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I-TASSER results for job id Rv3046c

[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
10.18 9 4zbfH 4M7 Rep, Mult 10,11,18,34,35,38,39,44,47,48,51,52,74
20.09 3 2d2mD OXY Rep, Mult 47,51
30.06 3 3dkpA ADP Rep, Mult 8,10,14,49,51,52,53
40.06 2 3ol3B IOD Rep, Mult 55,58,59,72
50.04 2 3kziA CLA Rep, Mult 51,55
60.03 1 3ol3A IOD Rep, Mult 10,11,14
70.03 1 3ol3B IOD Rep, Mult 17,20,74,87
80.03 1 3ol3B IOD Rep, Mult 50,57,80
90.02 1 3g5aA FMN Rep, Mult 30,31,35,48,52,80
100.02 1 2xzoA MG Rep, Mult 37,38,39,40,42,44
110.02 1 1s5lL CLA Rep, Mult 18,22

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
10.0602hyiI0.4773.940.0500.7263.6.4.13NA
20.0601in5A0.4674.010.0480.7583.6.4.12NA
30.0602db3A0.4933.900.0570.7823.6.4.1339
40.0602ocaA0.4843.920.0390.7503.6.4.1243
50.0602i7tA0.4334.560.0560.7503.1.27.-NA
60.0603i62A0.5464.190.0840.8633.6.4.13NA
70.0601pjrA0.4904.120.0660.7903.6.4.12NA
80.0602w00B0.5284.230.0610.9033.1.21.3NA
90.0601gl9B0.4803.900.0380.7585.99.1.3NA
100.0603n2oA0.4764.140.0950.7904.1.1.1954,75
110.0608ohmA0.4823.970.0590.7422.7.7.48NA
120.0603iceC0.4754.060.0750.7423.6.1.-46
130.0601nvbB0.4804.180.0760.7664.2.3.431
140.0601f20A0.4693.980.0430.7261.14.13.3912,78
150.0601tllA0.4903.990.0750.7741.14.13.39NA
160.0601auiA0.4723.990.0370.7903.1.3.16NA
170.0601rgqB0.2985.450.0350.6053.4.21.98NA
180.0602j6lB0.4564.320.0730.7741.2.1.31,1.2.1.3NA
190.0602is6A0.4833.930.0560.7823.6.4.12NA

