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I-TASSER results for job id Rv0898c

[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
10.11 31 1n1qA FEO Rep, Mult 56,60
20.11 42 3tveW NUC Rep, Mult 1,20,40,41,42,44,45,48,49,52,53,55,56,59,60,63
30.05 17 4qi1A MPG Rep, Mult 23,27,30,31,37,41,44,45,48,51
40.05 18 4zttF O Rep, Mult 19,22,47,50
50.04 12 1fbmB RTL Rep, Mult 47,51,54,58
60.04 11 1jm0A DMS Rep, Mult 18,19,22,47
70.04 11 1sumB FE Rep, Mult 52,53,56
80.03 10 5f1rA 42O Rep, Mult 59,60,63
90.03 11 4ryrA MPG Rep, Mult 20,23,24,27,44,48,51,55
100.03 13 4ytpD HEM Rep, Mult 17,20,23,24,51,55,56
110.02 6 1s5lz CLA Rep, Mult 23,24,27,28,51
120.02 8 2qaoX NUC Rep, Mult 37,40,41,42,48,49,52,53,56
130.02 5 2ypaB NUC Rep, Mult 50,53
140.02 8 3wu2D CLA Rep, Mult 17,20,23,24,51
150.01 3 3mgnD UUU Rep, Mult 18,21,22,25,26,29
160.00 1 1smyF MG Rep, Mult 86,87
170.00 1 2v01A CA Rep, Mult 46,50
180.00 1 2r3cA III Rep, Mult 73,76,77,80,84
190.00 2 3d5b2 MG Rep, Mult 12,58,59,62
200.00 1 2r5dC III Rep, Mult 13,16,17,20,24

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
10.1911urfA0.5372.510.0780.7242.7.11.1314,56
20.1403eabA0.5783.220.0260.8283.6.4.3NA
30.1391vp7B0.5011.940.0690.6093.1.11.612,14,20
40.0701wcrA0.6432.950.0990.9192.7.1.69NA
50.0602pfdB0.6912.810.1190.9662.1.2.5,4.3.1.450,54
60.0603kb9A0.6382.840.1280.9314.2.3.3724
70.0601i1iP0.6563.050.0710.9663.4.24.16NA
80.0601kqfC0.6302.590.0470.8051.2.1.2NA
90.0602epoA0.6293.440.0700.9193.2.1.5252
100.0601q0mD0.6433.210.0960.9431.15.1.114,17,56,58
110.0603dwcB0.6313.520.0120.9083.4.17.19NA
120.0601jkuA0.6492.730.0350.8161.11.1.6NA
130.0601o9iA0.6472.700.0350.8161.11.1.614,29
140.0602h1nA0.6483.140.0590.9663.4.24.-NA
150.0602oa6D0.6382.660.1190.8974.2.3.9NA
160.0603lomA0.6512.810.0800.9662.5.1.1052,57
170.0601jtnA0.3904.040.0660.5983.2.1.1723
180.0602dh4A0.6462.570.0600.8972.5.1.29NA
190.0603errA0.6372.610.0460.7826.1.1.1159,70
200.0602o36A0.6643.110.0810.9893.4.24.1555
210.0602zr3B0.6312.540.0920.7826.1.1.1121,53
220.0602ewgA0.6422.820.0240.8852.5.1.10NA
230.0602bq1I0.6643.460.0230.9891.17.4.1NA

