I-TASSER results

I-TASSER results for job id Rv2360c

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

Input Sequence in FASTA format

>protein (142 residues)
MPSLPDRLASILRDVLPAEEEPDGALTVRHDGTFASLRVVSIAEDLELVSLTQILAWDLP
LTKRLAEQVAKQARDINFGSVSLREKVSEKAARRSSGRPASNTADVMLRYNFPGTGLTDD
ALRTLILLVLETGATIRSALVG

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MPSLPDRLASILRDVLPAEEEPDGALTVRHDGTFASLRVVSIAEDLELVSLTQILAWDLPLTKRLAEQVAKQARDINFGSVSLREKVSEKAARRSSGRPASNTADVMLRYNFPGTGLTDDALRTLILLVLETGATIRSALVG
Prediction	CHHHHHHHHHHHHHHCCCEHCCCCEEEEEHCCEEEEEEEEEHCCCCEEEEEEEEHCCCCCCCHHHHHHHHHHHCCCCCCEEEEEEHCCCCCCCCCCCCCCCCEEEEEEEEHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCC
Conf.Score	8589999999998743456758985999998988999998747998478765544436899989999999987568755578888657766544567888876799999767888888757999999999989999999759
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MPSLPDRLASILRDVLPAEEEPDGALTVRHDGTFASLRVVSIAEDLELVSLTQILAWDLPLTKRLAEQVAKQARDINFGSVSLREKVSEKAARRSSGRPASNTADVMLRYNFPGTGLTDDALRTLILLVLETGATIRSALVG
Prediction	6651353035005522515447432020435413010201412661411201010013143376036304734552312102224434544445445555541110102121324414542021000000320451265248
	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

                   |                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CHHHHHHHHHHHHHHCCCEHCCCCEEEEEHCCEEEEEEEEEHCCCCEEEEEEEEHCCCCCCCHHHHHHHHHHHCCCCCCEEEEEEHCCCCCCCCCCCCCCCCEEEEEEEEHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCC
MPSLPDRLASILRDVLPAEEEPDGALTVRHDGTFASLRVVSIAEDLELVSLTQILAWDLPLTKRLAEQVAKQARDINFGSVSLREKVSEKAARRSSGRPASNTADVMLRYNFPGTGLTDDALRTLILLVLETGATIRSALVG

2y08A

0.15

0.14

0.96

0.67

MUSTER

DEAAFARLVRNHGRWFEQNSGPDSPW----CDLYSVLALTRSQSG-ALAMTTQLDATGPDAEKRLETYLAAVSEGVGVQPHSDTRRLPHSTRWPGIAGDGDMTGRAKIKAAYARRSFDDRQIGTLYTRLTSTDYDNPAGVVA

2plgA

0.12

0.11

0.88

0.83

dPPAS

LENAVEIIETVISSLHQVGQTDSGKIWFRYGSAEVFVQLSGHTEEDFLTIWSPVLPLPVADELALYRKLLTLNWLTTFEAHFAIAEE-----------------QVQVVASRTLGGITAGEISRLITIVATLADDYDDALRA

2plgA

0.12

0.11

0.85

0.97

wdPPAS

LENAVEIIETVISSLHQVGQTDSGKIWFRYGSAEVFVQLSGHTEE-DFLTIWSPV---LPVALALYRKLLTLNWLTTFEAHFAIAEE-----------------QVQVVASRTLGGITAGEISRLITIVATLADDYDDALRA

2plgA

0.13

0.11

0.86

0.95

wMUSTER

LENAVEIIETVISSLHQVGQTDSGKIWFRYGSAEVFVQLSGHTEE-DFLTIWSPVL-PLPVELALYRKLLTLNWLTTFEHFAIAEE------------------QVQVVASRTLGGITAGEISRLITIVATLADDYDDALRA

2plgA

0.13

0.11

0.84

0.87

wPPAS

LENAVEIIETVISSLHQVGQTDSGKIWFRYGSAEVFVQLSGHTEE-DFLTIWSPV---LPVALALYRKLLTLNWLTTFEHFAIAE-------------------QVQVVASRTLGGITAGEISRLITIVATLADDYDDALRA

2plgA

0.12

0.11

0.88

0.95

dPPAS2

LENAVEIIETVISSLHQVGQTDSGKIWFRYGSAEVFVQLSGHTEEDFLTIWSPVLPLPVADELALYRKLLTLNWLTTFEAHFAIAEE-----------------QVQVVASRTLGGITAGEISRLITIVATLADDYDDALRA

2plgA

0.13

0.11

0.84

0.83

PPAS

LENAVEIIETVISSLHQVGQTDSGKIWFRYGSAEVFVQLSGHTEE-DFLTIWSPV---LPVALALYRKLLTLNWLTTFEHFAIAE-------------------QVQVVASRTLGGITAGEISRLITIVATLADDYDDALRA

