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I-TASSER results for job id Rv0912

[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
10.09 4 2ix5A FAD Rep, Mult 53,55,56,96,97,99
20.08 3 5ajfA CU1 Rep, Mult 15,63,67,90,128
30.05 2 2ih1C 1EM Rep, Mult 68,75,79
40.02 1 2wpnB SBY Rep, Mult 13,16,41,42,68,71,72
50.02 1 4qi1C MPG Rep, Mult 59,62,92,100
60.02 1 2gceB UUU Rep, Mult 96,113,126
70.02 1 3uspA 05L Rep, Mult 38,40
80.02 1 3rkoL LFA Rep, Mult 15,18,19,61
90.02 1 1e3dB H2S Rep, Mult 65,90,93,94
100.02 1 2xtvA MC3 Rep, Mult 62,83,87,91
110.02 1 3k7tA GP7 Rep, Mult 7,8
120.02 1 2zalB ASP Rep, Mult 76,77,78
130.02 1 1hotB 16G Rep, Mult 72,75
140.02 1 2wsc1 CLA Rep, Mult 53,54,56,68,73
150.02 1 3tyhC CU Rep, Mult 100,101

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
10.0601bucA0.5644.000.1190.8321.3.99.2NA
20.0602wpnB0.5923.260.0570.8051.12.7.2124
30.0601y8pA0.5583.450.0570.7852.7.11.2NA
40.0601h2aL0.6073.690.0600.8461.12.2.1NA
50.0601qleA0.4814.260.1080.7251.9.3.1NA
60.0602pnrB0.5473.910.0700.7852.7.11.2NA
70.0602pnrF0.5473.860.0620.7852.7.11.256
80.0601h2rL0.6103.660.0600.8461.12.2.1NA
90.0602epoA0.5703.390.0410.7853.2.1.52NA
100.0603iam40.5653.560.0480.7921.6.99.560
110.0602yyjA0.5683.720.0320.8321.14.13.3NA
120.0603d2rB0.5653.420.0890.7922.7.11.2NA
130.0601u8vA0.5623.870.0570.8195.3.3.3NA
140.0601ivhA0.5654.080.0510.8521.3.99.10NA
150.0603i9wA0.5583.790.0360.7922.7.13.387
160.0601jqiA0.5754.000.0810.8461.3.99.2NA
170.0601frvB0.5403.690.0880.7851.12.2.1NA
180.0601ukwA0.5674.080.0800.8521.3.99.3NA
190.0601jqoA0.6013.800.0910.8394.1.1.31NA

