0.07	0.90	4w8aA	GO:0004553 GO:0005975 GO:0008152 GO:0016787 GO:0016798
15	0.07	0.508	4.59	0.11	0.87	3zmrA	GO:0000272 GO:0004553 GO:0005975 GO:0008152 GO:0009279 GO:0016020 GO:0016787 GO:0016798 GO:0033946 GO:0085030 GO:2000899
16	0.07	0.528	4.47	0.06	0.88	4xzbA	GO:0003860 GO:0004553 GO:0005975 GO:0008152 GO:0016020 GO:0016021 GO:0016787 GO:0016798
17	0.07	0.544	4.58	0.10	0.93	4eraA	GO:0001760 GO:0006568 GO:0016787 GO:0046872 GO:1904984
18	0.07	0.511	4.86	0.09	0.89	2jepA	GO:0004553 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0033946

Consensus prediction of GO terms

Molecular Function	GO:0016787	GO:0046872
GO-Score	0.46	0.38
Biological Processes	GO:0030245	GO:1904984	GO:1905004	GO:1905012	GO:0006569	GO:0051259
GO-Score	0.13	0.13	0.07	0.07	0.07	0.07
Cellular Component	GO:0070062	GO:0005829
GO-Score	0.07	0.07

(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.