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I-TASSER results for job id Rv0876c

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

 Input Sequence in FASTA format
 Predicted Secondary Structure
 Predicted Solvent Accessibility
 Predicted Normalized B-facotr
 Top 10 threading templates used by I-TASSER
 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.)
 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.)


 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
10.06 3 4zwbA MAL Rep, Mult 247,250,251,254,348,349,354,389,446,447,454,481
20.04 2 4oaaB TDG Rep, Mult 119,126,226,229,246,250,251,254,386,389,450,470,477
30.04 2 2wjpA AZI Rep, Mult 454,458,470
40.04 2 1n38A CH1 Rep, Mult 175,176,227,228,229,230
50.04 2 4zyrB 9PG Rep, Mult 119,126,222,246,250,251,254,386,389
60.02 1 4ay2A MG Rep, Mult 74,196
70.02 1 3nl5A TZE Rep, Mult 129,225
80.02 1 1n1hA MN Rep, Mult 102,103,104,241
90.02 1 3d1lA MPR Rep, Mult 405,408
100.02 1 3rkoN LFA Rep, Mult 131,147,148,151
110.02 1 3ukmA K Rep, Mult 220,229,310
120.02 1 5eqhA 5RF Rep, Mult 122,226,246,347,446,447,454,470,474,477,478
130.02 1 2zofA MN Rep, Mult 99,139,371
140.02 1 3orgA CL Rep, Mult 100,104,514
150.02 1 3rf3A III Rep, Mult 166,167,171,174
160.02 1 5aymA FE2 Rep, Mult 118,122,281,284,285
170.02 1 3rkoN LFA Rep, Mult 163,166,167,170,466,467
180.02 1 1jgtB MG Rep, Mult 102,196
190.02 1 5c65A Y01 Rep, Mult 160,331,342,346,350,476,479,484

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

RankCscoreECPDB
Hit
TM-scoreRMSDaIDENaCovEC NumberActive Site Residues
10.0601ea0A0.3068.100.0770.5251.4.1.13NA
20.0602pdaA0.3177.610.0700.5221.2.7.1NA
30.0601iduA0.3136.380.0490.4471.11.1.10NA
40.0602ivfA0.3198.230.0380.5551.17.99.2NA
50.0603gtgB0.3188.020.0560.5422.7.7.6147,151
60.0601lf6A0.3217.870.0300.5383.2.1.3NA
70.0601hi8A0.3148.120.0380.5442.7.7.48NA
80.0601ti2A0.3318.010.0450.5621.97.1.2NA
90.0601g8kA0.3137.620.0310.5071.20.98.1401
100.0601ofdA0.3337.450.0520.5331.4.7.1NA
110.0602r7oA0.3667.870.0460.6152.7.7.48208,209,212
120.0601llwA0.3207.690.0460.5241.4.7.1NA
130.0601g8kE0.3127.730.0310.5151.20.98.1NA
140.0601qhoA0.3197.680.0490.5203.2.1.133231
150.0601ti6A0.3328.010.0470.5621.97.1.2NA
160.0602j5wA0.3287.580.0520.5361.16.3.1NA
170.0601uwkA0.3237.590.0370.5164.2.1.49NA
180.0601n1hA0.3707.450.0500.5992.7.7.48NA
190.0602g49A0.3327.500.0310.5473.4.24.56NA

(a)CscoreEC is the confidence score for the EC number prediction. CscoreEC 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)RMSDa is the RMSD between residues that are structurally aligned by TM-align.
(d)IDENa 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

