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I-TASSER results for job id Rv3355c

[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 4 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
10.12 10 5dirC MLE Rep, Mult 14,17,18,50,54,88
20.07 6 4m70A III Rep, Mult 18,21,47,51
30.06 5 3ls1A ZN Rep, Mult 14,18,54
40.06 5 4w8pA III Rep, Mult 11,12,15,19,22,23,26,41,44,45,48,51,56,64
50.05 4 4qi1A MPG Rep, Mult 22,26,29,30,37,41,44,45,48,51
60.02 2 3rrpA LMR Rep, Mult 55,56,57,65
70.02 2 1bjyB CTC Rep, Mult 62,64,67
80.02 2 2ongA MN Rep, Mult 73,77
90.02 2 3mgrH RB Rep, Mult 54,55,57
100.02 2 4d2eD 78N Rep, Mult 10,13,14,78,81,85
110.01 1 2q67A CA Rep, Mult 51,52
120.01 1 2a9iA MN Rep, Mult 70,73
130.01 1 5ahzA BR Rep, Mult 7,11,65,70,73
140.01 1 5ezmA MPG Rep, Mult 43,88
150.01 1 1gwgA IOD Rep, Mult 28,29,32,37

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
10.0932w5jA0.4712.360.0490.6193.6.3.14NA
20.0781cxzB0.5492.200.1250.6492.7.11.13NA
30.0711a91A0.4932.530.0470.6603.6.3.14NA
40.0672h8aA0.6232.670.0680.8562.5.1.1810,64
50.0601fziA0.6742.610.0330.8971.14.13.25NA
60.0601mhyD0.6712.650.0430.8971.14.13.25NA
70.0603e04D0.7102.560.0880.9284.2.1.2NA
80.0603gzhA0.6442.970.0660.9074.3.2.2NA
90.0601dcnB0.6472.950.0450.9074.3.2.1NA
100.0601uzrB0.6322.790.0770.8761.17.4.1NA
110.0601yfmA0.6392.770.0650.9074.2.1.2NA
120.0603crlB0.6363.050.0890.9172.7.11.2NA
130.0602e9fB0.7102.810.0860.9494.3.2.1NA
140.0602qcxB0.6432.980.0650.8973.5.99.2NA
150.0603d2rB0.6343.350.0780.9282.7.11.2NA
160.0602pnrB0.6283.170.0670.9072.7.11.2NA
170.0601q5nA0.6543.210.1160.9285.5.1.281
180.0601yisA0.6663.010.0430.9384.3.2.253
190.0601xzpA0.6492.960.0540.9073.6.5.-52
200.0603gm1B0.6453.030.0760.9172.7.10.248,76
210.0601krqA0.6393.040.0340.8971.16.3.153
220.0602hvgA0.6513.040.0840.9284.3.2.2NA
230.0602v8tA0.6402.590.0780.8871.11.1.6NA

