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I-TASSER results for job id Rv0738

[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
10.63 9 2nsfA ZN Rep, Mult 43,112,116
20.05 1 3qnqA ZDM Rep, Mult 19,112,113,116,121

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
10.0601kblA0.4295.410.0570.7362.7.9.1NA
20.0601fbvA0.4323.830.0540.5886.3.2.19NA
30.0601ra0A0.4125.420.0520.7423.5.4.1NA
40.0601is2A0.4204.580.0530.6541.3.3.6NA
50.0601n1hA0.4224.780.0400.6592.7.7.4812
60.0602ix4A0.3255.490.0540.5772.3.1.41NA
70.0601kc7A0.4245.570.0430.7472.7.9.1132
80.0603b7wA0.4235.290.0520.7366.2.1.2NA
90.0601ua4A0.4275.220.0680.7252.7.1.14743,75
100.0601qi9B0.4265.510.0410.7531.11.1.1043,116
110.0602z8yP0.4484.110.0940.6702.3.1.16914
120.0602z8yD0.4395.370.0630.7251.2.7.4,1.2.99.2128
130.0602jkpB0.4385.450.0540.7693.2.1.20NA
140.0601w0iA0.4265.400.0840.7532.3.1.41NA
150.0601pz2A0.4195.470.0580.7423.2.1.5510
160.0602fonB0.3855.550.0580.6921.3.3.6NA
170.0601jqkF0.4914.580.0650.7361.2.99.2114
180.0603djlA0.4695.070.0480.7801.3.99.-NA
190.0601jdaA0.3355.240.0460.5773.2.1.60NA

(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
00.390.9311.890.180.992nsfA GO:0046872
10.070.5924.220.070.814x8bA GO:0004497 GO:0005506 GO:0016491 GO:0016705 GO:0046872 GO:0052699 GO:0055114
20.070.5752.880.090.703dkaB GO:0046872
30.060.3694.240.080.544xevA GO:0000165 GO:0000166 GO:0000302 GO:0001525 GO:0001556 GO:0001666 GO:0001954 GO:0002040 GO:0002250 GO:0002315 GO:0002376 GO:0002688 GO:0004672 GO:0004683 GO:0004713 GO:0004715 GO:0004871 GO:0004972 GO:0005102 GO:0005524 GO:0005634 GO:0005654 GO:0005737 GO:0005829 GO:0005856 GO:0005886 GO:0005925 GO:0005938 GO:0006461 GO:0006468 GO:0006915 GO:0006950 GO:0006968 GO:0006970 GO:0007015 GO:0007155 GO:0007165 GO:0007166 GO:0007172 GO:0007173 GO:0007204 GO:0007229 GO:0008284 GO:0008285 GO:0008360 GO:0009612 GO:0009725 GO:0009749 GO:0010226 GO:0010243 GO:0010595 GO:0010656 GO:0010752 GO:0010758 GO:0010976 GO:0014009 GO:0014069 GO:0016020 GO:0016301 GO:0016310 GO:0016740 GO:0017146 GO:0018108 GO:0030027 GO:0030054 GO:0030154 GO:0030155 GO:0030279 GO:0030307 GO:0030334 GO:0030335 GO:0030424 GO:0030425 GO:0030426 GO:0030500 GO:0030502 GO:0030826 GO:0030838 GO:0031175 GO:0031234 GO:0032270 GO:0032403 GO:0032960 GO:0033209 GO:0035235 GO:0035902 GO:0038083 GO:0042127 GO:0042220 GO:0042493 GO:0042542 GO:0042976 GO:0042995 GO:0043025 GO:0043066 GO:0043149 GO:0043267 GO:0043423 GO:0043507 GO:0043524 GO:0043534 GO:0043552 GO:0044297 GO:0045087 GO:0045121 GO:0045428 GO:0045429 GO:0045453 GO:0045471 GO:0045638 GO:0045727 GO:0045765 GO:0045766 GO:0045860 GO:0046330 GO:0046777 GO:0048010 GO:0048041 GO:0048471 GO:0050731 GO:0050848 GO:0051000 GO:0051279 GO:0051591 GO:0051592 GO:0051968 GO:0060291 GO:0060292 GO:0070098 GO:0070374 GO:0071300 GO:0071498 GO:0090630 GO:0097440 GO:2000058 GO:2000060 GO:2000114 GO:2000249 GO:2000310 GO:2000379 GO:2000463 GO:2000538 GO:2000573
40.060.3515.740.100.652x7gA GO:0000166 GO:0000245 GO:0000287 GO:0001525 GO:0004672 GO:0004674 GO:0005524 GO:0005634 GO:0005654 GO:0005730 GO:0005737 GO:0006397 GO:0006468 GO:0008284 GO:0008380 GO:0010628 GO:0016301 GO:0016310 GO:0016740 GO:0030154 GO:0035063 GO:0035556 GO:0043525 GO:0044822 GO:0045070 GO:0045071 GO:0045087 GO:0045787 GO:0048024 GO:0071889
50.060.3675.270.040.603fwnA GO:0004616 GO:0005829 GO:0006098 GO:0016491 GO:0019521 GO:0042802 GO:0042803 GO:0055114
60.060.3325.730.060.604kyoC GO:0003824 GO:0004760 GO:0005102 GO:0005739 GO:0005759 GO:0005777 GO:0005782 GO:0007219 GO:0008453 GO:0008483 GO:0009436 GO:0010498 GO:0016597 GO:0016740 GO:0019265 GO:0019448 GO:0030170 GO:0042803 GO:0042853 GO:0042866 GO:0043621 GO:0046487 GO:0046724 GO:0051384 GO:0051591
70.060.3355.790.060.601y1hX GO:0005783 GO:0005788 GO:0006687 GO:0016491 GO:0042803 GO:0043687 GO:0046872 GO:0055114
80.060.2896.110.040.562y3cA GO:0046872
90.060.3285.470.030.543b8gA GO:0004042 GO:0005737 GO:0006526 GO:0008080 GO:0008652 GO:0016740 GO:0016746
100.060.3065.450.040.534gh8A GO:0004146 GO:0005829 GO:0006545 GO:0006730 GO:0009165 GO:0016491 GO:0031427 GO:0042493 GO:0046654 GO:0046677 GO:0050661 GO:0055114
110.060.3125.450.050.571y4jB GO:0005783 GO:0005788 GO:0043687 GO:0046872
120.060.3595.890.070.691kfqA GO:0000287 GO:0004614 GO:0005737 GO:0005975 GO:0016853 GO:0016868 GO:0046872 GO:0071704
130.060.3415.640.070.635dn1A GO:0000105 GO:0000162 GO:0003824 GO:0003949 GO:0004640 GO:0005622 GO:0005737 GO:0008152 GO:0008652 GO:0009073 GO:0016853
140.060.3445.570.060.613amgB GO:0004553 GO:0005576 GO:0005975 GO:0006073 GO:0008152 GO:0008422 GO:0009251 GO:0009986 GO:0016787 GO:0016798
150.060.2395.400.060.404wp5A GO:0005634 GO:0051028
160.060.2885.990.030.562q17E GO:0046872
170.060.2855.160.080.474meeA GO:0005576 GO:0007155 GO:0009279 GO:0009405 GO:0009986 GO:0016020 GO:0016021 GO:0019867 GO:0042597
180.060.2515.890.060.484qzvB GO:0009405 GO:0016020 GO:0016021 GO:0016032 GO:0019012 GO:0019031 GO:0019062 GO:0033644 GO:0039663 GO:0044173 GO:0046718 GO:0046813 GO:0055036 GO:0061025