(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
00.230.6303.030.120.813x29A GO:0005198 GO:0005634 GO:0005737 GO:0005886 GO:0005923 GO:0016020 GO:0016021 GO:0016323 GO:0016338 GO:0019227 GO:0030054 GO:0042802 GO:0043296 GO:0043297
10.180.6723.130.120.874p79A GO:0005198 GO:0005886 GO:0005923 GO:0006810 GO:0006811 GO:0016020 GO:0016021 GO:0016328 GO:0016338 GO:0030054 GO:0042802
20.100.6713.880.090.954ywtA GO:0001523 GO:0005507 GO:0005576 GO:0005578 GO:0005615 GO:0005768 GO:0005796 GO:0005886 GO:0005887 GO:0006024 GO:0006027 GO:0007411 GO:0014037 GO:0016020 GO:0017134 GO:0030200 GO:0030203 GO:0031225 GO:0032288 GO:0040037 GO:0043202 GO:0043236 GO:0043395 GO:0045121 GO:0070062 GO:2001016
30.080.6063.900.060.894ad7C GO:0001523 GO:0005507 GO:0005576 GO:0005578 GO:0005615 GO:0005768 GO:0005796 GO:0005886 GO:0005887 GO:0006024 GO:0006027 GO:0007411 GO:0014037 GO:0016020 GO:0017134 GO:0030200 GO:0030203 GO:0031225 GO:0032288 GO:0040037 GO:0043202 GO:0043236 GO:0043395 GO:0045121 GO:0070062 GO:2001016
40.070.6373.900.040.913odnA GO:0005576 GO:0005578 GO:0005886 GO:0007224 GO:0007367 GO:0007411 GO:0007528 GO:0008101 GO:0008587 GO:0008589 GO:0009897 GO:0016020 GO:0016021 GO:0016055 GO:0017147 GO:0030177 GO:0030178 GO:0031225 GO:0031594 GO:0043395 GO:0045202 GO:0045570 GO:0045880 GO:0048190 GO:0048749 GO:0050908 GO:0098595
50.070.6553.650.110.914ad7A GO:0001523 GO:0005507 GO:0005576 GO:0005578 GO:0005615 GO:0005768 GO:0005796 GO:0005886 GO:0005887 GO:0006024 GO:0006027 GO:0007411 GO:0014037 GO:0016020 GO:0017134 GO:0030200 GO:0030203 GO:0031225 GO:0032288 GO:0040037 GO:0043202 GO:0043236 GO:0043395 GO:0045121 GO:0070062 GO:2001016
60.070.6043.760.040.874ywtB GO:0001523 GO:0005507 GO:0005576 GO:0005578 GO:0005615 GO:0005768 GO:0005796 GO:0005886 GO:0005887 GO:0006024 GO:0006027 GO:0007411 GO:0014037 GO:0016020 GO:0017134 GO:0030200 GO:0030203 GO:0031225 GO:0032288 GO:0040037 GO:0043202 GO:0043236 GO:0043395 GO:0045121 GO:0070062 GO:2001016
70.060.4784.910.050.873fieA GO:0004222 GO:0005576 GO:0006508 GO:0008233 GO:0008237 GO:0008270 GO:0008320 GO:0009405 GO:0016020 GO:0016021 GO:0016787 GO:0020002 GO:0030430 GO:0033644 GO:0044156 GO:0044164 GO:0044221 GO:0044231 GO:0046872 GO:0050827 GO:0051609 GO:0071806
80.060.3924.910.030.651wgzA GO:0004180 GO:0004181 GO:0006508 GO:0008233 GO:0008237 GO:0008270 GO:0016787 GO:0046872
90.060.3635.130.060.643fi0G GO:0000166 GO:0004812 GO:0004830 GO:0005524 GO:0005737 GO:0006412 GO:0006418 GO:0006436 GO:0016874
100.060.3185.010.050.542agaA GO:0000226 GO:0001012 GO:0004407 GO:0004843 GO:0005634 GO:0005654 GO:0005737 GO:0005759 GO:0005789 GO:0005829 GO:0006289 GO:0006351 GO:0006355 GO:0006508 GO:0006511 GO:0006515 GO:0007268 GO:0007399 GO:0008233 GO:0008234 GO:0008242 GO:0010810 GO:0016363 GO:0016579 GO:0016787 GO:0030036 GO:0031625 GO:0031966 GO:0034605 GO:0035520 GO:0035640 GO:0036459 GO:0042405 GO:0042802 GO:0043161 GO:0045104 GO:0051117 GO:0061578 GO:0070536 GO:0070932 GO:0071108 GO:0071218 GO:1904294 GO:1904379 GO:1990380
110.060.3245.000.020.523rt0C GO:0004864 GO:0004872 GO:0005634 GO:0005737 GO:0005886 GO:0009738 GO:0010427 GO:0016020 GO:0042803 GO:0043086 GO:0080163
120.060.3264.120.050.483o65E GO:0004843 GO:0005634 GO:0006351 GO:0006355 GO:0006508 GO:0008233 GO:0008234 GO:0008242 GO:0016579 GO:0016787 GO:0036459
130.060.2915.710.050.581ee1A GO:0000166 GO:0003952 GO:0005524 GO:0005737 GO:0008795 GO:0009435 GO:0016874 GO:0030435
140.060.2333.020.000.312m6yA GO:0000151 GO:0001664 GO:0005524 GO:0005634 GO:0005737 GO:0005739 GO:0005783 GO:0005829 GO:0006457 GO:0006986 GO:0007283 GO:0009408 GO:0016020 GO:0030317 GO:0030521 GO:0030544 GO:0031072 GO:0031397 GO:0031625 GO:0042769 GO:0043065 GO:0043066 GO:0043231 GO:0043508 GO:0046872 GO:0048471 GO:0050750 GO:0051082 GO:0051087 GO:0051223 GO:0055131 GO:0070062 GO:0070585 GO:0098554 GO:1901998
150.060.2974.660.070.472beiB GO:0004145 GO:0005737 GO:0008080 GO:0009447 GO:0016740 GO:0016746 GO:0032918 GO:0032919 GO:0032920 GO:0046204 GO:0070062
160.060.2603.480.060.351u2mA GO:0001530 GO:0005829 GO:0006457 GO:0022417 GO:0030288 GO:0032978 GO:0042597 GO:0043165 GO:0050821 GO:0051082 GO:0051085 GO:0065002
170.060.2653.590.060.374wb2C GO:0001701 GO:0002376 GO:0004866 GO:0005576 GO:0005579 GO:0005615 GO:0006954 GO:0006957 GO:0006958 GO:0010575 GO:0010760 GO:0010951 GO:0019835 GO:0045087 GO:0045766 GO:0070062 GO:0090197 GO:0098779
180.060.1834.460.030.292cw1A


Consensus prediction of GO terms
 
Molecular Function GO:0043394 GO:1901681 GO:0005198 GO:0042802 GO:0046914 GO:0050840 GO:0019838
GO-Score 0.47 0.47 0.37 0.37 0.35 0.35 0.35
Biological Processes GO:0097485 GO:0007409 GO:0007043 GO:0019226 GO:0098870 GO:0016338 GO:0044765 GO:0009968 GO:0030203 GO:0045597 GO:0048643 GO:0006026 GO:0090288 GO:2001014 GO:0044273 GO:0010001 GO:0007422 GO:0030201 GO:0010927 GO:0042552 GO:0040036 GO:0016101 GO:0006023 GO:0030167
GO-Score 0.47 0.47 0.46 0.46 0.46 0.37 0.36 0.35 0.35 0.35 0.35 0.35 0.35 0.35 0.35 0.35 0.35 0.35 0.35 0.35 0.35 0.35 0.35 0.35
Cellular Component GO:0031012 GO:0098590 GO:0016021 GO:0005923 GO:0005775 GO:1903561 GO:0044431 GO:0031226 GO:0098857 GO:0005764 GO:0031988
GO-Score 0.47 0.46 0.42 0.37 0.35 0.35 0.35 0.35 0.35 0.35 0.35

(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.