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I-TASSER results for job id Rv3135

[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
10.07 3 5da5E GOA Rep, Mult 37,41,76
20.05 2 4n7kL LDA Rep, Mult 30,31,90
30.05 2 2jj1G PIT Rep, Mult 42,45,46,49,50
40.05 2 2vs0B ZN Rep, Mult 36,84
50.04 2 1hjbA NUC Rep, Mult 71,72,75,76,78,79,82
60.02 1 3io4C CA Rep, Mult 94,97,98
70.02 1 3sjqC PHU Rep, Mult 100,103
80.02 1 1xrrA PRO Rep, Mult 68,72,101,107,108
90.02 1 1xvbB BBX Rep, Mult 27,31,105
100.02 1 3k7tA GP7 Rep, Mult 19,20
110.02 1 1f8rC UUU Rep, Mult 69,72
120.02 1 2hydA NA Rep, Mult 123,124,126,130
130.02 1 1vm1A TAZ Rep, Mult 3,9
140.02 1 2g381 III Rep, Mult 3,14,15,17,18,19,20,23,24,27,30,31,33,34,37,38,40,41,44,45,48,52,57,65,72,75,83,86,90,97
150.02 1 1xrpA III Rep, Mult 65,72,92,95,96,101
160.02 1 3c9iC XE Rep, Mult 97,100
170.02 1 3io6A CA Rep, Mult 9,12

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
10.1891cxzB0.4562.330.0470.5452.7.11.1338,42
20.1261urfA0.4612.730.1010.5762.7.11.1385
30.0601qd1B0.2564.660.0690.4552.1.2.5,4.3.1.4NA
40.0601tj7A0.5092.780.0710.6444.3.2.1NA
50.0601wleB0.5313.070.0380.6976.1.1.1143
60.0602iw5A0.5963.870.0380.9011.-.-.-NA
70.0601is2A0.5082.940.0630.6361.3.3.6NA
80.0603i9wA0.6072.980.0550.7882.7.13.333,38
90.0602pfdB0.5063.010.0540.6672.1.2.5,4.3.1.46
100.0602o6yA0.5063.840.0700.7204.3.1.-NA
110.0602b5uA0.6563.350.0530.9243.1.-.-32
120.0601w07B0.5482.560.0700.6591.3.3.6NA
130.0602fenD0.5023.110.0800.6515.5.1.2NA
140.0601z0hB0.2435.460.0000.4853.4.24.6974
150.0601vdkA0.5182.760.0560.6514.2.1.2NA
160.0602pmzQ0.5113.940.0440.7052.7.7.614,111
170.0601a31A0.3664.090.0440.5915.99.1.291
180.0601p49A0.5513.920.0420.8263.1.6.2NA
190.0602fonB0.5512.600.0630.6591.3.3.6NA
200.0601c3cA0.5012.640.0390.6294.3.2.2NA
210.0602zr3B0.5603.050.0160.7276.1.1.11NA

