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I-TASSER results for job id Rv2469c

[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
10.37 12 5fuvA ZN Rep, Mult 138,141,169,172
20.06 2 1zm8A MN Rep, Mult 150,173
30.03 1 1mvyA GLC Rep, Mult 172,173,177,184,185,194
40.03 1 1n38A CH1 Rep, Mult 149,150,151,152

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
10.0601ps9A0.4235.460.0570.7121.3.1.34NA
20.0603etcB0.4165.550.0570.6946.2.1.-NA
30.0601kblA0.4086.130.0350.7162.7.9.1NA
40.0602gbcA0.4045.980.0230.7073.4.14.5,3.4.15.5NA
50.0601kc7A0.4095.960.0400.7122.7.9.1179
60.0601iv8A0.4516.080.0330.8295.4.99.15NA
70.0601sliA0.3805.930.0250.6804.2.2.15,3.2.1.18NA
80.0603e7xA0.4205.380.0640.6986.1.1.13181
90.0602j5wA0.4276.440.0500.8021.16.3.1NA
100.0601w78A0.4185.660.0310.7166.3.2.17,6.3.2.12NA
110.0602shpA0.4055.710.0380.7033.1.3.48172,179
120.0601j38A0.4135.670.0730.7073.4.15.1147,150
130.0601g5aA0.4265.930.0490.7752.4.1.4NA
140.0601ordA0.4365.160.0750.7034.1.1.17NA
150.0601yr2A0.4285.680.0300.7303.4.21.26NA
160.0601n1hA0.4205.550.0290.7212.7.7.48NA
170.0602fhcA0.4185.540.0390.7033.2.1.41161
180.0602bf4A0.4095.910.0360.7211.6.2.4NA
190.0603g0bB0.4225.810.0370.7213.4.14.5NA