(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
00.300.5383.070.040.781t72A GO:0005315 GO:0005436 GO:0005737 GO:0005886 GO:0006810 GO:0006817 GO:0010629 GO:0015321 GO:0030643 GO:0035435 GO:0035725 GO:0042803 GO:0044341 GO:0045936 GO:0055085 GO:2000186
10.270.7592.430.090.951fioA GO:0000149 GO:0000329 GO:0005484 GO:0005546 GO:0005628 GO:0005886 GO:0006886 GO:0006906 GO:0012505 GO:0016020 GO:0016021 GO:0016192 GO:0030437 GO:0031201 GO:0031321 GO:0043325 GO:0048278 GO:0070300 GO:0080025
20.230.6312.280.060.743k9aA
30.180.6171.970.030.703p30A
40.160.5522.340.070.703cp1A GO:0005198 GO:0019031
50.160.7642.190.120.942bkpA GO:0006813 GO:0008324 GO:0098655
60.150.6432.750.070.944f7rD GO:0019904
70.150.6472.660.060.932o98B GO:0019904
80.150.7422.860.060.994zdrA GO:0000166 GO:0000287 GO:0001558 GO:0001894 GO:0001944 GO:0002039 GO:0004672 GO:0004674 GO:0005524 GO:0005615 GO:0005634 GO:0005654 GO:0005737 GO:0005739 GO:0005829 GO:0005913 GO:0005925 GO:0006468 GO:0006605 GO:0006914 GO:0006915 GO:0006974 GO:0007049 GO:0007050 GO:0007165 GO:0007283 GO:0007286 GO:0007409 GO:0008134 GO:0008285 GO:0010212 GO:0010508 GO:0010941 GO:0016020 GO:0016301 GO:0016310 GO:0016740 GO:0019901 GO:0019904 GO:0030010 GO:0030111 GO:0030154 GO:0030168 GO:0030275 GO:0030295 GO:0030308 GO:0030511 GO:0030659 GO:0031625 GO:0032147 GO:0036398 GO:0036399 GO:0042470 GO:0042593 GO:0042802 GO:0043066 GO:0043276 GO:0043488 GO:0044822 GO:0045059 GO:0046777 GO:0046872 GO:0048814 GO:0050731 GO:0050772 GO:0050852 GO:0051055 GO:0051645 GO:0051683 GO:0051896 GO:0060070 GO:0060770 GO:0061024 GO:0070062 GO:0071493 GO:0071902 GO:0072332 GO:0072562 GO:0090168 GO:0097484 GO:0098609 GO:0098641 GO:1900182 GO:1900740 GO:1901796 GO:1904262
90.140.7232.690.070.972xheB GO:0000149 GO:0005484 GO:0005886 GO:0006886 GO:0006887 GO:0006906 GO:0012505 GO:0016020 GO:0016021 GO:0016192 GO:0031201 GO:0048278
100.140.5573.370.080.954dnkB GO:0000165 GO:0003714 GO:0005634 GO:0005737 GO:0005739 GO:0005829 GO:0005913 GO:0005925 GO:0006605 GO:0008022 GO:0016020 GO:0016032 GO:0017053 GO:0019899 GO:0019904 GO:0030659 GO:0032403 GO:0035308 GO:0035329 GO:0042470 GO:0042826 GO:0043085 GO:0043234 GO:0043488 GO:0045744 GO:0045892 GO:0048471 GO:0050815 GO:0051219 GO:0051220 GO:0051291 GO:0061024 GO:0070062 GO:0098609 GO:0098641 GO:1900740
110.140.7502.720.070.992br9A GO:0000086 GO:0001764 GO:0003064 GO:0005737 GO:0005739 GO:0005829 GO:0005871 GO:0005913 GO:0005925 GO:0006605 GO:0015459 GO:0016020 GO:0016032 GO:0019899 GO:0019904 GO:0021762 GO:0021766 GO:0021987 GO:0023026 GO:0030424 GO:0030659 GO:0031625 GO:0032403 GO:0035308 GO:0035329 GO:0035556 GO:0042470 GO:0042826 GO:0043154 GO:0044325 GO:0044822 GO:0046982 GO:0050815 GO:0051219 GO:0060306 GO:0061024 GO:0070062 GO:0086013 GO:0086091 GO:0098609 GO:0098641 GO:1900034 GO:1900740 GO:1901016 GO:1902309
120.130.7122.850.050.971a37A GO:0005615 GO:0005634 GO:0005737 GO:0005925 GO:0008134 GO:0019901 GO:0019904 GO:0031625 GO:0042470 GO:0042802 GO:0044822 GO:0051683 GO:0070062 GO:0072562 GO:0090168
