[Home] [Server] [About] [Statistics] [Annotation]

I-TASSER results for job id Rv0207c

[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
10.08 4 1tauA ZN Rep, Mult 45,48,137,161
20.06 3 3l8hA MG Rep, Mult 45,50,161
30.06 3 1ul1X MG Rep, Mult 45,101,135,137
40.06 3 2z8yO XE Rep, Mult 43,140,157,164
50.04 2 3nmtB MG Rep, Mult 161,162
60.04 2 1z2bB VLB Rep, Mult 144,148,154,155,156,157
70.02 1 4j7cD ATP Rep, Mult 68,203
80.02 1 3sxnD COA Rep, Mult 201,202
90.02 1 3ke6A MN Rep, Mult 45,161,204
100.02 1 4hx2A 1AX Rep, Mult 36,151,152,153,175,176,177
110.02 1 3hkeB T13 Rep, Mult 160,189,191,192
120.02 1 1id8A DBI Rep, Mult 50,75,157,158,160,182,183,200,203,208
130.02 1 1ampA ZN Rep, Mult 143,161,201
140.02 1 1cqpB 803 Rep, Mult 40,180,212,216

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
10.0603d64B0.4925.110.0940.7443.3.1.170,72,74
20.0602yy7A0.4784.200.0890.6491.1.1.103NA
30.0601hlgA0.4604.870.0740.7113.1.1.3NA
40.0601fa9A0.4645.830.0490.7852.4.1.1NA
50.0601ileA0.4985.380.0710.7936.1.1.5NA
60.0603d64A0.4905.180.0880.7523.3.1.1145
70.0602i6aA0.5004.980.0320.7402.7.1.20NA
80.0601o0sA0.4845.590.0770.7851.1.1.38NA
90.0601eg7A0.4835.380.0870.7896.3.4.3NA
100.0603h9uC0.4895.030.0740.7363.3.1.1139
110.0601gqtB0.4864.580.0940.6862.7.1.15NA
120.0601gq2A0.4934.600.0450.7031.1.1.40NA
130.0601ffyA0.4995.420.0560.8146.1.1.5NA
140.0603g1uC0.4905.020.0940.7403.3.1.1NA
150.0603hmjA0.4964.870.0740.7402.3.1.86NA
160.0601fw8A0.4984.440.0630.6982.7.2.3188,202,211,214
170.0602a9yA0.4854.960.0600.7232.7.1.20NA
180.0602x42A0.4864.930.0590.7153.2.1.21NA
190.0601hlgB0.4604.870.0740.7113.1.1.3142,165,169

(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
00.220.4864.580.090.691gqtB GO:0000166 GO:0004747 GO:0005524 GO:0005737 GO:0005829 GO:0005975 GO:0006014 GO:0016301 GO:0016310 GO:0016740 GO:0016773 GO:0019303 GO:0046835 GO:0046872
10.160.4505.050.060.692btqA GO:0000166 GO:0003924 GO:0005200 GO:0005525 GO:0005874 GO:0007017
20.160.4854.960.060.722a9yA GO:0000166 GO:0004001 GO:0005524 GO:0006166 GO:0016301 GO:0016310 GO:0016740 GO:0016773 GO:0044209 GO:0046872
30.160.4784.930.090.714u7xA GO:0000166 GO:0004747 GO:0006014 GO:0008865 GO:0016301 GO:0016310 GO:0016740 GO:0016773 GO:0046835
40.070.5144.510.070.744eb6B GO:0000166 GO:0003924 GO:0005200 GO:0005525 GO:0005737 GO:0005856 GO:0005874 GO:0007017
50.070.4594.900.050.685flzC GO:0000166 GO:0000928 GO:0000930 GO:0003924 GO:0005200 GO:0005525 GO:0005634 GO:0005737 GO:0005816 GO:0005822 GO:0005824 GO:0005856 GO:0005874 GO:0007017 GO:0007020 GO:0030472 GO:0031122 GO:2000767
60.070.5144.600.080.734e69B GO:0000166 GO:0016301 GO:0016310 GO:0016740 GO:0016773
70.070.5184.330.110.733cb2A GO:0000086 GO:0000166 GO:0000212 GO:0000226 GO:0000242 GO:0000794 GO:0000930 GO:0003924 GO:0005200 GO:0005525 GO:0005737 GO:0005813 GO:0005814 GO:0005815 GO:0005827 GO:0005829 GO:0005856 GO:0005874 GO:0005876 GO:0005881 GO:0005929 GO:0007017 GO:0007020 GO:0031122 GO:0031252 GO:0031513 GO:0036064 GO:0045177 GO:0055037
80.070.4205.070.070.633r3sA GO:0000166 GO:0016491 GO:0046872 GO:0055114
90.070.4495.080.050.684i4tA GO:0000166 GO:0000226 GO:0003725 GO:0003924 GO:0005200 GO:0005525 GO:0005737 GO:0005856 GO:0005874 GO:0005881 GO:0007017 GO:0031625 GO:0043209 GO:0070062 GO:0071353
100.070.4804.450.140.682rbcA GO:0016301 GO:0016310 GO:0016740
110.070.4734.910.070.713ljsB GO:0000166 GO:0005524 GO:0016301 GO:0016310 GO:0016740 GO:0016773
120.070.4824.550.080.683in1A GO:0004747 GO:0006014 GO:0016301 GO:0016310 GO:0016740 GO:0016773 GO:0046835
130.070.4615.020.060.691tz3A GO:0000166 GO:0004747 GO:0006014 GO:0008715 GO:0008865 GO:0016301 GO:0016310 GO:0016740 GO:0016773 GO:0016787 GO:0046835
140.070.5144.510.040.744ffbB GO:0000070 GO:0000166 GO:0003924 GO:0005200 GO:0005525 GO:0005737 GO:0005816 GO:0005828 GO:0005856 GO:0005874 GO:0005880 GO:0005881 GO:0007017 GO:0030473 GO:0045143 GO:0045298 GO:0046677
150.070.4445.710.070.722c49A GO:0004747 GO:0006014 GO:0016301 GO:0016310 GO:0016740 GO:0016773 GO:0046835
160.070.4784.400.070.682btqB GO:0000166 GO:0003924 GO:0005200 GO:0005525 GO:0005874 GO:0007017
170.070.4744.590.080.683ikhA GO:0000166 GO:0004747 GO:0005524 GO:0005737 GO:0006014 GO:0016301 GO:0016310 GO:0016740 GO:0016773 GO:0019303 GO:0046835
180.070.4594.910.040.691vm7A GO:0004747 GO:0005524 GO:0005737 GO:0006014 GO:0016301 GO:0016310 GO:0016740 GO:0016773 GO:0019303 GO:0046835


Consensus prediction of GO terms
 
Molecular Function GO:0005198 GO:0017111 GO:0032561 GO:0005524 GO:0046872 GO:0004747 GO:0019206 GO:0004396
GO-Score 0.43 0.43 0.43 0.35 0.35 0.35 0.32 0.32
Biological Processes GO:0019323 GO:0046835 GO:0006014 GO:0006167 GO:0043174 GO:0032261
GO-Score 0.45 0.35 0.35 0.32 0.32 0.32
Cellular Component GO:0044444 GO:0015630 GO:0099513
GO-Score 0.45 0.43 0.43

(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.