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I-TASSER results for job id Rv2644c

[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
10.10 6 2vdoA III Rep, Mult 24,39,40,41,48
20.03 2 1lshB UPL Rep, Mult 27,37
30.03 2 1y9mA UUU Rep, Mult 16,18,22,44,45
40.03 2 4a99C MIY Rep, Mult 49,94,97,98,101
50.03 2 4gaqN MG Rep, Mult 84,86
60.03 2 1d2vC BR Rep, Mult 76,79
70.03 2 1sumB FE Rep, Mult 82,86,89
80.02 1 1s56B XE Rep, Mult 41,98,102
90.02 1 3ijeA UUU Rep, Mult 9,27,60,61
100.02 1 1bizB CAC Rep, Mult 12,13,25,92
110.02 1 3a9gA TRE Rep, Mult 3,5,6,8,11,12
120.02 1 2wse3 CLA Rep, Mult 20,79
130.02 1 3aebC EPH Rep, Mult 38,102
140.02 1 3fcsC IMD Rep, Mult 58,61,63,75
150.02 1 1dckA MN Rep, Mult 19,53,56
160.02 1 3vbiC BCT Rep, Mult 91,92
170.02 1 1tyeC CA Rep, Mult 49,51,53,79
180.02 1 2nvxB DUT Rep, Mult 75,76

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
10.0601wyvB0.4423.780.0340.6951.4.4.2NA
20.0601ps0A0.4344.520.0680.8381.1.1.2NA
30.0601ivyA0.4444.540.0300.8193.4.16.5NA
40.0601by8A0.4384.870.0490.8573.4.22.38NA
50.0602qr5A0.3994.790.0670.7433.4.19.1103
60.0601aorB0.4434.770.0410.8861.2.7.512,39,41
70.0601avpA0.4364.000.0390.7143.4.22.3948
80.0601yqdA0.4354.600.0830.8001.1.1.195NA
90.0601pl7A0.4394.650.0650.8091.1.1.1412,31
100.0603c7oA0.4344.600.0670.7813.2.1.5537
110.0601s4vB0.4374.720.0400.8383.4.22.-NA
120.0601aecA0.4364.690.0490.8383.4.22.14NA
130.0601m6dA0.4354.770.0890.8293.4.22.41NA
140.0603jxfB0.4434.400.0410.8093.1.3.48NA
150.0601cqdA0.4354.800.0400.8383.4.22.67NA
160.0601s6yA0.4384.630.0660.8383.2.1.8654
170.0603elqB0.4594.940.0520.8862.8.2.22NA
180.0601cqdC0.4354.800.0400.8383.4.22.6711,13
190.0608pchA0.4444.710.0400.8573.4.22.16NA