(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
00.070.5454.230.070.873i5xA GO:0000166 GO:0000372 GO:0000373 GO:0003676 GO:0003723 GO:0004004 GO:0004386 GO:0005524 GO:0005739 GO:0005759 GO:0006392 GO:0006397 GO:0006417 GO:0008380 GO:0010501 GO:0016787 GO:0033592 GO:0034337
10.070.5104.300.040.844w7sA GO:0000166 GO:0000384 GO:0000395 GO:0003676 GO:0003723 GO:0004004 GO:0004386 GO:0005524 GO:0005634 GO:0005682 GO:0005737 GO:0006397 GO:0006413 GO:0007059 GO:0008380 GO:0010468 GO:0010501 GO:0016787 GO:0036464
20.070.4923.900.050.771wrbA GO:0000166 GO:0003676 GO:0004386 GO:0005524 GO:0016787
30.070.4753.510.060.691fuuB GO:0000166 GO:0003676 GO:0003723 GO:0003743 GO:0004004 GO:0004386 GO:0005524 GO:0005737 GO:0005840 GO:0006412 GO:0006413 GO:0006446 GO:0008186 GO:0010468 GO:0010501 GO:0016281 GO:0016787
40.070.4693.570.040.694u7dC GO:0000166 GO:0000724 GO:0000733 GO:0003676 GO:0003677 GO:0003678 GO:0004003 GO:0004386 GO:0005524 GO:0005634 GO:0005654 GO:0005694 GO:0005737 GO:0006281 GO:0006310 GO:0008026 GO:0009378 GO:0016020 GO:0016787 GO:0032508 GO:0036310 GO:0043140
50.070.4603.810.110.701hv8A GO:0000166 GO:0003676 GO:0003723 GO:0004004 GO:0004386 GO:0005524 GO:0010501 GO:0016787
60.070.4643.720.080.723iuyA GO:0000166 GO:0003676 GO:0003723 GO:0004004 GO:0004386 GO:0005524 GO:0005634 GO:0010501 GO:0016787
70.070.4874.090.030.775elxA GO:0000166 GO:0003676 GO:0003723 GO:0004386 GO:0005524 GO:0005634 GO:0005643 GO:0005737 GO:0006810 GO:0015031 GO:0016020 GO:0016787 GO:0031965 GO:0051028
80.070.4693.580.070.693eiqD GO:0000166 GO:0000289 GO:0000339 GO:0003676 GO:0003723 GO:0003725 GO:0003729 GO:0003743 GO:0004004 GO:0004386 GO:0005524 GO:0005634 GO:0005737 GO:0005829 GO:0006412 GO:0006413 GO:0006446 GO:0008135 GO:0010468 GO:0010501 GO:0016020 GO:0016032 GO:0016281 GO:0016787 GO:0016887 GO:0031012 GO:0031100 GO:0044822 GO:0070062
90.070.4613.680.100.705dtuA GO:0000166 GO:0003676 GO:0004386 GO:0005524 GO:0016787
100.070.4843.610.070.741xtkA GO:0000166 GO:0000245 GO:0000346 GO:0000398 GO:0001889 GO:0003676 GO:0003723 GO:0004004 GO:0004386 GO:0005524 GO:0005634 GO:0005654 GO:0005681 GO:0005687 GO:0005688 GO:0005737 GO:0006369 GO:0006397 GO:0006405 GO:0006406 GO:0006810 GO:0008186 GO:0008380 GO:0010501 GO:0016363 GO:0016607 GO:0016787 GO:0016887 GO:0017070 GO:0030621 GO:0031124 GO:0032403 GO:0032786 GO:0043008 GO:0043234 GO:0044822 GO:0045727 GO:0046784 GO:0051028 GO:0061051 GO:1904707 GO:2000002 GO:2000573
110.070.4424.030.070.745jbjA GO:0003677 GO:0005524 GO:0016787 GO:0016817
120.070.4853.960.090.745jb2A GO:0003677 GO:0005524 GO:0016787 GO:0016817
130.070.4823.940.080.762pl3A GO:0000166 GO:0003676 GO:0003723 GO:0003724 GO:0004004 GO:0004386 GO:0005524 GO:0010501 GO:0016787 GO:0044822
140.070.4783.920.050.733ex7C GO:0000166 GO:0000184 GO:0000289 GO:0000398 GO:0003676 GO:0003723 GO:0003729 GO:0004004 GO:0004386 GO:0005524 GO:0005634 GO:0005654 GO:0005681 GO:0005737 GO:0005829 GO:0006364 GO:0006369 GO:0006397 GO:0006405 GO:0006406 GO:0006417 GO:0006810 GO:0008143 GO:0008306 GO:0008380 GO:0010501 GO:0010629 GO:0014070 GO:0016020 GO:0016259 GO:0016607 GO:0016787 GO:0017148 GO:0030425 GO:0030529 GO:0031124 GO:0035145 GO:0035368 GO:0035613 GO:0035640 GO:0043021 GO:0043025 GO:0044822 GO:0045727 GO:0048701 GO:0051028 GO:0071013 GO:0072715 GO:0090394 GO:1902415 GO:1904570 GO:1904574 GO:1990416
150.070.4773.710.060.731s2mA GO:0000166 GO:0000290 GO:0000932 GO:0003676 GO:0003682 GO:0003723 GO:0003729 GO:0004004 GO:0004386 GO:0005524 GO:0005737 GO:0006397 GO:0006417 GO:0006810 GO:0010494 GO:0010501 GO:0016787 GO:0017148 GO:0033962 GO:0034063 GO:0045900 GO:0051028 GO:0090079
160.070.4643.980.080.721gm5A GO:0000166 GO:0003676 GO:0004003 GO:0004004 GO:0004386 GO:0005524 GO:0006281 GO:0006310 GO:0006974 GO:0010501 GO:0016787 GO:0032508
170.070.4893.700.110.753b7gA GO:0000122 GO:0000166 GO:0000244 GO:0000387 GO:0003676 GO:0003677 GO:0004004 GO:0004386 GO:0005524 GO:0005634 GO:0005654 GO:0005737 GO:0005829 GO:0005856 GO:0006396 GO:0006397 GO:0008285 GO:0008380 GO:0010501 GO:0016020 GO:0016787 GO:0017053 GO:0019904 GO:0030674 GO:0032797 GO:0034719 GO:0042826 GO:0043065 GO:0045892 GO:0048477 GO:0050810 GO:0051170 GO:0070491 GO:0090571 GO:0097504
180.070.4713.520.090.722j0uB GO:0000166 GO:0000184 GO:0000289 GO:0000398 GO:0003676 GO:0003723 GO:0003729 GO:0004004 GO:0004386 GO:0005524 GO:0005634 GO:0005654 GO:0005681 GO:0005737 GO:0005829 GO:0006364 GO:0006369 GO:0006397 GO:0006405 GO:0006406 GO:0006417 GO:0006810 GO:0008143 GO:0008306 GO:0008380 GO:0010501 GO:0010629 GO:0014070 GO:0016020 GO:0016259 GO:0016607 GO:0016787 GO:0017148 GO:0030425 GO:0030529 GO:0031124 GO:0035145 GO:0035368 GO:0035613 GO:0035640 GO:0043021 GO:0043025 GO:0044822 GO:0045727 GO:0048701 GO:0051028 GO:0071013 GO:0072715 GO:0090394 GO:1902415 GO:1904570 GO:1904574 GO:1990416


Consensus prediction of GO terms
 
Molecular Function GO:0035639 GO:0032559 GO:0032550 GO:0003724 GO:0008186 GO:0008026
GO-Score 0.58 0.58 0.58 0.37 0.37 0.37
Biological Processes GO:0016070
GO-Score 0.37
Cellular Component GO:0044424
GO-Score 0.37

(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.