2plgA

0.13

0.11

0.86

0.78

Env-PPAS

LENAVEIIETVISSLHQVGQTDSGKIWFRYGSAEVFVQLSGHTEE-DFLTIWSPV-LPLPVALALYRKLLTLNWLTTFEHFAIAEE------------------QVQVVASRTLGGITAGEISRLITIVATLADDYDDALRA

4z0vA2

0.10

0.94

0.64

MUSTER

RAVFSDSLVPALEAF--------GLEGVFRIKQHEGLATFYRKSKFSLLSQHDISFYEALESDPLHKELLEKLVLYPSAQEKVLQRSSVLQVSVLQSTKDSSKRICVANTHLYWHPKGGYIRLIQMAVALAHIRHVSCDLYP

4g6tA

0.17

0.15

0.85

0.76

dPPAS

YKTLLDDFSRSLE-MQPLVFDDHGTCNMIIDNTFALTLSCDYARE----RLLLIGLLEPHKDIPQQCLLAGALNPLLNAGPGLGLDEKSGL--------------YHAYQSIPREKLSVPTLKREMAGLLEWMRGWREA---

(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=-1.38

Estimated TM-score = 0.54±0.15

Estimated RMSD = 7.6±4.3Å

Download Model 2

C-score=-2.04

Download Model 3

C-score=-4.35

Download Model 4

C-score=-4.92

Download Model 5

C-score=-2.73

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	2plgA	0.788	1.56	0.089	0.866
2	4h5bA	0.688	2.89	0.161	0.873
3	1s28A	0.649	2.86	0.103	0.824
4	1jyoA	0.641	3.15	0.107	0.852
5	2fm8A	0.640	3.00	0.101	0.838
6	3kxyA	0.632	3.49	0.129	0.873
7	1xkpC	0.631	2.91	0.132	0.796
8	3epuA	0.627	2.87	0.118	0.824
9	1ry9A	0.625	3.04	0.126	0.838
10	1n5bA	0.606	3.44	0.085	0.803

(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	0.13	7	3kxyK	III	Rep, Mult	11,21,25,27,28,29,30,31,36,52,107,123,127,130,131,134
2	0.06	3	1ocoB	HEA	Rep, Mult	127,128
3	0.04	2	1n5b0	III	Rep, Mult	47,49,51,67,70,71,73,74,81,82,84,107,109,111
4	0.04	2	3kxyL	III	Rep, Mult	27,29,30,31,123,127,130,132,134,135,138,139
5	0.04	2	3iovA	CA	Rep, Mult	119,121
6	0.02	1	2ux8A	G1P	Rep, Mult	46,55,58,106,110
7	0.02	1	3dwrA	0PA	Rep, Mult	38,40,49,50,51,52,109
8	0.02	1	2zxlB	NA	Rep, Mult	70,71,81
9	0.02	1	3fkqA	MG	Rep, Mult	36,44
10	0.02	1	1xrmA	III	Rep, Mult	122,125
11	0.02	1	3au2A	CA	Rep, Mult	45,47,105
12	0.02	1	5l8gV	CA	Rep, Mult	110,125,128
13	0.02	1	2q8zA	NUP	Rep, Mult	58,59,62
14	0.02	1	2e82C	IM3	Rep, Mult	28,30,34,38,84,114
15	0.02	1	1ry90	III	Rep, Mult	60,62,63,69,70,71,74,83,84

	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	0.066	2v6uA	0.457	3.83	0.083	0.669	4.2.1.96	NA
2	0.060	2g18G	0.508	4.53	0.078	0.810	1.3.7.5	NA
3	0.060	1zg7A	0.513	4.88	0.065	0.922	3.4.17.2	NA
4	0.060	2fk5A	0.503	4.18	0.089	0.803	4.1.2.17	NA
5	0.060	1v5vA	0.506	4.52	0.098	0.859	2.1.2.10	122
6	0.060	2v77A	0.528	4.77	0.065	0.930	3.4.17.1	NA
7	0.060	1jqgA	0.524	4.97	0.070	0.908	3.4.17.1	NA
8	0.060	3dgvA	0.539	4.61	0.058	0.873	3.4.17.20	NA
9	0.060	1cg2A	0.520	4.79	0.074	0.880	3.4.17.11	NA
10	0.060	3d68C	0.538	4.70	0.058	0.880	3.4.17.20	NA
11	0.060	3d66A	0.540	4.67	0.051	0.880	3.4.17.20	NA
12	0.060	1pcaA	0.532	4.57	0.047	0.887	3.4.17.1	NA
13	0.060	1d8hA	0.505	4.60	0.142	0.803	3.1.3.33	NA
14	0.060	2zofA	0.517	4.66	0.060	0.880	3.4.13.18	NA
15	0.060	3ij3A	0.519	4.55	0.074	0.901	3.4.11.1	137
16	0.060	1pytB	0.518	5.07	0.064	0.944	3.4.17.1	NA
17	0.060	1h8lA	0.531	4.68	0.071	0.915	3.4.17.22	NA
18	0.060	1iu8A	0.511	4.55	0.085	0.817	3.4.19.3	NA
19	0.060	1eqrA	0.531	3.70	0.041	0.768	6.1.1.12	38
20	0.060	2nsmA	0.536	4.78	0.086	0.930	3.4.17.3	125

