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I-TASSER results for job id Rv2862c

[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
10.07 4 2oqyA MG Rep, Mult 37,109,192
20.05 3 1xjnB DTP Rep, Mult 110,111,112,134,137,141
30.05 3 1xspA PPV Rep, Mult 42,83,84,87,104,109
40.03 2 2ih9B 5AX Rep, Mult 26,32
50.03 2 1rmgA MAN Rep, Mult 28,30,31,32,33
60.02 1 1xjnC DTP Rep, Mult 111,116,136,140,169
70.02 1 3sjqC PHU Rep, Mult 61,62
80.02 1 4fuoA ZN Rep, Mult 37,88
90.02 1 3qoqD NUC Rep, Mult 12,18
100.02 1 1w70B TFA Rep, Mult 131,180
110.02 1 1y9eB NAD Rep, Mult 128,129,177
120.02 1 3uomA CA Rep, Mult 15,17
130.02 1 3ap9A BGC Rep, Mult 12,86
140.02 1 1xjnA DTP Rep, Mult 34,50,58
150.02 1 1xjfA DTP Rep, Mult 169,170,171
160.02 1 1ofmA UUU Rep, Mult 107,110,133,186
170.02 1 3d1nP NUC Rep, Mult 136,191
180.02 1 2iq7A UUU Rep, Mult 105,109,130
190.02 1 2ol1B UMP Rep, Mult 52,53
200.02 1 2eb5A MG Rep, Mult 107,109,132

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
10.0601jtaA0.4475.380.0410.7944.2.2.2NA
20.0601oocB0.4505.320.0420.7894.2.2.236,109,128
30.0601airA0.4685.400.0450.8144.2.2.2NA
40.0601cb7B0.4485.790.0570.8095.4.99.1132
50.0601xjjA0.4535.430.0440.7731.17.4.125,104
60.0601nhcA0.4435.290.0630.7533.2.1.15167
70.0601ru4A0.4485.520.0820.7894.2.2.2NA
80.0603edyA0.4375.730.0240.7993.4.14.9NA
90.0602z8gB0.4435.930.0590.7733.2.1.57134
100.0601z45A0.4435.520.0560.7585.1.3.2,5.1.3.3NA
110.0601reqA0.4005.670.1100.7115.4.99.2116
120.0601rmgA0.4714.860.0610.7423.2.1.-NA
130.0601pclA0.4655.270.0610.8044.2.2.2NA
140.0603eqoA0.4615.700.0960.8453.2.1.5891
150.0601vblA0.4495.330.0600.7474.2.2.2NA
160.0601czfA0.4405.420.0560.7633.2.1.15NA
170.0601kcdA0.4495.250.0630.7533.2.1.1539
180.0601idjA0.4655.340.0620.8094.2.2.10134
190.0601ogmX0.4385.580.0510.7783.2.1.11NA

