I-TASSER results

I-TASSER results for job id Rv2719c

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

Input Sequence in FASTA format

>protein (165 residues)
MTPVRPPHTPDPLNLRGPLDGPRWRRAEPAQSRRPGRSRPGGAPLRYHRTGVGMSRTGHG
SRPVPPATTVGLALLAAAITLWLGLVAQFGQMITGGSADGSADSTGRVPDRLAVVRVETG
ESLYDVAVRVAPNAPTRQVADRIRELNGLQTPALAVGQTLIAPVG

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MTPVRPPHTPDPLNLRGPLDGPRWRRAEPAQSRRPGRSRPGGAPLRYHRTGVGMSRTGHGSRPVPPATTVGLALLAAAITLWLGLVAQFGQMITGGSADGSADSTGRVPDRLAVVRVETGESLYDVAVRVAPNAPTRQVADRIRELNGLQTPALAVGQTLIAPVG
Prediction	CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEHCCCCCCCEHCCCCEEEHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEHCCCCCHHHHHHHHCCCCCHHHHHHHHHHHHCCCCCCCCCCEEEEHCCC
Conf.Score	998888888877777677777766667776666677778877665457877645655677765555554555567889999999999999987645555556667788877589999599789999999888999999999999998999998889889996589
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MTPVRPPHTPDPLNLRGPLDGPRWRRAEPAQSRRPGRSRPGGAPLRYHRTGVGMSRTGHGSRPVPPATTVGLALLAAAITLWLGLVAQFGQMITGGSADGSADSTGRVPDRLAVVRVETGESLYDVAVRVAPNAPTRQVADRIRELNGLQTPALAVGQTLIAPVG
Prediction	754444445565454444474444447545555444664444343444543332333464444244432211111222222213312321231333334434444464464333030444220140055237744244004202612707574033313040348
	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

                   |                   |                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEHCCCCCCCEHCCCCEEEHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEHCCCCCHHHHHHHHCCCCCHHHHHHHHHHHHCCCCCCCCCCEEEEHCCC
MTPVRPPHTPDPLNLRGPLDGPRWRRAEPAQSRRPGRSRPGGAPLRYHRTGVGMSRTGHGSRPVPPATTVGLALLAAAITLWLGLVAQFGQMITGGSADGSADSTGRVPDRLAVVRVETGESLYDVAVRVAPNAPTRQVADRIRELNGLQTPALAVGQTLIAPVG

4b8vA

0.18

0.16

0.88

1.14

MUSTER

IVSVNKLANPNLIELGATLIIPENCSNPDNKSCVSTPAEPTETC----------VPGLPGSYTIVSGDT--LTNISQDFNITLDSLIAANTQIENPDA-TVPVCPSSQCEAVGTYNIVAGDLFVDLAATYH------TTIGQIKALNNVNPSKLKVGQQIILPQD

5fimA

0.14

0.13

0.88

1.20

dPPAS

----------------MGLFNFVKDAGEKLWDAVTGQHDKDDQAKKVQEHLNKTGIPDADKVNIQIADGKATVTGDGLSQEAKEKILVAVGNISGIASVDDQVKTATPATASQFYTVKSGDTLSAISKQVYGNAN---LYNKIFEANKLKSDKIYPGQVLRIPEE

4b8vA2

0.20

0.15

0.72

2.89

wdPPAS

-----------------------------------STPAEPTETCVPGLPGSYTIVSGDTLTNISQDFNITLDSLIAANTIENPDAIDVGQIITVPVCPSSQCEAV------GTYNIVAGDLFVDLAATYHTT------IGQIKALNNNVNSKLKVGQQIILPQD

4b8vA

0.19

0.18

0.92

1.78

wMUSTER

IVSVNKLANPNLIELGATLIIPE-NCSNPDNKSCVSTPAEPTETCVPGLPGSYTIVSGDTLTNISQDFNITLDSLIAANQIENPDAIDVGQIITVPVCPSSQCEAV------GTYNIVAGDLFVDLAATYH------TTIGQIKALNNVNPSKLKVGQQIILPQD

4b8vA

0.20

0.18

0.92

2.96

wPPAS

IVSVNKLANPNLIELGATLIIPE-NCSNPDNKSCVSTPAEPTETCVPGLPGSYTIVSGDTLTNISQDFNITLDSLIAANTIENPDAIDVGQIITVPVCPSSQCEAV------GTYNIVAGDLFVDLAATYHTT------IGQIKALNNNNPSKLKVGQQIILPQD

2mkxA

0.26

0.08

0.30

3.07

dPPAS2

-------------------------------------------------------------------------------------------------------------GTNTYYTVKSGDTLNKIAAQYGVS------VANLRSWNGISGDLIFVGQKLIVKKG

2mkxA

0.26

0.08

0.30

2.39

PPAS

-------------------------------------------------------------------------------------------------------------GTNTYYTVKSGDTLNKIAAQYG------VSVANLRSWNGISGDLIFVGQKLIVKKG