(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
00.420.9171.310.300.994kxrB GO:0005576 GO:0009405 GO:0009986
10.250.7392.300.070.913zx6A GO:0004871 GO:0004888 GO:0005886 GO:0005887 GO:0006935 GO:0007165 GO:0016020 GO:0016021 GO:0043200 GO:0043424 GO:0046872 GO:0048870
20.240.7032.650.050.913g67A GO:0004871 GO:0007165 GO:0016020
30.210.3632.130.120.424jzlA GO:0000139 GO:0002474 GO:0005739 GO:0005783 GO:0005784 GO:0005789 GO:0005811 GO:0005829 GO:0005887 GO:0006810 GO:0006886 GO:0006888 GO:0006915 GO:0006921 GO:0007204 GO:0007283 GO:0015031 GO:0016020 GO:0016021 GO:0016192 GO:0030136 GO:0032403 GO:0032471 GO:0032580 GO:0033116 GO:0035584 GO:0042288 GO:0043280 GO:0051561 GO:0070973 GO:0071556 GO:0097038 GO:1903071 GO:1904154 GO:2001244
40.190.6092.390.100.712vrzA GO:0005576 GO:0009405
50.160.6612.900.080.884xxxA GO:0005576 GO:0009405 GO:0044315
60.140.7252.390.160.893j83A GO:0005576 GO:0009405 GO:0044315
70.130.6843.120.080.951y2oA GO:0001726 GO:0005737 GO:0005829 GO:0005856 GO:0005886 GO:0005913 GO:0007009 GO:0007409 GO:0008022 GO:0008093 GO:0008286 GO:0008360 GO:0009617 GO:0014069 GO:0015629 GO:0016020 GO:0016358 GO:0030141 GO:0030165 GO:0030175 GO:0030838 GO:0032956 GO:0038096 GO:0042802 GO:0042995 GO:0043005 GO:0043025 GO:0043197 GO:0048010 GO:0048167 GO:0051017 GO:0051764 GO:0061003 GO:0070062 GO:0070064 GO:0097481 GO:0098609 GO:0098641 GO:2000251
80.110.7152.630.080.902ch7A GO:0004871 GO:0005886 GO:0006935 GO:0007165 GO:0016020 GO:0016021
90.110.4992.960.030.651envA GO:0000122 GO:0000790 GO:0000978 GO:0000981 GO:0001080 GO:0001084 GO:0001135 GO:0001190 GO:0001191 GO:0002223 GO:0003677 GO:0003682 GO:0003700 GO:0005198 GO:0005634 GO:0005667 GO:0006351 GO:0006355 GO:0006366 GO:0008652 GO:0010691 GO:0016020 GO:0016021 GO:0016032 GO:0019012 GO:0019031 GO:0019062 GO:0019064 GO:0019082 GO:0020002 GO:0030683 GO:0033644 GO:0039654 GO:0039663 GO:0042802 GO:0043565 GO:0044174 GO:0044175 GO:0045899 GO:0046718 GO:0055036 GO:0060261 GO:0075509 GO:0075512 GO:1903833
100.110.7102.840.050.892d1lA GO:0001701 GO:0002230 GO:0003779 GO:0003785 GO:0005102 GO:0005737 GO:0005856 GO:0005912 GO:0007009 GO:0007015 GO:0007399 GO:0007517 GO:0010960 GO:0015629 GO:0030036 GO:0030041 GO:0030282 GO:0032233 GO:0034334 GO:0042802 GO:0050680 GO:0051015 GO:0061333 GO:0071498 GO:0072001 GO:0072102 GO:0072160 GO:0098792 GO:2001013
110.110.4222.310.110.504bl6C GO:0003729 GO:0005737 GO:0005794 GO:0005829 GO:0005856 GO:0006810 GO:0007275 GO:0007293 GO:0007294 GO:0007309 GO:0007310 GO:0007312 GO:0007314 GO:0008103 GO:0008298 GO:0016325 GO:0017137 GO:0019233 GO:0030100 GO:0030154 GO:0030669 GO:0030727 GO:0032050 GO:0045502 GO:0048477 GO:0048488 GO:0050658 GO:0051028 GO:0070727 GO:2000302 GO:2000370
120.100.6603.310.040.923ok8A GO:0005543 GO:0005829 GO:0005886 GO:0007009 GO:0008093 GO:0008286 GO:0008289 GO:0012506 GO:0015629 GO:0016020 GO:0030054 GO:0030659 GO:0030838 GO:0031410 GO:0044291 GO:0051017 GO:0051764 GO:0061024 GO:0071439 GO:2000251
130.100.4652.840.060.612oszA GO:0005487 GO:0005634 GO:0005635 GO:0005643 GO:0006810 GO:0006913 GO:0008139 GO:0015031 GO:0016020 GO:0031965 GO:0042306 GO:0043234 GO:0051028 GO:0051260 GO:0051290 GO:0051291 GO:0070208
140.070.5153.070.060.674uxvA GO:0000921 GO:0005886 GO:0005940 GO:0007049 GO:0016020 GO:0016021 GO:0051301 GO:0051781
150.060.4272.260.060.512c2jA GO:0005737 GO:0006879 GO:0006950 GO:0008199 GO:0016491 GO:0046872 GO:0055114
160.060.3981.930.050.462npsD GO:0000139 GO:0005484 GO:0005769 GO:0005794 GO:0005802 GO:0005829 GO:0005886 GO:0006810 GO:0006886 GO:0006906 GO:0007032 GO:0015031 GO:0016020 GO:0016021 GO:0016192 GO:0019905 GO:0030136 GO:0031201 GO:0032456 GO:0032588 GO:0032880 GO:0042147 GO:0043195 GO:0045335 GO:0048193 GO:0048278 GO:0048471 GO:0090161 GO:1903827
170.060.4194.010.030.675a20A GO:0019012 GO:0019028 GO:0019076 GO:0046718 GO:0046729
180.060.4033.900.030.612jesA GO:0019012 GO:0019028 GO:0019076 GO:0046718 GO:0046729
190.060.3502.450.080.445fvlA GO:0000166 GO:0005524 GO:0005634 GO:0005768 GO:0006810 GO:0007033 GO:0008568 GO:0010008 GO:0015031 GO:0016020 GO:0016125 GO:0016236 GO:0016887 GO:0031122 GO:0032511 GO:0042802 GO:0042803 GO:0045053 GO:0045324 GO:0051260 GO:0070676 GO:1990621


Consensus prediction of GO terms
 
Molecular Function GO:0099600 GO:0043169 GO:0038023 GO:0019901 GO:0042287 GO:0044877
GO-Score 0.50 0.50 0.50 0.50 0.43 0.43
Biological Processes GO:0009405 GO:0001101 GO:1901700 GO:0010243 GO:0042330 GO:0006928 GO:0051674 GO:0051560 GO:0097194 GO:1902533 GO:0070972 GO:0048002 GO:0070863 GO:1904152 GO:1904294 GO:2001056 GO:1903069 GO:0051480 GO:0032469 GO:2001235 GO:0022411 GO:0048193 GO:0048232 GO:0043281 GO:0032436 GO:0019722 GO:2001242
GO-Score 0.53 0.50 0.50 0.50 0.50 0.50 0.50 0.43 0.43 0.43 0.43 0.43 0.43 0.43 0.43 0.43 0.43 0.43 0.43 0.43 0.43 0.43 0.43 0.43 0.43 0.43 0.43
Cellular Component GO:0005576 GO:0030176 GO:0048471 GO:0031985 GO:0005793 GO:0030135 GO:0071256 GO:0098553 GO:0043232 GO:0009986 GO:0005887
GO-Score 0.53 0.43 0.43 0.43 0.43 0.43 0.43 0.43 0.43 0.42 0.41

(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.