Consensus prediction of GO terms
 
Molecular Function GO:0046872
GO-Score 0.47
Biological Processes GO:0008284 GO:0045087 GO:0052699 GO:0055114 GO:0000245 GO:0010226 GO:0008360 GO:0007229 GO:0001556 GO:0045787 GO:0032960 GO:0030838 GO:2000573 GO:0043552 GO:0007173 GO:0070374 GO:0001954 GO:2000538 GO:0050848 GO:0042542 GO:0071300 GO:0048010 GO:0010595 GO:0071498 GO:0050731 GO:0045766 GO:0048041 GO:0045471 GO:0009725 GO:0043524 GO:0043507 GO:0030502 GO:0002040 GO:0060291 GO:2000249 GO:2000114 GO:0035063 GO:0006970 GO:0045453 GO:0042220 GO:0010758 GO:0002315 GO:0009749 GO:0008285 GO:0045638 GO:0007172 GO:0090630 GO:0014009 GO:2000060 GO:0001666 GO:0043525 GO:0060292 GO:0035235 GO:0002250 GO:0038083 GO:0045070 GO:2000463 GO:0010752 GO:0045071 GO:0030826 GO:0051591 GO:0043534 GO:0033209 GO:2000310 GO:0006968 GO:0042493 GO:0010656 GO:0010976 GO:0048024 GO:0043149 GO:0051000 GO:0043267 GO:0051592 GO:0042976 GO:0070098 GO:0051968 GO:0051279 GO:0045727 GO:0045429 GO:0009612 GO:0030307 GO:0035902
GO-Score 0.12 0.12 0.07 0.07 0.06 0.06 0.06 0.06 0.06 0.06 0.06 0.06 0.06 0.06 0.06 0.06 0.06 0.06 0.06 0.06 0.06 0.06 0.06 0.06 0.06 0.06 0.06 0.06 0.06 0.06 0.06 0.06 0.06 0.06 0.06 0.06 0.06 0.06 0.06 0.06 0.06 0.06 0.06 0.06 0.06 0.06 0.06 0.06 0.06 0.06 0.06 0.06 0.06 0.06 0.06 0.06 0.06 0.06 0.06 0.06 0.06 0.06 0.06 0.06 0.06 0.06 0.06 0.06 0.06 0.06 0.06 0.06 0.06 0.06 0.06 0.06 0.06 0.06 0.06 0.06 0.06 0.06
Cellular Component GO:0005654 GO:0045121 GO:0030027 GO:0030424 GO:0031234 GO:0005829 GO:0043025 GO:0048471 GO:0005856 GO:0005730 GO:0014069 GO:0005938 GO:0005925 GO:0017146 GO:0097440 GO:0030426
GO-Score 0.12 0.06 0.06 0.06 0.06 0.06 0.06 0.06 0.06 0.06 0.06 0.06 0.06 0.06 0.06 0.06

(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.