(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
00.060.3565.570.020.624b4uB GO:0000105 GO:0000166 GO:0003824 GO:0004477 GO:0004488 GO:0006164 GO:0006730 GO:0008152 GO:0008652 GO:0009086 GO:0009396 GO:0016491 GO:0016787 GO:0035999 GO:0055114
10.060.3296.150.050.634g41A GO:0003824 GO:0008152 GO:0008652 GO:0008782 GO:0008930 GO:0009086 GO:0009116 GO:0009164 GO:0016787 GO:0016798 GO:0019509
20.060.3335.670.070.595a2aA GO:0003824 GO:0004556 GO:0005975 GO:0008152 GO:0016020 GO:0016021 GO:0016787 GO:0016798
30.060.3425.910.050.634w8jA GO:0005102 GO:0006952 GO:0009405 GO:0030435
40.060.3355.640.050.603zh3A GO:0003824 GO:0005737 GO:0005829 GO:0007049 GO:0008360 GO:0008760 GO:0009252 GO:0016740 GO:0016765 GO:0019277 GO:0051301 GO:0071236 GO:0071555
50.060.2565.870.020.474bz4B GO:0046872
60.060.2605.090.010.433rofA GO:0004721 GO:0004725 GO:0006470 GO:0016787 GO:0035335
70.060.2895.860.090.544m9pA GO:0001664 GO:0001948 GO:0002576 GO:0003779 GO:0004871 GO:0005576 GO:0005634 GO:0005730 GO:0005737 GO:0005829 GO:0005856 GO:0005884 GO:0005886 GO:0005911 GO:0005913 GO:0005925 GO:0005938 GO:0007195 GO:0008134 GO:0015629 GO:0016020 GO:0016479 GO:0017048 GO:0017160 GO:0019900 GO:0030030 GO:0030168 GO:0030334 GO:0030863 GO:0031012 GO:0031267 GO:0031523 GO:0031532 GO:0031852 GO:0031941 GO:0032403 GO:0034329 GO:0034394 GO:0034988 GO:0042177 GO:0042384 GO:0042789 GO:0042803 GO:0042993 GO:0043025 GO:0043066 GO:0043113 GO:0043123 GO:0043198 GO:0043234 GO:0043433 GO:0044319 GO:0044822 GO:0045184 GO:0046332 GO:0048365 GO:0048471 GO:0050821 GO:0051015 GO:0051020 GO:0051220 GO:0051764 GO:0070062 GO:0070527 GO:0071526 GO:0090307 GO:0097440 GO:0098641 GO:1900026 GO:2001046
80.060.2846.150.050.551i9rH
90.060.2685.850.040.483v8oA GO:0003779 GO:0005737 GO:0005829 GO:0005856 GO:0005886 GO:0005925 GO:0008092 GO:0016020 GO:0016528 GO:0030018 GO:0030506 GO:0034329 GO:0042383 GO:0043034 GO:0048747 GO:0051015
100.060.2606.100.010.504av2A GO:0006810 GO:0008565 GO:0009279 GO:0009297 GO:0009306 GO:0015031 GO:0016020 GO:0019867 GO:0030420
110.060.2625.930.060.501lr5A GO:0004872 GO:0005783 GO:0005788 GO:0008270 GO:0009734 GO:0010011 GO:0046872
120.060.2634.760.020.412be3A GO:0015969
130.060.2595.390.020.444cl1D GO:0000166 GO:0001172 GO:0003723 GO:0003968 GO:0004197 GO:0004252 GO:0004386 GO:0005198 GO:0005524 GO:0006508 GO:0008026 GO:0008236 GO:0008270 GO:0016020 GO:0016021 GO:0016032 GO:0016740 GO:0016779 GO:0016787 GO:0017111 GO:0019012 GO:0019028 GO:0019031 GO:0019079 GO:0019087 GO:0039694 GO:0046872
140.060.2774.240.030.423mvkG GO:0005996 GO:0016853 GO:0048029
150.060.2286.060.030.423wo4C GO:0004872 GO:0005886 GO:0006954 GO:0006955 GO:0007165 GO:0007166 GO:0016020 GO:0016021 GO:0070301 GO:0071345
160.060.2384.940.060.374aqzA GO:0006810 GO:0008565 GO:0009279 GO:0009297 GO:0009306 GO:0015031 GO:0016020 GO:0019867 GO:0030420
170.060.2484.730.070.384v9fY GO:0000166 GO:0003677 GO:0003723 GO:0003735 GO:0005622 GO:0005840 GO:0006281 GO:0006412 GO:0019843 GO:0030529
180.060.2115.250.030.362i85A GO:0001525 GO:0001618 GO:0001945 GO:0002042 GO:0005102 GO:0005886 GO:0005887 GO:0005925 GO:0007155 GO:0007267 GO:0007275 GO:0007399 GO:0007411 GO:0009653 GO:0009887 GO:0010839 GO:0016020 GO:0016021 GO:0016032 GO:0030154 GO:0031295 GO:0046718 GO:0046875 GO:0048013 GO:0048514 GO:0050920 GO:0072178 GO:2000727


Consensus prediction of GO terms
 
Molecular Function GO:0008930 GO:0005102 GO:0004488 GO:0004477 GO:0000166 GO:0008782 GO:0008760 GO:0004556
GO-Score 0.06 0.06 0.06 0.06 0.06 0.06 0.06 0.06
Biological Processes GO:0000105 GO:0009252 GO:0006952 GO:0005975 GO:0006164 GO:0008360 GO:0019277 GO:0071555 GO:0055114 GO:0009405 GO:0035999 GO:0019509 GO:0030435 GO:0009396 GO:0007049 GO:0009164 GO:0071236 GO:0051301
GO-Score 0.06 0.06 0.06 0.06 0.06 0.06 0.06 0.06 0.06 0.06 0.06 0.06 0.06 0.06 0.06 0.06 0.06 0.06
Cellular Component GO:0016021 GO:0005829
GO-Score 0.06 0.06

(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.