(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	0.23	0.641	3.15	0.11	0.85	1jyoA	GO:0005737 GO:0009405 GO:0050708
1	0.23	0.586	2.93	0.16	0.77	1k3sA	GO:0005737 GO:0009405
2	0.21	0.631	2.91	0.13	0.80	1xkpC	GO:0005737 GO:0005886 GO:0016020 GO:0050708
3	0.18	0.688	2.89	0.16	0.87	4h5bA	GO:0016049
4	0.17	0.632	3.49	0.13	0.87	3kxyA	GO:0005737 GO:0005886 GO:0016020 GO:0016021 GO:0030254 GO:0045893 GO:0050708
5	0.17	0.586	3.25	0.12	0.80	4gf3A	GO:0005737 GO:0050708
6	0.16	0.627	2.87	0.12	0.82	3epuA	GO:0005737 GO:0050708
7	0.16	0.660	2.84	0.10	0.84	1s28A	GO:0005737 GO:0050708
8	0.16	0.599	3.61	0.16	0.84	4g6tA	GO:0005737 GO:0050708
9	0.15	0.640	3.00	0.10	0.84	2fm8A	GO:0009405
10	0.11	0.606	3.44	0.09	0.80	1n5bA	GO:0005737 GO:0006351 GO:0006355 GO:0009405 GO:0050708
11	0.11	0.573	3.51	0.11	0.77	4jmfB	GO:0005737 GO:0009405 GO:0050708
12	0.09	0.602	3.30	0.08	0.81	1xkpB	GO:0005737 GO:0005886 GO:0009306 GO:0016020
13	0.07	0.501	3.00	0.12	0.66	1k3eB	GO:0005737 GO:0009405 GO:0050708
14	0.07	0.625	3.04	0.13	0.84	1ry9A	GO:0009405
15	0.06	0.428	4.49	0.10	0.68	3doeA	GO:0000166 GO:0003924 GO:0005095 GO:0005525 GO:0005622 GO:0005634 GO:0005737 GO:0005739 GO:0005758 GO:0005759 GO:0005813 GO:0005815 GO:0005829 GO:0005856 GO:0007021 GO:0007049 GO:0007264 GO:0010811 GO:0016328 GO:0031113 GO:0031116 GO:0034260 GO:0050796 GO:0051297 GO:0051457 GO:0070062 GO:0070830 GO:0072372
16	0.06	0.411	4.54	0.07	0.68	4zi2A	GO:0000139 GO:0000166 GO:0000910 GO:0001822 GO:0003924 GO:0005525 GO:0005622 GO:0005634 GO:0005737 GO:0005794 GO:0005813 GO:0005815 GO:0005819 GO:0005856 GO:0005876 GO:0005881 GO:0005929 GO:0006810 GO:0006892 GO:0007049 GO:0007224 GO:0007264 GO:0008017 GO:0015031 GO:0016020 GO:0019003 GO:0030496 GO:0032391 GO:0042073 GO:0042461 GO:0042995 GO:0046872 GO:0051301 GO:0060271 GO:0070062 GO:0072372
17	0.06	0.368	4.39	0.06	0.59	2x77A	GO:0000166 GO:0005525 GO:0005622 GO:0005802 GO:0006622 GO:0007264 GO:0030100
18	0.06	0.347	4.57	0.09	0.57	4i1vA	GO:0000166 GO:0004140 GO:0005524 GO:0005737 GO:0015937 GO:0016301 GO:0016310 GO:0016740
19	0.06	0.276	4.67	0.05	0.48	4dzoB	GO:0000775 GO:0000776 GO:0000777 GO:0000922 GO:0005634 GO:0005643 GO:0005694 GO:0005737 GO:0005813 GO:0005815 GO:0005819 GO:0005829 GO:0005856 GO:0007049 GO:0007062 GO:0007067 GO:0007093 GO:0007094 GO:0015629 GO:0042130 GO:0048538 GO:0051301 GO:0072686 GO:0090235 GO:1901990
20	0.06	0.360	4.61	0.03	0.62	5aedA	GO:0003824 GO:0004553 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0030246

Consensus prediction of GO terms

Molecular Function
GO-Score
Biological Processes	GO:0050708	GO:0009405	GO:0040007	GO:0071806	GO:0010628	GO:1903508	GO:0006355
GO-Score	0.49	0.41	0.36	0.33	0.33	0.33	0.33
Cellular Component	GO:0005737	GO:0005886
GO-Score	0.61	0.34

(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.