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I-TASSER results for job id Rv2991

[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
10.53 26 1wv4A FMN Rep, Mult 40,41,42,43,45,54,55,59,60,61,132
20.09 6 4ybnB FAD Rep, Mult 76,84,86,87,88,90,143,145
30.04 3 1ty9A FMN Rep, Mult 29,72,90,141
40.03 2 3gasA UUU Rep, Mult 55,56,58,59,61,129,132
50.02 2 2iab0 III Rep, Mult 25,27,29,30,31,32,33,35,36,37,38,39,41,68,70,72,73,74,86,88,145
60.01 1 1w3rA 2MN Rep, Mult 40,41
70.01 1 2i02A FMN Rep, Mult 25,40,41,42,43,54,55,59,60,61,113,114
80.01 1 1vl70 III Rep, Mult 23,24,25,27,29,31,35,36,37,38,39,41,43,56,70,72,74,86,113

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
10.0661nrgA0.6293.330.1460.7911.4.3.5136
20.0601kigH0.4404.270.0660.6323.4.21.689
30.0601bruP0.4254.100.0440.6073.4.21.71NA
40.0602qy0C0.2494.450.0470.3933.4.21.41,3.4.21.4256,60
50.0601rtkA0.4264.040.0410.6263.4.21.4793
60.0602a2jA0.6472.960.1460.7851.4.3.5NA
70.0601c5mD0.4404.130.0740.6263.4.21.6NA
80.0601gpzA0.4134.180.1170.6073.4.21.4188
90.0602iphA0.4143.750.0480.5773.4.22.6693
100.0601pfxC0.4394.180.0450.6263.4.21.2238
110.0601wv4A0.6212.600.1740.7181.4.3.5NA
120.0602ok5A0.4274.080.0400.6263.4.21.4788
130.0601dlmB0.4394.570.0400.6811.13.11.1NA
140.0601autC0.4354.190.0430.6263.4.21.6964
150.0601ci0A0.6253.350.1450.7911.4.3.5136
160.0601yc0A0.4144.090.0280.6013.4.21.-86
170.0601ym0A0.4134.130.0800.6013.4.21.-NA
180.0601ty9B0.6443.050.1300.7911.4.-.-29,37,72,145
190.0601eltA0.4194.140.0370.5953.4.21.36NA
200.0601dlmA0.4354.580.0480.6811.13.11.1NA