(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
00.070.4374.290.040.754irzA GO:0003366 GO:0005886 GO:0005925 GO:0007155 GO:0007159 GO:0007160 GO:0007229 GO:0008305 GO:0009986 GO:0016020 GO:0016021 GO:0034113 GO:0034446 GO:0034669 GO:0035987 GO:0043113 GO:0046872 GO:0050839 GO:0050901 GO:0070062 GO:0090074
10.070.4134.460.060.743k6sC GO:0004872 GO:0005886 GO:0007155 GO:0007229 GO:0008305 GO:0009887 GO:0009986 GO:0016020 GO:0016021 GO:0030198 GO:0034113 GO:0046872 GO:0050900 GO:1903955
20.060.4124.450.050.764nenA GO:0004872 GO:0005886 GO:0007155 GO:0007229 GO:0008305 GO:0009887 GO:0009986 GO:0016020 GO:0016021 GO:0030198 GO:0034113 GO:0046872 GO:0050900 GO:1903955
30.060.4124.470.050.754nehA GO:0004872 GO:0005886 GO:0007155 GO:0007229 GO:0008305 GO:0009887 GO:0009986 GO:0016020 GO:0016021 GO:0030198 GO:0034113 GO:0046872 GO:0050900 GO:1903955
40.060.4164.170.030.735e6uA GO:0002291 GO:0005886 GO:0006928 GO:0006954 GO:0007155 GO:0007157 GO:0007159 GO:0007160 GO:0007165 GO:0007229 GO:0008305 GO:0009986 GO:0016020 GO:0016021 GO:0016337 GO:0030198 GO:0030369 GO:0032403 GO:0034687 GO:0043113 GO:0046872 GO:0046982 GO:0050776 GO:0050839 GO:0050900 GO:0070062
50.060.3095.290.040.663gzaA GO:0004560 GO:0005975
60.060.4934.000.040.834g1eA GO:0001525 GO:0001568 GO:0001618 GO:0001846 GO:0001968 GO:0002020 GO:0002479 GO:0005080 GO:0005245 GO:0005622 GO:0005886 GO:0005887 GO:0005925 GO:0007155 GO:0007160 GO:0007229 GO:0008284 GO:0008305 GO:0009897 GO:0009986 GO:0010745 GO:0010888 GO:0015026 GO:0016020 GO:0016021 GO:0016032 GO:0016049 GO:0016477 GO:0017134 GO:0019960 GO:0030198 GO:0030335 GO:0031258 GO:0031527 GO:0031528 GO:0031589 GO:0031994 GO:0032369 GO:0032587 GO:0033690 GO:0034113 GO:0034446 GO:0034683 GO:0034684 GO:0034686 GO:0035867 GO:0035987 GO:0038027 GO:0038132 GO:0043277 GO:0045335 GO:0045715 GO:0045785 GO:0046718 GO:0046872 GO:0048010 GO:0050431 GO:0050748 GO:0050764 GO:0050840 GO:0050900 GO:0050919 GO:0052066 GO:0070062 GO:0070371 GO:0070588 GO:0097192 GO:1990430 GO:2000425 GO:2000536 GO:2001237
70.060.5013.980.040.833fcsA GO:0002576 GO:0002687 GO:0005886 GO:0005887 GO:0005925 GO:0007155 GO:0007160 GO:0007229 GO:0008305 GO:0009897 GO:0009986 GO:0016020 GO:0016021 GO:0030198 GO:0031092 GO:0042802 GO:0046872 GO:0050840 GO:0070051 GO:0070062 GO:0070527 GO:0072562
80.060.3345.020.070.704pbpB GO:0005576 GO:0046872
90.060.3794.930.030.735fbyA GO:0005634 GO:0006508 GO:0008233
100.060.4983.770.060.833vi3A GO:0001525 GO:0001618 GO:0001726 GO:0005154 GO:0005161 GO:0005178 GO:0005737 GO:0005783 GO:0005794 GO:0005886 GO:0005911 GO:0005925 GO:0007044 GO:0007155 GO:0007157 GO:0007159 GO:0007229 GO:0007613 GO:0008305 GO:0009897 GO:0009986 GO:0010811 GO:0016020 GO:0016021 GO:0016032 GO:0030198 GO:0030335 GO:0030949 GO:0031410 GO:0031589 GO:0032587 GO:0033631 GO:0034113 GO:0035313 GO:0035987 GO:0043184 GO:0045202 GO:0046718 GO:0046872 GO:0050731 GO:0050839 GO:0050900 GO:0071062 GO:1903672 GO:2000811
110.060.3034.330.030.502ns6A GO:0046872
120.060.2914.830.030.521nogA
130.060.3044.120.060.522jsoA GO:0046677
140.060.2845.440.040.601rh8A GO:0001222 GO:0005509 GO:0005522 GO:0005544 GO:0005802 GO:0007010 GO:0007416 GO:0016080 GO:0030054 GO:0030133 GO:0030424 GO:0030425 GO:0030426 GO:0031594 GO:0043005 GO:0043025 GO:0043195 GO:0044316 GO:0044317 GO:0045202 GO:0046872 GO:0048471 GO:0048786 GO:0048788 GO:0060077 GO:0097470
150.060.2815.000.050.583r2nD GO:0003824 GO:0004126 GO:0008270 GO:0009972 GO:0016787
160.060.3155.080.100.662ftzA GO:0004161 GO:0004311 GO:0004337 GO:0008299 GO:0016740 GO:0033386
170.060.2614.020.030.432dmxA GO:0005634 GO:0005829 GO:0044183 GO:0051082 GO:0051087 GO:0061077 GO:0090084
180.060.2914.860.020.574h7lB GO:0046872


Consensus prediction of GO terms
 
Molecular Function GO:0043169 GO:0060089
GO-Score 0.57 0.36
Biological Processes GO:0007166 GO:0016337 GO:0016477 GO:0043062 GO:0002376 GO:0009653 GO:0010822 GO:1903749 GO:1903214 GO:0090316 GO:0048513
GO-Score 0.57 0.47 0.47 0.47 0.47 0.36 0.36 0.36 0.36 0.36 0.36
Cellular Component GO:0098802 GO:0005887 GO:0098636
GO-Score 0.57 0.57 0.57

(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.