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I-TASSER results for job id Rv1251c

[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
10.22 11 2xzoA UUU Rep, Mult 748,768,769,770,771,772,773,774,875,902,942,943,1065,1067,1102
20.09 4 3cmvB MG Rep, Mult 773,799,803,874
30.07 4 2gjkA MG Rep, Mult 773,875,1065
40.05 3 4b3gA NUC Rep, Mult 584,629,630,631,656,697,699,700,703,796,797,798,820,823,854,856,906,990,991,1033,1034,1059,1061,1088,1089
50.04 2 2gk6A PO4 Rep, Mult 768,769,772,902,943,1065,1102
60.04 2 5eaxA NUC Rep, Mult 177,179,197,205,206,329,330,353,479,568,608,609,610,632,654,675,692,694,697,796,797,798,823,856,857,906,909,1032,1033,1034,1059,1061,1062,1087,1088,1089,1095
70.03 2 3cmvB ANP Rep, Mult 768,769,771,772,773,774,804,807
80.02 1 2ckjC FES Rep, Mult 876,877,880,918,919,920,921

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
10.0601k32A0.2598.950.0290.3923.4.21.-NA
20.0603dy5A0.2568.710.0400.3781.13.11.40,4.2.1.92NA
30.0601ofdA0.2659.100.0470.4031.4.7.1NA
40.0601ea0A0.26810.040.0480.4451.4.1.13NA
50.0601n1hA0.2719.450.0420.4242.7.7.48NA
60.0602vdcA0.2759.460.0530.4341.4.1.13NA
70.0602vumA0.2659.410.0430.4142.7.7.6918,926
80.0603iydD0.2749.860.0380.4462.7.7.6NA
90.0601w36D0.3045.570.1370.3633.1.11.5766,770,875,920,938,1065
100.0603h0gA0.2659.420.0290.4102.7.7.6811
110.0603b9jI0.0805.720.0640.0981.17.1.4,1.17.3.2742,755
120.0601l5jA0.2568.940.0410.3894.2.1.3NA
130.0602fhbA0.2759.480.0340.4293.2.1.41NA
140.0602vdcF0.2769.510.0470.4371.4.1.13NA
150.0601fo4A0.2939.570.0530.4621.17.1.4NA
160.0602e1qA0.2959.460.0390.4601.17.3.2,1.17.1.4NA
170.0603b9jC0.1988.880.0340.3001.17.3.2,1.17.1.4NA
180.0602fgeA0.2549.570.0380.4043.4.24.-NA
190.0602fhcA0.2769.620.0450.4423.2.1.41NA

