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I-TASSER results for job id Rv0857

[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 26 3nmnA PYV Rep, Mult 59,69,72,74,85,87,93,96,132,136,137
20.09 11 4reiA 3MV Rep, Mult 29,59,61,72,74,85,98,114,136,137
30.09 11 4ryvA ZEA Rep, Mult 14,16,26,29,30,83,85,100,102,112,114,137,138,141
40.04 5 4a81A 2AN Rep, Mult 14,16,29,85,100,114,116,133,136,137,140,141
50.03 4 2qimA ZEA Rep, Mult 29,30,35,74,83,85,100,141
60.02 3 3tl1A JRO Rep, Mult 61,64,70,72,87,93,96,116,128,129,132,133,136
70.01 1 2qimA ZEA Rep, Mult 10,11,12,125,130,131
80.01 1 2xs4A MG Rep, Mult 37,40
90.01 1 3cz3B NUC Rep, Mult 123,124
100.01 2 4ryvA ZEA Rep, Mult 12,14,116,118,130,131,134
110.01 2 2bnwA NUC Rep, Mult 109,110,112,113
120.01 1 1bv10 III Rep, Mult 27,30,31,33,34,36,37,45,46,47,48,78,80
130.01 1 2bq8X ZN Rep, Mult 27,31
140.01 1 2wyiB PG0 Rep, Mult 139,142

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
10.0601t7nA0.5095.010.0480.8732.3.1.7NA
20.0601ndoA0.6103.860.1150.8981.14.12.1227,35,142
30.0601q23B0.5184.770.0490.8472.3.1.28NA
40.0602ihwA0.5164.920.0540.8412.3.1.168NA
50.0601dpbA0.5094.620.0700.8022.3.1.12NA
60.0601bibA0.5073.990.1080.7076.3.4.15NA
70.0601ciaA0.5144.640.0490.8222.3.1.28NA
80.0601z01A0.6323.330.0590.8221.14.13.6142
90.0601xl7B0.4954.520.0580.7962.3.1.137NA
100.0602fy3A0.5024.970.0280.8472.3.1.6NA
110.0602ewnA0.5273.820.0970.7206.3.4.15NA
120.0602vq5A0.6873.430.0680.9174.2.1.7846
130.0603l60A0.5244.500.0550.8152.3.1.12NA
140.0601b5sE0.5074.850.0690.8282.3.1.1229,97
150.0602ii4A0.5184.760.0600.8342.3.1.16861,120,131
160.0602b1xA0.6093.870.0770.8731.14.12.12NA
170.0602x4mA0.4855.220.0380.7963.4.23.48NA
180.0602de6B0.6333.840.0670.8661.14.12.-31
190.0601im0A0.4914.570.0300.7833.1.1.32,3.1.1.4NA