Homologous GO templates in PDB 
RankCscoreGOTM-scoreRMSDaIDENaCovPDB HitAssociated GO Terms
00.110.6113.360.090.693o7qA GO:0005886 GO:0005887 GO:0005975 GO:0006004 GO:0006810 GO:0008643 GO:0015150 GO:0015293 GO:0015517 GO:0015518 GO:0015535 GO:0015751 GO:0015756 GO:0015757 GO:0016020 GO:0016021 GO:0055085
10.110.5094.810.090.652xutA GO:0005215 GO:0006810 GO:0006857 GO:0015197 GO:0015833 GO:0016020 GO:0016021
20.090.5295.110.130.695ayoA GO:0005381 GO:0016020 GO:0016021 GO:0034755
30.090.5454.900.080.704uvmA GO:0005215 GO:0006810 GO:0006857 GO:0015197 GO:0015833 GO:0016020 GO:0016021
40.070.6214.130.080.744gbyA GO:0005215 GO:0005886 GO:0005887 GO:0006810 GO:0008643 GO:0015293 GO:0015519 GO:0015753 GO:0016020 GO:0016021 GO:0022857 GO:0022891 GO:0055085
50.070.6063.650.110.714zw9A GO:0005215 GO:0005355 GO:0005536 GO:0005886 GO:0005887 GO:0005975 GO:0006810 GO:0008643 GO:0015758 GO:0016020 GO:0016021 GO:0019852 GO:0022857 GO:0022891 GO:0033300 GO:0055056 GO:0055085 GO:0070062 GO:0070837 GO:1904659
60.070.5454.910.090.704xnjA GO:0005215 GO:0006810 GO:0006857 GO:0015197 GO:0015833 GO:0016020 GO:0016021 GO:0042802
70.070.6053.930.090.714ybqB GO:0003044 GO:0005215 GO:0005353 GO:0005355 GO:0005886 GO:0005887 GO:0006810 GO:0008643 GO:0015755 GO:0015758 GO:0016020 GO:0016021 GO:0016324 GO:0022857 GO:0022891 GO:0042383 GO:0055085 GO:0070061 GO:0071332 GO:1904659 GO:1990539
80.070.5395.270.090.715a2nA GO:0005215 GO:0005886 GO:0006810 GO:0006857 GO:0009414 GO:0009635 GO:0009734 GO:0010167 GO:0015112 GO:0015293 GO:0015706 GO:0016020 GO:0016021 GO:0042128 GO:0055085
90.070.5195.030.080.674q65A GO:0005215 GO:0005886 GO:0005887 GO:0006810 GO:0006857 GO:0015031 GO:0015197 GO:0015333 GO:0015833 GO:0015992 GO:0016020 GO:0016021 GO:0042936 GO:0042938
100.070.5654.550.080.705eqgA GO:0000139 GO:0001939 GO:0005215 GO:0005355 GO:0005622 GO:0005737 GO:0005829 GO:0005886 GO:0005887 GO:0005901 GO:0005911 GO:0005989 GO:0006461 GO:0006810 GO:0006970 GO:0008643 GO:0015758 GO:0016020 GO:0016021 GO:0016323 GO:0016324 GO:0019852 GO:0019900 GO:0022857 GO:0022891 GO:0030496 GO:0030864 GO:0031982 GO:0033300 GO:0042149 GO:0042470 GO:0042802 GO:0042908 GO:0042910 GO:0043621 GO:0045121 GO:0050796 GO:0055056 GO:0055085 GO:0070062 GO:0070837 GO:0072562 GO:1904659
110.070.5445.390.090.734ikvA GO:0005215 GO:0006810 GO:0006857 GO:0015197 GO:0015833 GO:0016020 GO:0016021
120.070.5215.580.070.704tpgA GO:0005215 GO:0005427 GO:0006810 GO:0006857 GO:0015197 GO:0015833 GO:0016020 GO:0016021 GO:0035672 GO:0042802
130.070.5654.250.090.694zp0A GO:0005215 GO:0005886 GO:0005887 GO:0006810 GO:0006855 GO:0015238 GO:0015385 GO:0015386 GO:0016020 GO:0016021 GO:0030641 GO:0035725 GO:0046677 GO:0055085 GO:0071805