(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
00.100.6633.900.130.884ogeA GO:0003676 GO:0003677 GO:0003723 GO:0004518 GO:0004519 GO:0016787 GO:0046872 GO:0051607 GO:0090305
10.070.5654.510.070.775axwA GO:0003677 GO:0003723 GO:0004518 GO:0004519 GO:0016787 GO:0043571 GO:0046872 GO:0051607 GO:0090305
20.060.3395.860.060.594exmC GO:0003796 GO:0003824 GO:0008152 GO:0009253 GO:0016787 GO:0016798 GO:0016998 GO:0019076 GO:0019835 GO:0030430 GO:0042742
30.060.4884.880.100.724oo8A GO:0003677 GO:0003723 GO:0004518 GO:0004519 GO:0004520 GO:0004527 GO:0008408 GO:0016787 GO:0043571 GO:0046872 GO:0051607 GO:0090305
40.060.4765.160.090.724zt9A GO:0003677 GO:0003723 GO:0004518 GO:0004519 GO:0004520 GO:0004527 GO:0008408 GO:0016787 GO:0043571 GO:0046872 GO:0051607 GO:0090305
50.060.2886.260.050.543mq4A GO:0001642 GO:0001661 GO:0001662 GO:0004871 GO:0004930 GO:0005245 GO:0005246 GO:0005509 GO:0005886 GO:0005887 GO:0005938 GO:0007165 GO:0007186 GO:0007194 GO:0007196 GO:0007268 GO:0007605 GO:0007608 GO:0007613 GO:0007614 GO:0008066 GO:0008306 GO:0010855 GO:0014050 GO:0016020 GO:0016021 GO:0016595 GO:0019226 GO:0030165 GO:0030424 GO:0030425 GO:0030534 GO:0030818 GO:0031279 GO:0032279 GO:0033555 GO:0042734 GO:0043198 GO:0043235 GO:0045211 GO:0048786 GO:0050877 GO:0050896 GO:0051966 GO:0070588 GO:0070905
60.060.3636.280.020.684cmpA GO:0003677 GO:0003723 GO:0004518 GO:0004519 GO:0004520 GO:0004527 GO:0008408 GO:0016787 GO:0043571 GO:0046872 GO:0051607 GO:0090305
70.060.3245.660.030.544phuA GO:0003796 GO:0003824 GO:0004871 GO:0004930 GO:0005085 GO:0005886 GO:0005887 GO:0007165 GO:0007186 GO:0008152 GO:0008289 GO:0009253 GO:0016020 GO:0016021 GO:0016787 GO:0016798 GO:0016998 GO:0019076 GO:0019835 GO:0030073 GO:0030430 GO:0032024 GO:0042593 GO:0042742 GO:0043547 GO:0045125 GO:0051928 GO:0070542
80.060.4985.300.090.774zt0A GO:0003677 GO:0003723 GO:0004518 GO:0004519 GO:0004520 GO:0004527 GO:0008408 GO:0016787 GO:0043571 GO:0046872 GO:0051607 GO:0090305
90.060.3026.560.040.584oo8D GO:0003677 GO:0003723 GO:0004518 GO:0004519 GO:0004520 GO:0004527 GO:0008408 GO:0016787 GO:0043571 GO:0046872 GO:0051607 GO:0090305
100.060.3785.690.040.644zt9C GO:0003677 GO:0003723 GO:0004518 GO:0004519 GO:0004520 GO:0004527 GO:0008408 GO:0016787 GO:0043571 GO:0046872 GO:0051607 GO:0090305
110.060.3266.110.040.595i0nA GO:0000166 GO:0000287 GO:0002561 GO:0003796 GO:0003824 GO:0004430 GO:0005524 GO:0005739 GO:0005765 GO:0005768 GO:0005794 GO:0005829 GO:0005886 GO:0005887 GO:0006661 GO:0008152 GO:0009253 GO:0016020 GO:0016023 GO:0016301 GO:0016310 GO:0016740 GO:0016787 GO:0016798 GO:0016998 GO:0019835 GO:0030054 GO:0030425 GO:0030672 GO:0031083 GO:0031224 GO:0031410 GO:0031901 GO:0032403 GO:0035651 GO:0035838 GO:0042734 GO:0042742 GO:0042995 GO:0043005 GO:0043025 GO:0043204 GO:0043231 GO:0043234 GO:0044231 GO:0045121 GO:0045202 GO:0046854 GO:0070382 GO:0098779
120.060.3066.140.030.552ppqA GO:0000166 GO:0004413 GO:0005524 GO:0008652 GO:0009088 GO:0016301 GO:0016310 GO:0016740
130.060.3186.500.040.634cmqB GO:0003677 GO:0003723 GO:0004518 GO:0004519 GO:0004520 GO:0004527 GO:0008408 GO:0016787 GO:0043571 GO:0046872 GO:0051607 GO:0090305
140.060.3005.700.050.512qb0B GO:0003796 GO:0003824 GO:0008152 GO:0009253 GO:0016787 GO:0016798 GO:0016998 GO:0019076 GO:0019835 GO:0030430 GO:0042742
150.060.3165.830.030.584n9nA GO:0000978 GO:0000981 GO:0001077 GO:0003677 GO:0003796 GO:0003824 GO:0005634 GO:0006351 GO:0006355 GO:0006366 GO:0008152 GO:0008270 GO:0009253 GO:0016020 GO:0016787 GO:0016798 GO:0016998 GO:0019076 GO:0019835 GO:0030430 GO:0035961 GO:0035969 GO:0042742 GO:0045944 GO:0046872 GO:0048471 GO:0071456 GO:1904741
160.060.3135.320.110.514xesA GO:0001659 GO:0003085 GO:0003254 GO:0003796 GO:0003824 GO:0004871 GO:0004930 GO:0005737 GO:0005739 GO:0005783 GO:0005794 GO:0005886 GO:0005887 GO:0007165 GO:0007186 GO:0007218 GO:0007612 GO:0008152 GO:0008344 GO:0009253 GO:0009898 GO:0009986 GO:0014049 GO:0014054 GO:0016020 GO:0016021 GO:0016492 GO:0016787 GO:0016798 GO:0016998 GO:0019076 GO:0019835 GO:0030424 GO:0030425 GO:0030430 GO:0032280 GO:0033993 GO:0042742 GO:0042803 GO:0043025 GO:0043065 GO:0043066 GO:0043195 GO:0043197 GO:0043198 GO:0043204 GO:0043576 GO:0043679 GO:0044309 GO:0045121 GO:0045202 GO:0046982 GO:0047485 GO:0050965 GO:0051280 GO:0051281 GO:0051930 GO:0060732 GO:0070779 GO:0071545 GO:0090238 GO:0097151 GO:0098900 GO:1990123 GO:2001259
170.060.2905.410.020.484n6kA GO:0006810 GO:0030288
180.060.2927.100.030.634qrzA GO:0005215 GO:0006810


Consensus prediction of GO terms
 
Molecular Function GO:0043169 GO:0004518 GO:0003676
GO-Score 0.52 0.52 0.52
Biological Processes GO:0009615 GO:0002252 GO:0098542 GO:0043570
GO-Score 0.52 0.52 0.52 0.36
Cellular Component GO:0030430
GO-Score 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.