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I-TASSER results for job id Rv2926c

[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 6 3wmnA MQ8 Rep, Mult 149,153
20.07 4 3sqgD M43 Rep, Mult 77,78,140,143,160
30.07 4 3gwzD CA Rep, Mult 143,147
40.06 3 3gtgA ZN Rep, Mult 96,99,159,170
50.04 2 5d91A 8K6 Rep, Mult 138,141
60.04 2 1ocoB HEA Rep, Mult 145,146
70.04 2 4lqhA MG Rep, Mult 142,143
80.02 1 3b08B ZN Rep, Mult 159,163,167,170
90.02 1 2xjmH CO Rep, Mult 183,186
100.02 1 1focA HEM Rep, Mult 159,163
110.02 1 1hbmA NA Rep, Mult 168,170,171,172,173

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
10.0602e1qA0.4046.170.0490.7441.17.3.2,1.17.1.4NA
20.0601djnA0.4205.750.1030.7341.5.8.2,1.5.99.7NA
30.0605acnA0.4285.980.0260.7784.2.1.3NA
40.0602pdaA0.4225.740.0270.7341.2.7.1121
50.0601yscA0.4285.390.0630.7253.4.16.5NA
60.0602v4wD0.3306.270.0700.6232.3.3.1084,154
70.0602pahA0.3246.770.0340.6711.14.16.1NA
80.0602tmdA0.4195.890.0740.7541.5.8.2NA
90.0601c7sA0.3636.320.0450.7153.2.1.52NA
100.0602j5wA0.4265.750.0670.7301.16.3.1NA
110.0601e6yA0.4585.580.0560.7782.8.4.1152
120.0601asqA0.4325.470.0480.7341.10.3.392
130.0602e52A0.4285.560.0450.7303.1.21.4142
140.0602p4qA0.4245.980.0420.7781.1.1.44152
150.0602gtqA0.4214.730.0500.6523.4.11.2NA
160.0601j0mA0.3575.940.0380.6424.2.2.12193
170.0602vn7A0.4356.080.0690.8073.2.1.3NA
180.0601ayxA0.4255.810.0740.7633.2.1.3NA
190.0601ug9A0.4195.810.0480.7493.2.1.70NA

