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I-TASSER results for job id Rv2809

[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 1tkoB FE Rep, Mult 61,64
20.06 3 2xkpA AKG Rep, Mult 70,73
30.06 3 3au2A CA Rep, Mult 52,54
40.04 2 1crxB NUC Rep, Mult 65,69
50.04 2 3l19A CA Rep, Mult 48,50,52,54,65
60.04 2 1d2z0 III Rep, Mult 68,70,72,83,84,86
70.02 1 2wtfA CA Rep, Mult 45,48
80.02 1 5hpmC CY3 Rep, Mult 1,97
90.02 1 2nsn0 III Rep, Mult 14,15,23,24,31,82,83,86,87,88,89,90,91
100.02 1 3telA MN Rep, Mult 25,27,29
110.02 1 4edgA MN Rep, Mult 25,48
120.02 1 1cc1L FCO Rep, Mult 67,70,74,75,99,102
130.02 1 3ug6A MG Rep, Mult 9,25
140.02 1 1j7lA MG Rep, Mult 36,48
150.02 1 1hotB 16G Rep, Mult 18,19
160.02 1 3attA MG Rep, Mult 54,56

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
10.0601jkyA0.4664.320.1040.8353.4.24.83NA
20.0601iysA0.4564.090.0780.7773.5.2.6NA
30.0601rp5A0.4663.760.0570.7773.4.-.-NA
40.0603fwlA0.4784.130.0870.8162.4.1.129NA
50.0602hgsA0.4714.090.1360.8066.3.2.3NA
60.0602zr3B0.4923.990.0770.8256.1.1.1179,80
70.0601uwkA0.4804.700.0320.9034.2.1.49NA
80.0601cc1L0.4804.740.0300.9031.12.99.666
90.0602dq3A0.4854.070.0900.8256.1.1.1138,69
100.0603bfdA0.4494.020.0630.7863.5.2.6NA
110.0603itbD0.4664.290.0600.8063.4.16.49
120.0602p3xA0.4674.670.0590.8741.10.3.164
130.0601iyqA0.4604.070.0780.7773.5.2.613
140.0602v4wD0.4674.510.0320.8162.3.3.10NA
150.0601fn7A0.4613.790.0630.7484.2.99.18,3.2.2.-NA
160.0601xteA0.4673.840.0610.7482.7.11.130
170.0603cg7A0.4644.130.0750.7863.1.-.-NA
180.0601zxvA0.4724.380.0630.8353.4.24.83NA
190.0603lggA0.4924.480.0310.8743.5.4.4NA