(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
00.210.7532.450.050.975c1fA GO:0001786 GO:0005547 GO:0005737 GO:0005826 GO:0005829 GO:0005856 GO:0007049 GO:0007067 GO:0051301 GO:0070273 GO:1903475
10.200.7791.910.050.952v0oA GO:0001786 GO:0005546 GO:0005886 GO:0005905 GO:0006897 GO:0010324 GO:0016020 GO:0030136 GO:0035091 GO:0048268 GO:0072583 GO:0072659
20.180.6952.540.060.942efkA GO:0001891 GO:0005086 GO:0005096 GO:0005654 GO:0005737 GO:0005764 GO:0005794 GO:0005802 GO:0005829 GO:0005856 GO:0005886 GO:0005938 GO:0006897 GO:0007154 GO:0007165 GO:0008289 GO:0016020 GO:0016192 GO:0030036 GO:0042802 GO:0042995 GO:0043231 GO:0043547 GO:0048471 GO:0051056 GO:0070062
30.180.7222.620.040.963q0kD GO:0005215 GO:0005654 GO:0005737 GO:0005768 GO:0005769 GO:0005829 GO:0005856 GO:0005886 GO:0005901 GO:0005911 GO:0005913 GO:0005925 GO:0006897 GO:0008092 GO:0008289 GO:0016020 GO:0019898 GO:0030036 GO:0030100 GO:0030659 GO:0031410 GO:0032587 GO:0036010 GO:0042802 GO:0042995 GO:0043231 GO:0045806 GO:0048858 GO:0055038 GO:0070062 GO:0070300 GO:0070836 GO:0072584 GO:0097320 GO:0098609 GO:0098641
40.180.7312.470.050.963syvC GO:0005654 GO:0005737 GO:0005768 GO:0005802 GO:0005886 GO:0006897 GO:0008092 GO:0008289 GO:0016020 GO:0019855 GO:0045806 GO:0051044 GO:0051926 GO:0070062 GO:0097320
50.180.7642.360.040.971i49A GO:0001726 GO:0005525 GO:0005737 GO:0005829 GO:0005886 GO:0005913 GO:0005938 GO:0006928 GO:0007264 GO:0019904 GO:0030032 GO:0030036 GO:0030742 GO:0031529 GO:0032588 GO:0034315 GO:0048365 GO:0070273 GO:0098609 GO:0098641
60.170.7012.690.040.963i2wA GO:0000281 GO:0005543 GO:0005768 GO:0005829 GO:0005886 GO:0007053 GO:0007112 GO:0007269 GO:0008289 GO:0030100 GO:0030496 GO:0032154 GO:0036090 GO:0045211 GO:0045887 GO:0048488 GO:0061024 GO:0071212
70.170.6902.930.070.963m3wB GO:0005654 GO:0005737 GO:0005768 GO:0005802 GO:0005886 GO:0006897 GO:0008092 GO:0008289 GO:0016020 GO:0019855 GO:0045806 GO:0051044 GO:0051926 GO:0070062 GO:0097320
80.160.7222.700.040.964bneA GO:0005737 GO:0005768 GO:0005769 GO:0005802 GO:0005829 GO:0005856 GO:0005886 GO:0005901 GO:0005925 GO:0006897 GO:0008092 GO:0008289 GO:0016020 GO:0030036 GO:0030054 GO:0030100 GO:0030659 GO:0031410 GO:0032587 GO:0042995 GO:0045806 GO:0055038 GO:0070300 GO:0070836 GO:0097320
90.160.6992.710.040.963i2wB GO:0000281 GO:0005543 GO:0005768 GO:0005829 GO:0005886 GO:0007053 GO:0007112 GO:0007269 GO:0008289 GO:0030100 GO:0030496 GO:0032154 GO:0036090 GO:0045211 GO:0045887 GO:0048488 GO:0061024 GO:0071212
100.150.7412.310.040.962eflA GO:0005086 GO:0005737 GO:0005764 GO:0005802 GO:0005856 GO:0005886 GO:0005905 GO:0005938 GO:0006897 GO:0008289 GO:0016020 GO:0016023 GO:0016192 GO:0031410 GO:0042802 GO:0043547
110.140.7222.560.070.963syvB GO:0005654 GO:0005737 GO:0005768 GO:0005802 GO:0005886 GO:0006897 GO:0008092 GO:0008289 GO:0016020 GO:0019855 GO:0045806 GO:0051044 GO:0051926 GO:0070062 GO:0097320
120.130.7402.590.030.973g9gA GO:0000144 GO:0000147 GO:0001400 GO:0004857 GO:0005934 GO:0005935 GO:0006897 GO:0007049 GO:0032185 GO:0042802 GO:0043086 GO:0061645
130.120.8101.830.100.935f15A GO:0016020 GO:0016021 GO:0016740
140.110.7232.600.020.963haiA GO:0005543 GO:0005737 GO:0005768 GO:0005829 GO:0005886 GO:0006897 GO:0007015 GO:0008092 GO:0008289 GO:0016020 GO:0030054 GO:0030100 GO:0030137 GO:0030659 GO:0031410 GO:0032587 GO:0042995 GO:0043005 GO:0043209 GO:0043679 GO:0045202 GO:0045806 GO:0048471 GO:0048488 GO:0048666 GO:0048812 GO:0072657 GO:0090002 GO:0097320 GO:1900006
150.090.6892.700.040.964wpeA GO:0000142 GO:0000144 GO:0000281 GO:0000917 GO:0005737 GO:0005856 GO:0005935 GO:0007049 GO:0007067 GO:0008092 GO:0044697 GO:0051301 GO:0090339
160.070.7352.660.070.963qniA GO:0005543 GO:0005737 GO:0005768 GO:0005829 GO:0005886 GO:0006897 GO:0007015 GO:0008092 GO:0008289 GO:0016020 GO:0030054 GO:0030100 GO:0030137 GO:0030659 GO:0031410 GO:0032587 GO:0042995 GO:0043005 GO:0043209 GO:0043679 GO:0045202 GO:0045806 GO:0048471 GO:0048488 GO:0048666 GO:0048812 GO:0072657 GO:0090002 GO:0097320 GO:1900006
170.070.6263.150.020.931ya9A GO:0001523 GO:0001540 GO:0001937 GO:0002021 GO:0005319 GO:0005543 GO:0005576 GO:0005615 GO:0005634 GO:0005783 GO:0005794 GO:0005829 GO:0005886 GO:0006629 GO:0006641 GO:0006695 GO:0006707 GO:0006810 GO:0006869 GO:0006874 GO:0006898 GO:0006979 GO:0007186 GO:0007263 GO:0008104 GO:0008201 GO:0008203 GO:0008289 GO:0010468 GO:0010544 GO:0010873 GO:0010875 GO:0015485 GO:0015909 GO:0016020 GO:0016209 GO:0017038 GO:0017127 GO:0019068 GO:0019433 GO:0019934 GO:0030195 GO:0030516 GO:0030828 GO:0031012 GO:0031103 GO:0032374 GO:0032489 GO:0032805 GO:0033344 GO:0033700 GO:0034361 GO:0034362 GO:0034363 GO:0034364 GO:0034372 GO:0034374 GO:0034375 GO:0034380 GO:0034382 GO:0034384 GO:0034447 GO:0042157 GO:0042158 GO:0042159 GO:0042311 GO:0042627 GO:0042632 GO:0042802 GO:0042803 GO:0043407 GO:0043524 GO:0043537 GO:0043691 GO:0044794 GO:0045541 GO:0046889 GO:0046911 GO:0048156 GO:0048844 GO:0050728 GO:0050750 GO:0051000 GO:0051044 GO:0051055 GO:0051651 GO:0055088 GO:0055089 GO:0060228 GO:0060999 GO:0061000 GO:0070062 GO:0070326 GO:0071813 GO:0072358 GO:0072562 GO:0090370 GO:0097113 GO:0097114 GO:0098869 GO:1900221 GO:1901214 GO:1901215 GO:1901216 GO:1901627 GO:1901628 GO:1901630 GO:1901631 GO:1902004 GO:1902430 GO:1902947 GO:1902951 GO:1902952 GO:1902995 GO:1902998 GO:1902999 GO:1903001 GO:1903002 GO:1903561
180.070.4062.920.000.583iu6A GO:0000228 GO:0003677 GO:0003682 GO:0005634 GO:0005654 GO:0006338 GO:0006351 GO:0006355 GO:0007067 GO:0008285 GO:0016568 GO:0090544