(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
00.070.4575.670.040.804h1gA GO:0000166 GO:0003777 GO:0005215 GO:0005363 GO:0005524 GO:0005874 GO:0006810 GO:0007018 GO:0008017 GO:0015768
10.070.4535.640.050.781e6vA GO:0015948 GO:0016740 GO:0046872 GO:0050524
20.070.4575.590.050.781e6yA GO:0015948 GO:0016740 GO:0046872 GO:0050524
30.070.4535.760.070.781hbmA GO:0015948 GO:0016740 GO:0046872 GO:0050524
40.060.4145.580.060.714qvhA GO:0000287 GO:0005215 GO:0005363 GO:0005886 GO:0006810 GO:0006974 GO:0008643 GO:0008897 GO:0009239 GO:0009366 GO:0015768 GO:0016740 GO:0016780 GO:0019540 GO:0030288 GO:0034289 GO:0042597 GO:0042956 GO:0043190 GO:0055052 GO:0060326 GO:1901982 GO:1990060
50.060.3935.750.060.694nufA GO:0000122 GO:0003677 GO:0003707 GO:0003714 GO:0005215 GO:0005363 GO:0005634 GO:0005737 GO:0006351 GO:0006355 GO:0006810 GO:0007219 GO:0008134 GO:0009749 GO:0010628 GO:0010629 GO:0015768 GO:0019904 GO:0031100 GO:0032024 GO:0032403 GO:0042803 GO:0042974 GO:0042975 GO:0043234 GO:0043401 GO:0043433 GO:0045892 GO:0046965 GO:0046966
60.060.4345.260.050.733py7A GO:0001725 GO:0003677 GO:0005178 GO:0005215 GO:0005363 GO:0005654 GO:0005737 GO:0005829 GO:0005856 GO:0005875 GO:0005886 GO:0005925 GO:0005938 GO:0006351 GO:0006355 GO:0006810 GO:0006936 GO:0006974 GO:0007155 GO:0007160 GO:0007165 GO:0007172 GO:0007173 GO:0007179 GO:0008013 GO:0008270 GO:0008643 GO:0015768 GO:0016032 GO:0017166 GO:0019901 GO:0030027 GO:0030054 GO:0030288 GO:0032403 GO:0034289 GO:0034614 GO:0042025 GO:0042597 GO:0042956 GO:0043190 GO:0044204 GO:0046872 GO:0048010 GO:0055052 GO:0060326 GO:0060396 GO:1901982 GO:1990060
70.060.3235.970.050.574aouA GO:0000166 GO:0000287 GO:0004450 GO:0006099 GO:0006102 GO:0016491 GO:0016616 GO:0046872 GO:0051287 GO:0055114
80.060.3496.200.060.664blbB GO:0000122 GO:0001501 GO:0001843 GO:0001947 GO:0003281 GO:0003714 GO:0004871 GO:0005215 GO:0005363 GO:0005634 GO:0005654 GO:0005737 GO:0005829 GO:0005929 GO:0006355 GO:0006508 GO:0006810 GO:0006974 GO:0007165 GO:0007275 GO:0007368 GO:0008013 GO:0008134 GO:0008643 GO:0015768 GO:0019901 GO:0021513 GO:0021775 GO:0021776 GO:0030288 GO:0034289 GO:0035904 GO:0042597 GO:0042956 GO:0042992 GO:0042994 GO:0043190 GO:0043433 GO:0043588 GO:0045668 GO:0045879 GO:0055052 GO:0060326 GO:0060976 GO:0072372 GO:0097542 GO:0097546 GO:1901621 GO:1901982 GO:1990060 GO:2000059
90.060.3235.970.040.591v8jA GO:0000166 GO:0000775 GO:0000776 GO:0000777 GO:0003777 GO:0005524 GO:0005634 GO:0005694 GO:0005737 GO:0005856 GO:0005871 GO:0005874 GO:0005881 GO:0007018 GO:0007019 GO:0007049 GO:0007059 GO:0007067 GO:0007080 GO:0008017 GO:0015630 GO:0016020 GO:0016887 GO:0030951 GO:0035371 GO:0051010 GO:0051301 GO:0051983
100.060.3595.550.040.634ifpA GO:0000166 GO:0002376 GO:0005215 GO:0005363 GO:0005524 GO:0005622 GO:0005634 GO:0005737 GO:0005829 GO:0006810 GO:0006915 GO:0006919 GO:0006954 GO:0006974 GO:0008643 GO:0008656 GO:0015768 GO:0019899 GO:0019904 GO:0030288 GO:0032495 GO:0034289 GO:0042597 GO:0042742 GO:0042956 GO:0042981 GO:0043190 GO:0045087 GO:0050718 GO:0050727 GO:0051402 GO:0055052 GO:0060326 GO:0061702 GO:0072558 GO:1901982 GO:1990060
110.060.3176.230.070.602h58A GO:0000166 GO:0003777 GO:0005524 GO:0005737 GO:0005794 GO:0005813 GO:0005815 GO:0005856 GO:0005871 GO:0005874 GO:0005912 GO:0005915 GO:0007017 GO:0007018 GO:0007030 GO:0007601 GO:0008017 GO:0008569 GO:0016020 GO:0016887 GO:0030054 GO:0030659 GO:0031410 GO:0045218 GO:0070062 GO:0090136
120.060.3885.640.060.671y4cA GO:0005215 GO:0005363 GO:0006810 GO:0006974 GO:0008643 GO:0015768 GO:0030288 GO:0034289 GO:0042597 GO:0042956 GO:0043190 GO:0055052 GO:0060326 GO:1901982 GO:1990060
130.060.3585.900.030.641a0dA GO:0000287 GO:0005737 GO:0005975 GO:0006098 GO:0009045 GO:0016853 GO:0042732 GO:0046872
140.060.3676.050.030.694w7sA GO:0000166 GO:0000384 GO:0000395 GO:0003676 GO:0003723 GO:0004004 GO:0004386 GO:0005524 GO:0005634 GO:0005682 GO:0005737 GO:0006397 GO:0006413 GO:0007059 GO:0008380 GO:0010468 GO:0010501 GO:0016787 GO:0036464
150.060.3396.230.030.654aoyA GO:0000287 GO:0004450 GO:0006099 GO:0006102 GO:0016491 GO:0016616 GO:0046872 GO:0051287 GO:0055114
160.060.2996.180.030.584hs7A GO:0005363 GO:0015768
170.060.3626.070.030.665azaA GO:0004576 GO:0005215 GO:0005363 GO:0006486 GO:0006810 GO:0006974 GO:0008643 GO:0015768 GO:0016020 GO:0016021 GO:0016740 GO:0030288 GO:0034289 GO:0042597 GO:0042956 GO:0043190 GO:0055052 GO:0060326 GO:1901982 GO:1990060
180.060.3445.780.080.604c57A GO:0000166 GO:0004672 GO:0004674 GO:0005524 GO:0005737 GO:0005794 GO:0005829 GO:0005925 GO:0006468 GO:0006898 GO:0007029 GO:0007030 GO:0007049 GO:0010977 GO:0016020 GO:0016301 GO:0016310 GO:0016740 GO:0030054 GO:0030332 GO:0031982 GO:0043231 GO:0048471 GO:0072318 GO:0072583 GO:0072600 GO:0090002 GO:0090160


Consensus prediction of GO terms
 
Molecular Function GO:0050497 GO:0043169
GO-Score 0.37 0.37
Biological Processes GO:0009061 GO:0015975 GO:0015947 GO:0043447
GO-Score 0.37 0.37 0.37 0.37
Cellular Component GO:0055052 GO:0030288 GO:0005874 GO:0009366 GO:1990060
GO-Score 0.07 0.07 0.07 0.07 0.07

(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.