(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
00.110.5463.520.170.832mjmA GO:0000166 GO:0000979 GO:0002376 GO:0005524 GO:0005634 GO:0005737 GO:0005829 GO:0032088 GO:0043549 GO:0045087 GO:0045345 GO:0045944 GO:0051607 GO:0060335 GO:0060339 GO:0060340
10.070.5703.850.120.942cxfA GO:0005737 GO:0007015 GO:0007275 GO:0007399 GO:0012505 GO:0016020 GO:0030027 GO:0030054 GO:0030154 GO:0030175 GO:0030335 GO:0030424 GO:0030425 GO:0030426 GO:0042995 GO:0043025 GO:0043204 GO:0045773 GO:0050770 GO:0050771 GO:0050772 GO:0071437 GO:0090316 GO:2000114
20.070.5443.920.100.923cwzB GO:0000139 GO:0005085 GO:0005262 GO:0005794 GO:0005802 GO:0005829 GO:0016020 GO:0017112 GO:0017137 GO:0030904 GO:0042147 GO:0043547 GO:0050982 GO:0070588
30.070.5533.760.100.904giwA GO:0000209 GO:0003779 GO:0005070 GO:0005634 GO:0005737 GO:0005768 GO:0005769 GO:0005794 GO:0005856 GO:0005874 GO:0005886 GO:0009967 GO:0014069 GO:0015630 GO:0016020 GO:0016023 GO:0030054 GO:0031410 GO:0045202 GO:0045211
40.070.5273.870.090.832of5H GO:0005123 GO:0005634 GO:0005654 GO:0005737 GO:0005794 GO:0005829 GO:0006915 GO:0006919 GO:0006974 GO:0006977 GO:0007165 GO:0042981 GO:0043065 GO:0043066 GO:0051092 GO:1902043 GO:2001235 GO:2001238
50.070.5243.440.110.834o6xA GO:0000281 GO:0005200 GO:0005737 GO:0005764 GO:0005783 GO:0005794 GO:0005829 GO:0005856 GO:0005886 GO:0005923 GO:0006888 GO:0007009 GO:0007016 GO:0007165 GO:0007409 GO:0007411 GO:0007528 GO:0008092 GO:0008093 GO:0009925 GO:0009986 GO:0010628 GO:0010650 GO:0010765 GO:0010960 GO:0014704 GO:0014731 GO:0016020 GO:0016323 GO:0016328 GO:0016529 GO:0019228 GO:0030018 GO:0030054 GO:0030315 GO:0030424 GO:0030425 GO:0030507 GO:0030674 GO:0031594 GO:0033268 GO:0033270 GO:0034112 GO:0042383 GO:0042995 GO:0043001 GO:0043005 GO:0043034 GO:0043194 GO:0043266 GO:0044325 GO:0045184 GO:0045202 GO:0045211 GO:0045296 GO:0045838 GO:0050808 GO:0071286 GO:0071709 GO:0072659 GO:0072660 GO:0072661 GO:0090314 GO:1900827 GO:1902260 GO:2000651 GO:2001259
60.070.5383.450.070.811dgnA GO:0004869 GO:0006954 GO:0010466 GO:0010951 GO:0030414 GO:0042981
70.070.5043.640.120.792dbdA GO:0000166 GO:0000187 GO:0002376 GO:0002606 GO:0005524 GO:0005737 GO:0005829 GO:0005886 GO:0006915 GO:0006919 GO:0006952 GO:0006954 GO:0007165 GO:0007254 GO:0008656 GO:0009595 GO:0010942 GO:0016020 GO:0016045 GO:0016323 GO:0016324 GO:0032731 GO:0032755 GO:0032760 GO:0032874 GO:0035556 GO:0042228 GO:0042742 GO:0042802 GO:0042803 GO:0042834 GO:0042981 GO:0043123 GO:0043280 GO:0045087 GO:0046330 GO:0050700 GO:0050830 GO:0051000 GO:0051092 GO:0051259 GO:0070374 GO:0070423 GO:0071225 GO:1901224 GO:1904417
80.070.4773.920.090.785fnaA GO:0001666 GO:0004175 GO:0004197 GO:0005576 GO:0005737 GO:0005739 GO:0005829 GO:0006508 GO:0006915 GO:0006919 GO:0007165 GO:0008233 GO:0008234 GO:0008656 GO:0009617 GO:0010506 GO:0016485 GO:0016787 GO:0032496 GO:0032611 GO:0033198 GO:0042981 GO:0043123 GO:0050715 GO:0050717 GO:0050718 GO:0050727 GO:0051882 GO:0060081 GO:0070269 GO:0071260 GO:0071310 GO:0072557 GO:0072558 GO:0072559 GO:0097153 GO:0097169 GO:0097300 GO:1901998
90.070.4654.040.100.804ikmA GO:0005215 GO:0005363 GO:0005634 GO:0005654 GO:0005737 GO:0006810 GO:0006915 GO:0006919 GO:0006974 GO:0008643 GO:0008656 GO:0015768 GO:0030288 GO:0032089 GO:0034289 GO:0042597 GO:0042803 GO:0042956 GO:0042981 GO:0043124 GO:0043190 GO:0043280 GO:0050718 GO:0055052 GO:0060326 GO:0072559 GO:1901982 GO:1990060
100.070.4454.410.090.833crdA GO:0002020 GO:0005634 GO:0005737 GO:0005829 GO:0006915 GO:0006919 GO:0006977 GO:0007165 GO:0008625 GO:0030674 GO:0042981 GO:0070513 GO:0071260 GO:2001235
110.060.4045.060.040.813fg3A GO:0003824 GO:0004096 GO:0005506 GO:0005737 GO:0006629 GO:0006631 GO:0006633 GO:0008152 GO:0016020 GO:0016491 GO:0016702 GO:0016829 GO:0019369 GO:0020037 GO:0031408 GO:0046872 GO:0047677 GO:0047987 GO:0051213 GO:0055114 GO:0098869
120.060.4344.250.070.763dy5A GO:0003824 GO:0004096 GO:0005506 GO:0005737 GO:0006629 GO:0006631 GO:0006633 GO:0008152 GO:0016020 GO:0016491 GO:0016702 GO:0016829 GO:0019369 GO:0020037 GO:0031408 GO:0046872 GO:0047677 GO:0047987 GO:0051213 GO:0055114 GO:0098869
130.060.3634.470.030.695exeC GO:0003824 GO:0016491 GO:0016625 GO:0030976 GO:0033611 GO:0046872 GO:0051536 GO:0051539 GO:0055114
140.060.4014.350.050.743vf1A GO:0005506 GO:0016491 GO:0016702 GO:0046872 GO:0051213 GO:0055114
150.060.4004.750.020.752x5dD GO:0003824 GO:0008483 GO:0009058 GO:0016740 GO:0030170
160.060.3504.710.040.604cybJ GO:0005623 GO:0006879 GO:0006950 GO:0008199 GO:0016722 GO:0046872 GO:0055114
170.060.3344.750.090.631z6uA GO:0003677 GO:0004842 GO:0005634 GO:0005654 GO:0005720 GO:0006511 GO:0007049 GO:0008270 GO:0008283 GO:0010216 GO:0016567 GO:0016874 GO:0030154 GO:0042393 GO:0046872 GO:0051726 GO:0051865 GO:0061630 GO:0071158 GO:0090308
180.060.3324.590.030.612ofiA GO:0003824 GO:0006281 GO:0006284 GO:0008152 GO:0008725 GO:0016787 GO:0016798 GO:0046872
190.060.3074.000.120.501wfqA GO:0003676 GO:0003677 GO:0003723 GO:0005737 GO:0005743 GO:0005794 GO:0005886 GO:0006355 GO:0008584 GO:0044822 GO:0070937 GO:0070966
200.060.3083.760.050.482djrA GO:0003677 GO:0046872


Consensus prediction of GO terms
 
Molecular Function GO:0005524 GO:0000979 GO:0017137 GO:0005262 GO:0005070 GO:0017112 GO:0003779 GO:0005123
GO-Score 0.11 0.11 0.07 0.07 0.07 0.07 0.07 0.07
Biological Processes GO:0045944 GO:0032088 GO:0060339 GO:0060340 GO:0043549 GO:0045345 GO:0060335 GO:0051607 GO:0090316 GO:0007015 GO:2000114 GO:0045773 GO:0050771 GO:0030335 GO:0051092 GO:0043547 GO:0006977 GO:0042147 GO:0000209 GO:0006919 GO:0070588 GO:0050982 GO:0043066 GO:1902043
GO-Score 0.11 0.11 0.11 0.11 0.11 0.11 0.11 0.11 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07
Cellular Component GO:0043231 GO:0044444 GO:0012505
GO-Score 0.44 0.44 0.37

(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.