2mkxA

0.26

0.08

0.30

2.36

Env-PPAS

-------------------------------------------------------------------------------------------------------------GTNTYYTVKSGDTLNKIAAQYG------VSVANLRSWNGISGDLIFVGQKLIVKKG

5fimA

0.14

0.12

0.85

1.10

MUSTER

--------------------VKDAGEKLWDAVTGQHDKDDQAKKVQEHLNKTGI--PDADKVNIQIADGKATVTGDGLSQEAKEKILVAVGNISGIASVDDQVKTATPATASQFYTVKSGDTLSAISKQVYGNAN---LYNKIFEANKLKSDKIYPGQVLRIPEE

4uz2A

0.22

0.13

0.58

1.13

dPPAS

------------------------------------------------------------QATYTVAPGDTLYSIARRYGTTVEELMRLNGL---ESFLLQPGQVLKLPSRERTHVVAPGDTLFSLARRYGTT------VEALMRLNGLSSPEIKVGQVLRLPEE

(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=-1.31

Estimated TM-score = 0.55±0.15

Estimated RMSD = 7.8±4.4Å

Download Model 2

C-score=-2.51

Download Model 3

C-score=-3.29

Download Model 4

C-score=-4.05

Download Model 5

C-score=-3.70

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	4b8vA	0.847	1.56	0.197	0.921
2	5fqeA	0.471	5.25	0.032	0.830
3	2vtfA	0.457	5.21	0.078	0.800
4	3i04A2	0.434	4.77	0.052	0.727
5	2zxhA	0.433	4.86	0.043	0.746
6	4m5dA2	0.432	5.09	0.086	0.746
7	3uk7A	0.431	5.00	0.030	0.746
8	4zmuA	0.429	4.41	0.044	0.679
9	3wiqA	0.429	5.28	0.044	0.739
10	5axgA	0.428	5.28	0.033	0.782

(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	0.12	4	4b8vA	NAG	Rep, Mult	15,117,118,120,121,154
2	0.07	3	3gwzD	CA	Rep, Mult	121,125
3	0.05	2	4b8vA	NAG	Rep, Mult	11,12,13,122,123,124,140,151,152
4	0.05	2	4b8vA	NAG	Rep, Mult	13,14,15,122,151,152,153,154
5	0.04	2	3fu3A	IMD	Rep, Mult	122,123,140,141,144
6	0.04	2	3fahA	GOL	Rep, Mult	127,131,140,144
7	0.04	2	3fu0A	22F	Rep, Mult	115,117,123,127,128,163
8	0.04	2	3ftwA	IMD	Rep, Mult	143,144,147,160
9	0.02	1	4gaqG	NUC	Rep, Mult	156,157
10	0.02	1	1fbmD	RTL	Rep, Mult	149,154
11	0.02	1	3v3xA	MTN	Rep, Mult	159,160
12	0.02	1	1a34A	U	Rep, Mult	119,120

