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I-TASSER results for job id Rv0178

[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 3 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 5 1jdbE GLN Rep, Mult 126,127,138,139,142
20.07 4 3ov4B EQU Rep, Mult 124,158,196,198,200,212,216,232,236
30.05 3 4akyA 4LL Rep, Mult 128,129,130,131,158,162,198,214,234
40.05 3 3fkaC UNL Rep, Mult 124,128,196,214,216,232
50.04 2 3soaA DB8 Rep, Mult 182,192,219,232
60.04 2 2ibfA III Rep, Mult 133,134,136,137,140,155,159
70.02 1 1c3oA GLN Rep, Mult 129,130,155,157
80.02 1 3fk7A 4DM Rep, Mult 124,128
90.02 1 1a9x1 III Rep, Mult 120,121,124,125,147,148
100.02 1 3atsA CA Rep, Mult 19,22,23
110.02 1 2vn9B GVD Rep, Mult 178,180,195,214,216,240
120.02 1 2ljcB RIM Rep, Mult 85,88
130.02 1 1nr5B CO Rep, Mult 142,149
140.02 1 2c3wA GLC Rep, Mult 227,233,234,235
150.02 1 3cf8B QUE Rep, Mult 193,195

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
10.0601yiqA0.4385.590.0590.6891.1.99.-189
20.0601g72A0.4355.840.1030.7301.1.99.8NA
30.0602uv8G0.3906.200.0340.6842.3.1.86NA
40.0604stdA0.4123.280.0620.5164.2.1.94NA
50.0601ofdA0.3736.540.0470.6931.4.7.1NA
60.0601fo4A0.3616.710.0480.6931.17.1.4NA
70.0602vkzG0.3946.110.0400.6722.3.1.38,3.1.2.14NA
80.0601lrwA0.4415.600.0790.7131.1.99.8189
90.0602w68C0.2835.100.0440.4263.2.1.18NA
100.0603gzxB0.4053.940.0850.5411.14.12.18NA
110.0602ebsB0.3955.960.0290.6563.2.1.150NA
120.0603b9jC0.3606.390.0320.6391.17.3.2,1.17.1.4NA
130.0602e1qA0.3636.560.0630.6931.17.3.2,1.17.1.4NA
140.0602d0vA0.4435.760.0680.7251.1.99.8189
150.0601eulA0.3826.250.0630.6843.6.3.8NA
160.0601bxrA0.4246.140.0290.7586.3.5.5119
170.0602r7oA0.4046.000.0600.7092.7.7.48140
180.0602v7oA0.2386.520.0410.4392.7.11.17134,135
190.0601o0sA0.4246.240.0700.7501.1.1.38NA