140.070.5644.570.090.704yb9D GO:0003044 GO:0005215 GO:0005353 GO:0005886 GO:0005887 GO:0006810 GO:0008643 GO:0009750 GO:0015755 GO:0016020 GO:0016021 GO:0016324 GO:0022857 GO:0022891 GO:0042383 GO:0055085 GO:0070061 GO:0071332 GO:1990539
150.070.5554.510.060.684j05A GO:0005215 GO:0016020 GO:0016021 GO:0022857 GO:0055085
160.070.5495.490.070.744oh3A GO:0005215 GO:0005886 GO:0006810 GO:0006857 GO:0009414 GO:0009635 GO:0009734 GO:0010167 GO:0015112 GO:0015293 GO:0015706 GO:0016020 GO:0016021 GO:0042128 GO:0055085
170.070.5574.640.100.694ldsA GO:0005215 GO:0006810 GO:0016020 GO:0016021 GO:0022857 GO:0022891 GO:0055085
180.070.5515.430.090.744oh3B GO:0005215 GO:0005886 GO:0006810 GO:0006857 GO:0009414 GO:0009635 GO:0009734 GO:0010167 GO:0015112 GO:0015293 GO:0015706 GO:0016020 GO:0016021 GO:0042128 GO:0055085
190.070.5444.850.080.694ja4A GO:0005215 GO:0005886 GO:0005887 GO:0006810 GO:0008643 GO:0015293 GO:0015519 GO:0015753 GO:0016020 GO:0016021 GO:0022857 GO:0022891 GO:0055085
200.070.5315.350.100.712cfpA GO:0005351 GO:0005886 GO:0005887 GO:0006810 GO:0008643 GO:0015293 GO:0015528 GO:0015767 GO:0015992 GO:0016020 GO:0016021 GO:0030395 GO:0055085
210.070.5024.850.080.642gfpA GO:0005886 GO:0006810 GO:0006855 GO:0015238 GO:0015893 GO:0016020 GO:0016021 GO:0055085
220.060.2227.470.040.361dceA GO:0004659 GO:0004663 GO:0005968 GO:0008270 GO:0008318 GO:0016740 GO:0017137 GO:0018342 GO:0018344
230.060.2587.290.050.415i1mV GO:0000220 GO:0000324 GO:0000329 GO:0005773 GO:0005774 GO:0006461 GO:0006797 GO:0006810 GO:0006811 GO:0007035 GO:0015078 GO:0015986 GO:0015991 GO:0015992 GO:0016020 GO:0016021 GO:0016049 GO:0033179 GO:0046961 GO:0051117 GO:0070072
240.060.2348.420.050.422d0oA GO:0000166 GO:0005524 GO:0046872
250.060.2287.460.060.371pquA GO:0003942 GO:0004073 GO:0005737 GO:0006520 GO:0008652 GO:0009085 GO:0009086 GO:0009088 GO:0009089 GO:0009097 GO:0016491 GO:0016620 GO:0019877 GO:0046983 GO:0050661 GO:0051287 GO:0055114 GO:0071266
260.060.2426.810.070.364jevB GO:0003824 GO:0003992 GO:0005737 GO:0005829 GO:0006520 GO:0006525 GO:0006526 GO:0008483 GO:0008652 GO:0009016 GO:0009085 GO:0009089 GO:0016740 GO:0030170 GO:0042802
270.060.2096.970.040.322f8lA GO:0003677 GO:0006306 GO:0008170 GO:0046872 GO:0051536 GO:0051539


Consensus prediction of GO terms
 
Molecular Function GO:0022892 GO:0015291
GO-Score 0.38 0.35
Biological Processes GO:0015833 GO:0044765 GO:0044763
GO-Score 0.38 0.35 0.35
Cellular Component GO:0016021 GO:0031226
GO-Score 0.39 0.35

(a)CscoreGO 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)RMSDa is the RMSD between residues that are structurally aligned by TM-align.
(d)IDENa 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 CscoreGO 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.