	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	3k2iA	0.408	5.42	0.046	0.764	3.1.2.2	NA
2	0.060	1c7sA	0.410	5.59	0.054	0.782	3.2.1.52	127
3	0.060	2dkcA	0.412	5.36	0.065	0.746	5.4.2.3	51,112
4	0.060	1ybhA	0.410	5.57	0.032	0.764	2.2.1.6	NA
5	0.060	1v10A	0.414	5.68	0.065	0.794	1.10.3.2	NA
6	0.060	2e1pA	0.419	5.35	0.070	0.709	3.4.21.62	NA
7	0.060	1gw6A	0.425	5.05	0.038	0.758	3.3.2.6	NA
8	0.060	1pxvA	0.365	5.39	0.034	0.685	3.4.22.-	NA
9	0.060	2j5wA	0.417	5.62	0.068	0.794	1.16.3.1	NA
10	0.060	2o8rA	0.411	5.14	0.067	0.715	2.7.4.1	140
11	0.060	1e5tA	0.390	5.73	0.062	0.727	3.4.21.26	NA
12	0.060	1gpeB	0.416	5.31	0.026	0.758	1.1.3.4	NA
13	0.060	2j62A	0.296	5.87	0.045	0.588	3.2.1.52	123,151
14	0.060	2gmjA	0.416	5.21	0.067	0.727	1.5.5.1	NA
15	0.060	2cqsA	0.435	5.54	0.051	0.788	2.4.1.20	121
16	0.060	1clcA	0.406	5.45	0.023	0.733	3.2.1.4	NA
17	0.060	1qbaA	0.415	5.33	0.070	0.764	3.2.1.52	67
18	0.060	3dt7A	0.410	5.33	0.062	0.746	4.1.1.32	NA
19	0.060	3ig5A	0.415	5.04	0.058	0.721	6.3.2.2	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	0.09	0.280	1.73	0.26	0.31	2ltfA	GO:0019012
1	0.06	0.290	3.38	0.08	0.37	2djpA
2	0.06	0.395	4.15	0.11	0.56	4a52A	GO:0008360 GO:0009252 GO:0016740 GO:0016757 GO:0016787 GO:0030435 GO:0031160 GO:0071555
3	0.06	0.364	5.20	0.07	0.64	4j1yA	GO:0002376 GO:0004252 GO:0005509 GO:0005576 GO:0006508 GO:0006956 GO:0006958 GO:0008233 GO:0008236 GO:0016787 GO:0042802 GO:0045087 GO:0046872 GO:0070062 GO:0072562
4	0.06	0.375	3.87	0.07	0.51	5jceB	GO:0005886 GO:0006952 GO:0008061 GO:0016020 GO:0016021 GO:0043621
5	0.06	0.304	5.42	0.05	0.53	2w91A	GO:0005576 GO:0005618 GO:0005737 GO:0016020 GO:0033925
6	0.06	0.277	5.88	0.02	0.54	4k87A	GO:0000166 GO:0003723 GO:0003824 GO:0004812 GO:0004818 GO:0004827 GO:0005524 GO:0005737 GO:0005829 GO:0006412 GO:0006417 GO:0006418 GO:0006424 GO:0006433 GO:0006461 GO:0008152 GO:0016020 GO:0016874 GO:0016876 GO:0017101 GO:0017148 GO:0030529 GO:0035613 GO:0043039 GO:0051020 GO:0071346 GO:0097452
7	0.06	0.347	3.36	0.06	0.44	4s3kA	GO:0004553 GO:0004568 GO:0005975 GO:0006032 GO:0008152 GO:0016787 GO:0016798
8	0.06	0.356	4.71	0.05	0.59	1a0gB	GO:0003824 GO:0008152 GO:0008483 GO:0016740 GO:0019478 GO:0030170 GO:0046416 GO:0046437 GO:0047810
9	0.06	0.315	4.75	0.04	0.47	2l9yA	GO:0005975 GO:0043581
10	0.06	0.401	5.18	0.03	0.71	4s3jB	GO:0004553 GO:0004568 GO:0005975 GO:0006032
11	0.06	0.323	3.62	0.08	0.44	5c8oA	GO:0005975 GO:0043581
12	0.06	0.297	5.72	0.03	0.56	3n5lA	GO:0015604 GO:0015716 GO:0042916 GO:0042917 GO:0043190 GO:0055085
13	0.06	0.316	5.40	0.03	0.56	3daqA	GO:0003824 GO:0005737 GO:0008152 GO:0008652 GO:0008840 GO:0009085 GO:0009089 GO:0016829 GO:0019877
14	0.06	0.259	4.03	0.07	0.38	3gefA	GO:0005198 GO:0005634 GO:0005635 GO:0005638 GO:0005652 GO:0005654 GO:0005737 GO:0005829 GO:0005882 GO:0006997 GO:0006998 GO:0007077 GO:0007084 GO:0007283 GO:0007517 GO:0008157 GO:0009612 GO:0016363 GO:0016607 GO:0030334 GO:0030951 GO:0031012 GO:0031965 GO:0034504 GO:0035105 GO:0036498 GO:0045669 GO:0048471 GO:0055015 GO:0071456 GO:0090201 GO:0090343 GO:1900180 GO:1904178 GO:2001237
15	0.06	0.267	1.41	0.15	0.28	5bumA	GO:0004553 GO:0005975 GO:0008152 GO:0016787 GO:0016798
16	0.06	0.286	5.42	0.04	0.53	4hsjA	GO:0000334 GO:0005506 GO:0006569 GO:0008198 GO:0009435 GO:0016491 GO:0019363 GO:0019805 GO:0034354 GO:0043420 GO:0046872 GO:0051213 GO:0055114
17	0.06	0.266	2.07	0.26	0.30	2mkxA	GO:0003824 GO:0004040 GO:0005576 GO:0007049 GO:0008152 GO:0016787 GO:0016798 GO:0019835 GO:0042742 GO:0051301 GO:0071555
18	0.06	0.291	5.85	0.03	0.59	3it8D	GO:0004674 GO:0006468 GO:0006508 GO:0008233

Consensus prediction of GO terms

Molecular Function	GO:0042802	GO:0008061	GO:0043621	GO:0016757	GO:0005509	GO:0004252
GO-Score	0.06	0.06	0.06	0.06	0.06	0.06
Biological Processes	GO:0009252	GO:0030435	GO:0008360	GO:0006958	GO:0006508	GO:0071555	GO:0045087
GO-Score	0.06	0.06	0.06	0.06	0.06	0.06	0.06
Cellular Component	GO:0019012	GO:0031160	GO:0005886	GO:0016021	GO:0070062	GO:0072562
GO-Score	0.09	0.06	0.06	0.06	0.06	0.06

(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.