Consensus prediction of GO terms
 
Molecular Function GO:1902936 GO:0001786 GO:0005085 GO:0030695 GO:0008047 GO:0045296 GO:0098632 GO:0043168 GO:0005246 GO:0008200 GO:0042802 GO:0008092
GO-Score 0.39 0.37 0.36 0.36 0.36 0.36 0.36 0.36 0.36 0.36 0.33 0.33
Biological Processes GO:0000280 GO:0000915 GO:1902407 GO:0043623 GO:1990778 GO:0072657 GO:0006898 GO:0043087 GO:0007264 GO:0051345 GO:1902531 GO:0044854 GO:0007155 GO:0032990 GO:0000902 GO:0030030 GO:0072665 GO:0051043 GO:0043271 GO:0045732 GO:0031331 GO:0045862 GO:0051924 GO:0097320 GO:0045806
GO-Score 0.42 0.42 0.42 0.39 0.39 0.39 0.39 0.36 0.36 0.36 0.36 0.36 0.36 0.36 0.36 0.36 0.36 0.36 0.36 0.36 0.36 0.36 0.36 0.33 0.33
Cellular Component GO:0005829 GO:0005654 GO:0070062 GO:0030864 GO:0032155 GO:0070938 GO:0030135 GO:0000323 GO:0005924 GO:0044853 GO:0010008 GO:0044433 GO:0055037 GO:0005911 GO:0031253 GO:0001726 GO:0012506 GO:0031256 GO:0005802
GO-Score 0.47 0.45 0.45 0.42 0.42 0.42 0.39 0.36 0.36 0.36 0.36 0.36 0.36 0.36 0.36 0.36 0.36 0.36 0.33

(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.