(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
00.690.9281.000.900.961rfeA GO:0004733 GO:0010181 GO:0016491 GO:0042823 GO:0055114
10.390.6982.570.220.844qvbB GO:0004733 GO:0010181 GO:0016491 GO:0030170 GO:0042803 GO:0042816 GO:0042823 GO:0055114
20.360.6682.560.160.752fhqA GO:0010181 GO:0016491 GO:0055114
30.350.6752.070.170.763db0B GO:0010181 GO:0016491 GO:0055114
40.300.6712.940.180.833tgvA GO:0004733 GO:0010181 GO:0016491 GO:0042823 GO:0055114
50.280.6382.640.240.763f7eA GO:0004733 GO:0010181 GO:0016491 GO:0042823 GO:0055114
60.260.6582.420.140.762i02A GO:0000166 GO:0010181 GO:0016491 GO:0055114
70.260.6682.530.170.772re7A GO:0010181 GO:0016491 GO:0055114
80.250.6403.260.160.813dmbA GO:0010181 GO:0016491 GO:0055114
90.250.6522.650.150.773fkhD GO:0010181 GO:0016491 GO:0055114
100.250.6892.900.180.823dnhA GO:0010181 GO:0016491 GO:0055114
110.250.7652.400.130.892furA GO:0010181 GO:0016491 GO:0055114
120.250.6562.230.180.753u5wA GO:0010181 GO:0016491 GO:0055114
130.240.7742.600.110.934ybnA GO:0010181 GO:0016491 GO:0055114
140.240.7292.970.140.892x1kA GO:0010181 GO:0016491 GO:0055114
150.230.6843.110.170.835bncA GO:0010181 GO:0016491 GO:0055114
160.230.6952.670.130.822arzA GO:0010181 GO:0016491 GO:0055114
170.230.6333.040.170.772ou5A GO:0000166 GO:0010181 GO:0016491 GO:0055114
180.220.6682.460.180.772htiA GO:0000166 GO:0010181 GO:0016491 GO:0055114
190.200.6552.630.180.772hq9B GO:0000166 GO:0010181 GO:0016491 GO:0055114
200.190.7302.620.110.862fg9A GO:0000166 GO:0010181 GO:0016491 GO:0055114
210.180.6642.400.170.771vl7A GO:0004733 GO:0010181 GO:0016491 GO:0042823 GO:0055114
220.180.7422.950.090.902ol5B GO:0010181 GO:0016491 GO:0055114
230.170.6472.370.190.733ec6A GO:0000166 GO:0003677 GO:0010181 GO:0016491 GO:0055114
240.070.6183.510.140.792qeaA GO:0010181 GO:0016491 GO:0046872 GO:0055114
250.060.3265.630.030.621gviA GO:0003824 GO:0004553 GO:0005975
260.060.4134.180.120.611gpzA GO:0002376 GO:0004252 GO:0005509 GO:0005576 GO:0006508 GO:0006955 GO:0006956 GO:0006958 GO:0008233 GO:0008236 GO:0016787 GO:0045087 GO:0070062 GO:0072562
270.060.3304.900.030.562p52A GO:0000060 GO:0000122 GO:0000733 GO:0000785 GO:0000790 GO:0000977 GO:0000979 GO:0000981 GO:0001046 GO:0001077 GO:0001085 GO:0001228 GO:0001701 GO:0001756 GO:0001836 GO:0002020 GO:0002039 GO:0002309 GO:0002326 GO:0002360 GO:0002931 GO:0003677 GO:0003682 GO:0003684 GO:0003700 GO:0005507 GO:0005524 GO:0005634 GO:0005654 GO:0005657 GO:0005667 GO:0005669 GO:0005730 GO:0005737 GO:0005739 GO:0005759 GO:0005783 GO:0005829 GO:0006289 GO:0006302 GO:0006351 GO:0006355 GO:0006357 GO:0006366 GO:0006461 GO:0006915 GO:0006974 GO:0006977 GO:0006978 GO:0006979 GO:0006983 GO:0007049 GO:0007050 GO:0007179 GO:0007275 GO:0007369 GO:0007406 GO:0007417 GO:0007507 GO:0007569 GO:0007623 GO:0008104 GO:0008134 GO:0008156 GO:0008285 GO:0008340 GO:0009303 GO:0009411 GO:0009651 GO:0009792 GO:0010165 GO:0010332 GO:0010628 GO:0010629 GO:0010666 GO:0012501 GO:0016032 GO:0016363 GO:0016604 GO:0016605 GO:0019899 GO:0019901 GO:0019903 GO:0021549 GO:0030308 GO:0030330 GO:0030512 GO:0030971 GO:0031052 GO:0031065 GO:0031497 GO:0031571 GO:0031625 GO:0032461 GO:0033077 GO:0034103 GO:0034613 GO:0034644 GO:0035033 GO:0035035 GO:0035264 GO:0035794 GO:0035861 GO:0042127 GO:0042149 GO:0042493 GO:0042771 GO:0042802 GO:0042981 GO:0043065 GO:0043066 GO:0043153 GO:0043234 GO:0043504 GO:0043523 GO:0043525 GO:0043621 GO:0044212 GO:0045861 GO:0045892 GO:0045893 GO:0045930 GO:0045944 GO:0046872 GO:0046982 GO:0047485 GO:0048147 GO:0048511 GO:0048512 GO:0048568 GO:0050731 GO:0050821 GO:0051087 GO:0051262 GO:0051276 GO:0051402 GO:0051721 GO:0051726 GO:0051974 GO:0060411 GO:0061419 GO:0070059 GO:0070243 GO:0070245 GO:0070266 GO:0071158 GO:0071479 GO:0071480 GO:0071494 GO:0071850 GO:0072332 GO:0072363 GO:0090200 GO:0090343 GO:0090399 GO:0090403 GO:0097252 GO:0097371 GO:1900119 GO:1901525 GO:1902108 GO:1902253 GO:1904024 GO:1990144 GO:1990440 GO:2000269 GO:2000378 GO:2000379 GO:2000772 GO:2001244


Consensus prediction of GO terms
 
Molecular Function GO:0010181 GO:0004733 GO:0030170 GO:0042803
GO-Score 0.94 0.87 0.39 0.39
Biological Processes GO:0055114 GO:0042823 GO:0042816
GO-Score 0.94 0.87 0.39
Cellular Component
GO-Score

(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.