(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
00.070.4664.630.080.674rzmB GO:0016853 GO:0017000
10.060.4443.800.060.563soaA GO:0000082 GO:0000165 GO:0000166 GO:0002931 GO:0004672 GO:0004674 GO:0004683 GO:0005088 GO:0005516 GO:0005524 GO:0005634 GO:0005654 GO:0005739 GO:0005829 GO:0005886 GO:0006468 GO:0006816 GO:0007223 GO:0010666 GO:0016020 GO:0016301 GO:0016310 GO:0016740 GO:0018105 GO:0030054 GO:0030666 GO:0035254 GO:0038166 GO:0042734 GO:0042803 GO:0043547 GO:0045202 GO:0046777 GO:0046928 GO:0048168 GO:0051092 GO:0051928 GO:0060333 GO:0097481 GO:1900034 GO:1902108
20.060.4494.390.030.634xzzA GO:0016740
30.060.4153.330.120.515ig5F GO:0000166 GO:0004672 GO:0004674 GO:0004683 GO:0005516 GO:0005524 GO:0006468 GO:0016301 GO:0016310 GO:0016740
40.060.4152.990.100.502ux0A GO:0000082 GO:0000165 GO:0000166 GO:0004672 GO:0004674 GO:0004683 GO:0004723 GO:0005088 GO:0005516 GO:0005524 GO:0005654 GO:0005829 GO:0005886 GO:0006468 GO:0006470 GO:0006816 GO:0007275 GO:0007399 GO:0014733 GO:0016020 GO:0016301 GO:0016310 GO:0016529 GO:0016740 GO:0030073 GO:0030154 GO:0030666 GO:0033017 GO:0042803 GO:0043547 GO:0046777 GO:0051259 GO:0051924 GO:0060333 GO:0097481 GO:1900034 GO:1901897
50.060.4132.650.120.485ig4E GO:0000166 GO:0004672 GO:0004674 GO:0004683 GO:0005516 GO:0005524 GO:0006468 GO:0016301 GO:0016310 GO:0016740
60.060.3982.800.100.475ig0A GO:0000166 GO:0004672 GO:0004674 GO:0004683 GO:0005516 GO:0005524 GO:0006468 GO:0016301 GO:0016310 GO:0016740
70.060.4002.870.110.482w2cH GO:0000082 GO:0000165 GO:0000166 GO:0001558 GO:0001666 GO:0002026 GO:0002028 GO:0003254 GO:0004672 GO:0004674 GO:0004683 GO:0005088 GO:0005516 GO:0005524 GO:0005634 GO:0005654 GO:0005737 GO:0005829 GO:0005886 GO:0006357 GO:0006468 GO:0006816 GO:0008016 GO:0010389 GO:0010613 GO:0010649 GO:0010666 GO:0010880 GO:0010881 GO:0014704 GO:0014911 GO:0016020 GO:0016301 GO:0016310 GO:0016529 GO:0016740 GO:0018105 GO:0018107 GO:0019871 GO:0030007 GO:0030315 GO:0030666 GO:0031432 GO:0031594 GO:0032469 GO:0033017 GO:0034704 GO:0035022 GO:0042383 GO:0042803 GO:0043025 GO:0043194 GO:0043234 GO:0043547 GO:0044325 GO:0046777 GO:0048471 GO:0048661 GO:0050998 GO:0051259 GO:0055119 GO:0060048 GO:0060314 GO:0060333 GO:0060341 GO:0061049 GO:0070374 GO:0071277 GO:0086003 GO:0086091 GO:0098901 GO:0098909 GO:1900034 GO:1901725 GO:1901844 GO:1901897 GO:1902306 GO:1902514 GO:2000650
80.060.3973.970.120.533h51A GO:0004683 GO:0005516 GO:0006468
90.060.3982.910.100.482f86B GO:0000165 GO:0000166 GO:0004672 GO:0004674 GO:0004683 GO:0005516 GO:0005524 GO:0005737 GO:0006468 GO:0010628 GO:0016301 GO:0016310 GO:0016740 GO:0018105 GO:0018107 GO:0030424 GO:0042995 GO:0043005 GO:0043204 GO:0044325 GO:0046872 GO:0072375 GO:1904115
100.060.3553.880.080.475cxoB GO:0016787
110.060.3376.250.050.594uakA GO:0000166 GO:0000287 GO:0004672 GO:0004674 GO:0005524 GO:0005737 GO:0005856 GO:0005886 GO:0005911 GO:0006468 GO:0007010 GO:0007163 GO:0007165 GO:0016020 GO:0016301 GO:0016310 GO:0016477 GO:0016740 GO:0017048 GO:0030036 GO:0030054 GO:0031032 GO:0031252 GO:0031532 GO:0035556 GO:0042641 GO:0046872 GO:0070062
120.060.3753.340.070.463b7cA GO:0004067 GO:0016787
130.060.3495.920.050.593nynA GO:0000166 GO:0002029 GO:0004672 GO:0004674 GO:0004703 GO:0005524 GO:0005829 GO:0005886 GO:0006468 GO:0007165 GO:0008277 GO:0010360 GO:0016020 GO:0016055 GO:0016301 GO:0016310 GO:0016740 GO:0047696
140.060.3594.120.060.484xb5A GO:0005622 GO:0006810 GO:0007165 GO:0009579 GO:0009881 GO:0016020 GO:0016037 GO:0018298 GO:0030089 GO:0031404 GO:0042651 GO:0050896
150.060.3603.220.080.451buqA GO:0004769 GO:0005622 GO:0006629 GO:0006810 GO:0008202 GO:0016853
160.060.3713.500.060.463wmdB GO:0016853
170.060.3733.240.080.453t8nB GO:0004769 GO:0006629 GO:0008202 GO:0016853
180.060.3476.090.050.592acxB GO:0000166 GO:0002029 GO:0004672 GO:0004674 GO:0004703 GO:0005524 GO:0005829 GO:0005886 GO:0006468 GO:0007165 GO:0008277 GO:0010360 GO:0016020 GO:0016055 GO:0016301 GO:0016310 GO:0016740 GO:0047696


Consensus prediction of GO terms
 
Molecular Function GO:0005515 GO:0035639 GO:0032550 GO:0004674 GO:0032559
GO-Score 0.36 0.36 0.36 0.36 0.36
Biological Processes GO:0006464 GO:0016310
GO-Score 0.36 0.36
Cellular Component GO:0005829 GO:0005654 GO:0030666 GO:0014069 GO:0042734 GO:0030054 GO:0033017 GO:0005739
GO-Score 0.12 0.12 0.12 0.12 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.