130.120.7452.540.080.953c98B GO:0000149 GO:0001948 GO:0001956 GO:0005484 GO:0005886 GO:0006810 GO:0006836 GO:0006886 GO:0006887 GO:0008021 GO:0008076 GO:0009629 GO:0010701 GO:0010807 GO:0016020 GO:0016021 GO:0016081 GO:0016192 GO:0017022 GO:0017156 GO:0017157 GO:0019855 GO:0019869 GO:0019900 GO:0019904 GO:0030054 GO:0030141 GO:0030672 GO:0030674 GO:0031201 GO:0031410 GO:0031629 GO:0032028 GO:0032940 GO:0033605 GO:0042641 GO:0043005 GO:0043008 GO:0043229 GO:0043234 GO:0044325 GO:0045202 GO:0045921 GO:0045956 GO:0046982 GO:0047485 GO:0048306 GO:0070032 GO:0070033 GO:0070044 GO:2000463
140.110.5592.510.070.713wfvA GO:0005198 GO:0016020 GO:0016021 GO:0016032 GO:0019012 GO:0019031 GO:0019062 GO:0020002 GO:0033644 GO:0039663 GO:0044174 GO:0044175 GO:0046718 GO:0055036
150.100.6412.790.050.942npmA GO:0019904
160.090.7482.540.050.982btpA GO:0005737 GO:0005739 GO:0005829 GO:0005925 GO:0006605 GO:0007264 GO:0008022 GO:0016020 GO:0019904 GO:0021762 GO:0030659 GO:0034766 GO:0043234 GO:0044325 GO:0045892 GO:0047485 GO:0061024 GO:0070062 GO:0071889 GO:1900740
170.090.5863.320.080.933efzB GO:0019904
180.070.6432.750.060.943axyC GO:0005634 GO:0005737 GO:0019904
190.070.6482.840.060.944dx0A GO:0019904
200.070.6522.850.070.944jc3A GO:0000079 GO:0001836 GO:0003334 GO:0005576 GO:0005615 GO:0005634 GO:0005737 GO:0005739 GO:0005829 GO:0005913 GO:0006469 GO:0006977 GO:0007165 GO:0008426 GO:0008630 GO:0010482 GO:0010839 GO:0019901 GO:0019904 GO:0030216 GO:0030307 GO:0030659 GO:0031424 GO:0043154 GO:0043588 GO:0045606 GO:0046827 GO:0051219 GO:0051726 GO:0061024 GO:0061436 GO:0070062 GO:0071901 GO:0098609 GO:0098641 GO:1900740
210.070.6492.800.080.944j6sB GO:0000086 GO:0005080 GO:0005159 GO:0005737 GO:0005739 GO:0005829 GO:0005925 GO:0006469 GO:0006605 GO:0008426 GO:0009966 GO:0016020 GO:0019904 GO:0030659 GO:0030971 GO:0031988 GO:0032869 GO:0043209 GO:0044822 GO:0045664 GO:0048167 GO:0061024 GO:0070062 GO:0071901 GO:1900740
220.070.4443.620.090.784apcB GO:0000166 GO:0000242 GO:0004672 GO:0004674 GO:0004702 GO:0004713 GO:0005524 GO:0005634 GO:0005737 GO:0005813 GO:0005815 GO:0005856 GO:0006468 GO:0007049 GO:0007067 GO:0016301 GO:0016310 GO:0016740 GO:0018108 GO:0023014 GO:0030030 GO:0042384 GO:0046872 GO:0051301


Consensus prediction of GO terms
 
Molecular Function GO:1902936 GO:0043168 GO:0005315 GO:0042803 GO:0005436 GO:0015321
GO-Score 0.53 0.53 0.30 0.30 0.30 0.30
Biological Processes GO:0046907 GO:0090174 GO:0016192 GO:0034613 GO:0015031 GO:0016050 GO:0030437 GO:0010927 GO:0022406 GO:0030643 GO:0010629 GO:2000186 GO:0045936 GO:0035725 GO:0044341
GO-Score 0.53 0.53 0.53 0.53 0.53 0.53 0.53 0.53 0.53 0.30 0.30 0.30 0.30 0.30 0.30
Cellular Component GO:0042764 GO:0000324 GO:0098796 GO:0098852 GO:0005886 GO:0031224 GO:0036338
GO-Score 0.53 0.53 0.53 0.53 0.49 0.42 0.32

(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.