(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
00.300.8481.850.190.952rerA GO:0003824 GO:0008152 GO:0008168 GO:0008171 GO:0016740 GO:0017000 GO:0032259
10.250.8062.220.070.931em2A GO:0005737 GO:0005739 GO:0005765 GO:0005768 GO:0006629 GO:0006694 GO:0006701 GO:0006810 GO:0006839 GO:0006869 GO:0008202 GO:0008203 GO:0008289 GO:0015485 GO:0016020 GO:0016021 GO:0031902
20.230.7772.430.180.903p0lA GO:0005739 GO:0005758 GO:0005829 GO:0006082 GO:0006694 GO:0006699 GO:0006700 GO:0006701 GO:0006703 GO:0006810 GO:0006869 GO:0007420 GO:0007584 GO:0007623 GO:0008203 GO:0008211 GO:0008289 GO:0008584 GO:0009635 GO:0009636 GO:0010033 GO:0010212 GO:0010288 GO:0010628 GO:0014070 GO:0014823 GO:0015485 GO:0016101 GO:0017085 GO:0017127 GO:0017143 GO:0018879 GO:0018894 GO:0018958 GO:0018963 GO:0030061 GO:0031667 GO:0032367 GO:0032869 GO:0034698 GO:0035094 GO:0035457 GO:0042493 GO:0042542 GO:0042747 GO:0043005 GO:0043025 GO:0043434 GO:0043524 GO:0043627 GO:0044255 GO:0044321 GO:0044344 GO:0045471 GO:0046677 GO:0048168 GO:0048545 GO:0050769 GO:0050810 GO:0051412 GO:0060992 GO:0061370 GO:0071222 GO:0071236 GO:0071248 GO:0071276 GO:0071312 GO:0071320 GO:0071333 GO:0071346 GO:0071371 GO:0071372 GO:0071373 GO:0071378 GO:0071407 GO:0071549 GO:0071560 GO:0071872
30.190.7722.590.070.925brlA GO:0005739 GO:0005783 GO:0005829 GO:0006810 GO:0006869 GO:0008289 GO:0015485 GO:0016023 GO:0034435
40.190.7712.580.090.942r55A GO:0005829 GO:0006700 GO:0006810 GO:0006869 GO:0008289 GO:0032052
50.160.7922.480.080.942mouA GO:0006810 GO:0006869 GO:0008289
60.150.7393.270.140.943fo5A GO:0005737 GO:0005829 GO:0006631 GO:0008289 GO:0009266 GO:0009409 GO:0016787 GO:0035338 GO:0035556 GO:0047617 GO:0052689 GO:0070062
70.130.7142.760.130.871z94B GO:0006950
80.070.5983.590.140.802kewA GO:0006950
90.060.3765.620.070.723l2nA GO:0004180 GO:0004181 GO:0006508 GO:0008270 GO:0046872
100.060.4034.950.080.694iilA GO:0005886 GO:0016020
110.060.3285.330.060.543rd7B GO:0006637 GO:0047617
120.060.3205.140.060.554d4zB GO:0004497 GO:0005829 GO:0008612 GO:0016491 GO:0019135 GO:0046872 GO:0055114
130.060.3545.720.050.652qk4B GO:0000166 GO:0003360 GO:0003824 GO:0004637 GO:0004641 GO:0004644 GO:0005524 GO:0005737 GO:0005829 GO:0006164 GO:0006189 GO:0006544 GO:0008152 GO:0009058 GO:0009113 GO:0009156 GO:0009168 GO:0010033 GO:0010035 GO:0016740 GO:0016742 GO:0016874 GO:0021549 GO:0021987 GO:0046654 GO:0046872 GO:0070062
140.060.3245.300.030.591z05A GO:0003700 GO:0006355 GO:0046872
150.060.2755.480.060.521lldA GO:0003824 GO:0004459 GO:0005737 GO:0005975 GO:0006096 GO:0016491 GO:0016616 GO:0019752 GO:0055114
160.060.2535.260.070.474v6wAI GO:0000462 GO:0003735 GO:0005622 GO:0005840 GO:0006412 GO:0022008 GO:0022627 GO:0030529 GO:0035167
170.060.3555.160.040.645bsmA GO:0000166 GO:0003824 GO:0005524 GO:0008152 GO:0009698 GO:0016207 GO:0016874
180.060.2343.200.040.294iylA GO:0003723 GO:0003735 GO:0005622 GO:0005840 GO:0006412 GO:0019843 GO:0030529
190.060.2134.510.040.341ihjB GO:0005198 GO:0005516 GO:0005886 GO:0007601 GO:0007602 GO:0007605 GO:0008104 GO:0009881 GO:0016020 GO:0016027 GO:0016028 GO:0016059 GO:0017022 GO:0030159 GO:0031473 GO:0050896 GO:0050962 GO:0071482


Consensus prediction of GO terms
 
Molecular Function GO:0015485 GO:0015248 GO:0033293 GO:0008171
GO-Score 0.54 0.47 0.38 0.30
Biological Processes GO:0071385 GO:0071559 GO:0071548 GO:0043066 GO:0071241 GO:0001678 GO:0071870 GO:0071331 GO:0000302 GO:0046890 GO:0008210 GO:0007417 GO:0010604 GO:0071871 GO:1901215 GO:0042537 GO:0034699 GO:0032354 GO:0009749 GO:0050767 GO:0051591 GO:0043648 GO:0051962 GO:0050802 GO:0046483 GO:0009314 GO:0071375 GO:0006721 GO:1901617 GO:0097305 GO:0072330 GO:0032868 GO:0060416 GO:0071345 GO:0071363 GO:0071774 GO:0032496 GO:0071219 GO:0006805 GO:0030301 GO:0031667 GO:0060322 GO:0035455 GO:0032366 GO:0046686 GO:1901655 GO:0051385 GO:0071371 GO:0009404 GO:0010468 GO:0010720 GO:0043523 GO:0034341 GO:0008406 GO:0046546 GO:0043279 GO:0019218 GO:0008206 GO:0048167 GO:0006701 GO:0008203 GO:0034434 GO:0032259 GO:0017000
GO-Score 0.47 0.47 0.47 0.47 0.47 0.47 0.47 0.47 0.47 0.47 0.47 0.47 0.47 0.47 0.47 0.47 0.47 0.47 0.47 0.47 0.47 0.47 0.47 0.47 0.47 0.47 0.47 0.47 0.47 0.47 0.47 0.47 0.47 0.47 0.47 0.47 0.47 0.47 0.47 0.47 0.47 0.47 0.47 0.47 0.47 0.47 0.47 0.47 0.47 0.47 0.47 0.47 0.47 0.47 0.47 0.47 0.47 0.47 0.47 0.42 0.42 0.39 0.30 0.30
Cellular Component GO:0098852 GO:0005764 GO:0010008 GO:0005770 GO:0005829 GO:0031970 GO:0044297 GO:0005743 GO:0044455 GO:0036477 GO:0042995 GO:0031224 GO:0031988 GO:0031410
GO-Score 0.50 0.50 0.50 0.50 0.50 0.47 0.47 0.47 0.47 0.47 0.47 0.40 0.39 0.39

(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.