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I-TASSER results for job id Rv1711

[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
10.55 12 1ksvA U Rep, Mult 117,118,119,122,149,197,203,204,205,206,219
20.22 4 3dh3A NUC Rep, Mult 15,17,18,27,28,29,32,49,51,86,89,90,111,113,116,117,119,120,122,132,135,136,139,140,149,200,203,204,205,206,219,221
30.19 9 3lwoA NUC Rep, Mult 88,114,115,116,117,119,120,149,174,176,200,204,205,206,219,221
40.02 1 3mm6D SF4 Rep, Mult 177,200,201,203,204,206,207,208
50.02 1 4nz6A DLY Rep, Mult 117,118,119,122,149,219
60.02 1 3lwrA RQA Rep, Mult 88,117,119

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
10.1621ze2B0.4242.950.2050.5004.2.1.70119,149
20.1411k8wA0.5623.100.1480.6654.2.1.70119,149
30.1071s71B0.5243.960.2310.6694.2.1.70119,149
40.0603gipA0.3945.690.0350.6653.5.1.8222
50.0602gv9B0.4225.400.1110.6652.7.7.7NA
60.0602v4jD0.4306.060.0320.7361.8.99.381
70.0603mtjA0.4185.640.0930.6771.1.1.320,38
80.0601chmA0.4245.460.0550.6773.5.3.325,27,34
90.0601rm6A0.4016.320.0370.7131.3.99.20NA
100.0603gh4A0.3956.340.0830.7173.2.1.52NA
110.0604kbpA0.3985.830.0300.6613.1.3.2NA
120.0603fwmA0.4045.840.0420.6892.4.1.129,NA
130.0601js4A0.4075.210.0620.6183.2.1.4NA
140.0603c20B0.3696.150.0670.6502.7.2.4110,112
150.0601k1dA0.3875.440.0600.6183.5.2.-185
160.0601yifA0.4115.600.0380.6733.2.1.37NA
170.0603fwlA0.4125.440.0360.6612.4.1.129NA
180.0603l24A0.3965.950.0480.6773.1.8.2,3.4.13.9,3.1.8.1250
190.0603c7bE0.4205.860.0720.7051.8.99.3NA

(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
00.540.8631.990.400.944lgtA GO:0000455 GO:0001522 GO:0003723 GO:0005829 GO:0006364 GO:0009451 GO:0009982 GO:0016853 GO:0016866
10.440.8991.050.340.923dh3B GO:0000455 GO:0001522 GO:0003723 GO:0005829 GO:0006364 GO:0009451 GO:0009982 GO:0016853 GO:0016866
20.410.6423.040.260.741kskA GO:0000455 GO:0001522 GO:0003723 GO:0005829 GO:0006364 GO:0009451 GO:0009982 GO:0016853 GO:0016866
30.340.6723.240.310.791vioA GO:0000455 GO:0001522 GO:0003723 GO:0005829 GO:0006364 GO:0009451 GO:0009982 GO:0016853 GO:0016866
40.320.5972.140.340.652omlA GO:0000455 GO:0001522 GO:0003723 GO:0005829 GO:0006364 GO:0009451 GO:0009982 GO:0016853 GO:0016866
50.060.3106.280.060.533wv6A GO:0002376 GO:0002519 GO:0004871 GO:0005534 GO:0005576 GO:0005615 GO:0005622 GO:0005634 GO:0005737 GO:0006935 GO:0006954 GO:0007565 GO:0010628 GO:0010629 GO:0019899 GO:0030246 GO:0032496 GO:0032673 GO:0032674 GO:0032682 GO:0032689 GO:0032720 GO:0032753 GO:0032834 GO:0034134 GO:0034142 GO:0038066 GO:0042346 GO:0043123 GO:0043305 GO:0045953 GO:0046007 GO:0046598 GO:0048030 GO:0050718 GO:0051092 GO:0060135 GO:0070062 GO:0070241 GO:0070371 GO:0070374 GO:0070555 GO:0071346 GO:0071636 GO:0071639 GO:0097029 GO:0098586 GO:1900744 GO:1902715 GO:1904469 GO:2000484 GO:2000510 GO:2000562 GO:2000563 GO:2000667 GO:2000670 GO:2000778 GO:2001181 GO:2001184 GO:2001190 GO:2001200 GO:2001269
60.060.2826.310.040.503ppsA GO:0005507 GO:0016491 GO:0046872 GO:0052716 GO:0055114
70.060.3676.380.050.653i01A GO:0003824 GO:0006091 GO:0015977 GO:0016151 GO:0016491 GO:0018492 GO:0043885 GO:0046872 GO:0051536 GO:0051539 GO:0055114
80.060.2695.660.050.443j9wAD GO:0003723 GO:0003735 GO:0005622 GO:0005840 GO:0006412 GO:0015935 GO:0019843 GO:0030529 GO:0045903
90.060.3146.290.040.552blfA GO:0016491 GO:0030151 GO:0042128 GO:0055114
100.060.2384.510.140.314a2iD GO:0000900 GO:0003723 GO:0003735 GO:0005622 GO:0005829 GO:0005840 GO:0006351 GO:0006353 GO:0006355 GO:0006412 GO:0006417 GO:0015935 GO:0019843 GO:0022627 GO:0030529 GO:0031564 GO:0045903 GO:0045947 GO:0046677 GO:0048027 GO:1990145
110.060.3316.260.030.584fn5A GO:0000166 GO:0003746 GO:0003924 GO:0005525 GO:0005622 GO:0005737 GO:0006412 GO:0006414
120.060.2596.110.050.454givA GO:0000070 GO:0000413 GO:0000794 GO:0003755 GO:0005634 GO:0005940 GO:0006457 GO:0016853 GO:0016925 GO:0031386 GO:0042802 GO:0046872
130.060.2686.290.040.483v7oB GO:0003723 GO:0006351 GO:0019012 GO:0019013 GO:0030430 GO:0046872
140.060.2454.400.170.354aqyD GO:0003723 GO:0003735 GO:0005622 GO:0005840 GO:0006412 GO:0015935 GO:0019843 GO:0030529 GO:0046872
150.060.2365.280.040.373ktsA GO:0003723 GO:0006071 GO:0006351 GO:0006355 GO:0009607
160.060.2023.080.150.242k6pA GO:0003723
170.060.2084.800.080.304y0bA GO:0009507 GO:0009532 GO:0009536 GO:0009570 GO:0009579 GO:0009941 GO:0019538
180.060.2274.800.100.333jteA GO:0000160 GO:0003824 GO:0005622


Consensus prediction of GO terms
 
Molecular Function GO:0009982 GO:0003723
GO-Score 0.93 0.93
Biological Processes GO:0000455
GO-Score 0.93
Cellular Component GO:0005829
GO-Score 0.93

(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.