(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
00.340.4414.340.150.492wjyA GO:0000166 GO:0000184 GO:0000294 GO:0000723 GO:0000784 GO:0000785 GO:0000932 GO:0000956 GO:0003677 GO:0003682 GO:0003723 GO:0004004 GO:0004386 GO:0005524 GO:0005634 GO:0005654 GO:0005737 GO:0005829 GO:0006260 GO:0006281 GO:0006406 GO:0006449 GO:0008270 GO:0009048 GO:0016787 GO:0032201 GO:0035145 GO:0042162 GO:0044530 GO:0044822 GO:0046872 GO:0061014 GO:0061158 GO:0071044 GO:0071222 GO:0071347
10.230.4244.950.140.492xzlA GO:0000166 GO:0000184 GO:0000956 GO:0003677 GO:0004004 GO:0004386 GO:0005524 GO:0005634 GO:0005737 GO:0005739 GO:0005844 GO:0006310 GO:0006449 GO:0006452 GO:0008270 GO:0008298 GO:0016567 GO:0016787 GO:0016887 GO:0030466 GO:0043024 GO:0046872 GO:0070478
20.160.8191.930.160.845eanA GO:0000076 GO:0000166 GO:0000723 GO:0000729 GO:0000784 GO:0003677 GO:0003678 GO:0003824 GO:0004386 GO:0004518 GO:0004519 GO:0005524 GO:0005634 GO:0005739 GO:0005760 GO:0006260 GO:0006264 GO:0006281 GO:0006284 GO:0006974 GO:0008152 GO:0016787 GO:0016890 GO:0017108 GO:0032508 GO:0033567 GO:0042645 GO:0043137 GO:0043139 GO:0043142 GO:0043504 GO:0045740 GO:0046872 GO:0051536 GO:0051539 GO:0090305 GO:1902990
30.130.3055.190.140.363gp8A GO:0000166 GO:0003677 GO:0004003 GO:0004386 GO:0005524 GO:0008094 GO:0016787 GO:0032508 GO:0043141
40.070.4453.330.190.484b3fX GO:0000049 GO:0000166 GO:0003676 GO:0003677 GO:0003678 GO:0003697 GO:0003723 GO:0004386 GO:0005524 GO:0005634 GO:0005737 GO:0006260 GO:0006281 GO:0006310 GO:0006351 GO:0006355 GO:0006357 GO:0006412 GO:0008026 GO:0008094 GO:0008134 GO:0008186 GO:0008270 GO:0016020 GO:0016787 GO:0030424 GO:0030426 GO:0030529 GO:0032508 GO:0032575 GO:0032797 GO:0042995 GO:0043022 GO:0043141 GO:0046872 GO:0051260
50.060.4525.940.120.544pj3A GO:0000398 GO:0003723 GO:0005634 GO:0005654 GO:0005681 GO:0006283 GO:0006397 GO:0008380 GO:0016020 GO:0044822 GO:0071013
60.060.1968.210.040.281ii0B GO:0000166 GO:0005524 GO:0015446 GO:0016787 GO:0016887 GO:0046685 GO:0071722 GO:0098655 GO:0098656
70.060.3085.770.140.373k70D GO:0000166 GO:0000724 GO:0003677 GO:0004003 GO:0004386 GO:0004518 GO:0004519 GO:0004527 GO:0005524 GO:0006281 GO:0006302 GO:0006310 GO:0006974 GO:0008854 GO:0009338 GO:0016787 GO:0032508 GO:0043142 GO:0090305
80.060.1597.460.030.223dm5A GO:0000166 GO:0003723 GO:0003924 GO:0005525 GO:0005737 GO:0006612 GO:0006614 GO:0008312 GO:0030529 GO:0048500
90.060.1647.320.040.224flnB GO:0004252 GO:0006508 GO:0008233 GO:0008236 GO:0009507 GO:0009533 GO:0009535 GO:0009536 GO:0009570 GO:0009579 GO:0009658 GO:0009941 GO:0010206 GO:0016020 GO:0016787 GO:0030163
100.060.1465.730.060.181sxjC GO:0000166 GO:0003677 GO:0003689 GO:0005524 GO:0005634 GO:0005663 GO:0005829 GO:0006260 GO:0006272 GO:0006298 GO:0007049 GO:0007062 GO:0016887 GO:0031389 GO:0031390 GO:0031391
110.060.1426.060.060.184xgcA GO:0000166 GO:0003677 GO:0003682 GO:0005524 GO:0005634 GO:0005664 GO:0006260 GO:0006261 GO:0006270 GO:0006277 GO:0006342 GO:0008283 GO:0019233 GO:0022008 GO:0042023
120.060.1176.820.020.151zu5B GO:0000166 GO:0003924 GO:0005525 GO:0005737 GO:0005886 GO:0006612 GO:0006614 GO:0016020 GO:0031226
130.060.1306.280.070.163dmdB GO:0000166 GO:0003924 GO:0005525 GO:0005737 GO:0005886 GO:0006612 GO:0006614 GO:0016020 GO:0031226
140.060.1296.740.060.173hteE GO:0000166 GO:0004176 GO:0005524 GO:0005759 GO:0005829 GO:0006457 GO:0006508 GO:0008270 GO:0016032 GO:0016887 GO:0030163 GO:0042802 GO:0043335 GO:0046872 GO:0046983 GO:0051082 GO:0051301 GO:0051704
150.060.1506.060.080.191sxjD GO:0000076 GO:0000166 GO:0003677 GO:0003689 GO:0005524 GO:0005634 GO:0005663 GO:0006260 GO:0006272 GO:0006298 GO:0007049 GO:0007062 GO:0017076 GO:0031389 GO:0031390 GO:0031391
160.060.1226.840.040.165l3wA GO:0000166 GO:0003924 GO:0005525 GO:0005737 GO:0005886 GO:0006612 GO:0006614 GO:0016020 GO:0031226
170.060.1307.540.040.184ja0D GO:0004639 GO:0005524 GO:0006164 GO:0006189
180.060.1146.200.060.142yhsA GO:0000166 GO:0003924 GO:0005525 GO:0005737 GO:0005829 GO:0005886 GO:0006612 GO:0006614 GO:0016020 GO:0031226


Consensus prediction of GO terms
 
Molecular Function GO:0005524 GO:0008270 GO:0004004 GO:0043021 GO:0043139 GO:0004003 GO:0044822 GO:0003682 GO:0042162 GO:0051536 GO:0016888 GO:0048256
GO-Score 0.66 0.52 0.49 0.46 0.38 0.38 0.34 0.34 0.34 0.33 0.33 0.33
Biological Processes GO:0000184 GO:0006449 GO:0043928 GO:0070727 GO:0006414 GO:0032446 GO:0034427 GO:0006342 GO:0032201 GO:0071347 GO:0006406 GO:0009048 GO:0061014 GO:0061158 GO:0071044 GO:0000294 GO:0071222 GO:0010557 GO:0031328 GO:0006302 GO:0051054 GO:0031570 GO:0033567 GO:0032042 GO:1903047 GO:0006275 GO:0032508
GO-Score 0.49 0.49 0.46 0.46 0.46 0.46 0.46 0.46 0.34 0.34 0.34 0.34 0.34 0.34 0.34 0.34 0.34 0.33 0.33 0.33 0.33 0.33 0.33 0.33 0.33 0.33 0.32
Cellular Component GO:0000784 GO:0000932 GO:0005654 GO:0005829 GO:0000785 GO:0035145 GO:0044530 GO:0009295 GO:0005759 GO:0098798 GO:0042575
GO-Score 0.45 0.34 0.34 0.34 0.34 0.34 0.34 0.33 0.33 0.33 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.