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I-TASSER results for job id Rv3103c

[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 4fe1F CLA Rep, Mult 25,29
20.07 3 4v1fA BQ1 Rep, Mult 31,32,35
30.05 2 3e0dA CA Rep, Mult 62,64
40.05 2 3fbyA CA Rep, Mult 62,64,66,68,70,73,76
50.05 2 2efbA UUU Rep, Mult 131,133,134
60.02 1 2j5mA MAN Rep, Mult 81,83
70.02 1 4h2sC PNS Rep, Mult 20,21
80.02 1 2cixA MAN Rep, Mult 85,87
90.02 1 2wl3A CA Rep, Mult 63,107
100.02 1 3pcaM DHB Rep, Mult 61,68
110.02 1 2wsc2 CLA Rep, Mult 19,145
120.02 1 5er5A ET Rep, Mult 36,37
130.02 1 1lgb1 III Rep, Mult 115,116,117,118,119,120,121,122,123,124,128,129,130,137,138
140.02 1 2w6dB CPL Rep, Mult 94,95,96,97,98

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
10.0605r1rA0.2014.670.0410.3451.17.4.1NA
20.0601l1lA0.2343.540.0140.3311.17.4.2NA
30.0601ekjG0.2373.690.0800.3384.2.1.1NA
40.0601wd9A0.1903.960.0470.2833.5.3.15NA
50.0601mc0A0.2014.360.0830.3243.1.4.1784
60.0601n1hA0.2353.460.0340.3172.7.7.48NA
70.0602dewX0.2384.550.0250.3933.5.3.15NA
80.0603daxA0.2383.720.0200.3381.14.13.17NA
90.0602ofgX0.2573.970.0160.3723.6.3.5NA
100.0603b43A0.3654.520.0680.6002.7.11.1131,133
110.0602d4eC0.2394.170.0630.3591.2.1.60NA
120.0602pziA0.2563.860.1030.3932.7.11.1NA
130.0601eulA0.2045.060.0220.3793.6.3.8NA
140.0602q3zA0.2324.310.0190.3792.3.2.13NA
150.0601uxvA0.2334.320.0770.3521.2.1.9129
160.0601p1jA0.2344.070.0190.3655.5.1.4NA
170.0602vkzG0.2544.690.0210.4212.3.1.38,3.1.2.14NA
180.0601qrjB0.2393.280.0330.3243.1.26.4129
190.0603hz3A0.2384.910.0560.4212.4.1.5NA

(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
00.070.6341.900.090.731mv3A GO:0005634 GO:0005737 GO:0006897 GO:0006997 GO:0007275 GO:0008283 GO:0015629 GO:0016020 GO:0016032 GO:0030018 GO:0030100 GO:0030154 GO:0030315 GO:0030424 GO:0031674 GO:0033268 GO:0042692 GO:0042802 GO:0043065 GO:0043194 GO:0045664 GO:0048156 GO:0048711 GO:0051015 GO:0060987 GO:0060988 GO:0070063 GO:0071156
10.060.1654.800.010.262vgeA GO:0000122 GO:0003215 GO:0003229 GO:0003714 GO:0005634 GO:0005654 GO:0005737 GO:0005913 GO:0006351 GO:0006355 GO:0006915 GO:0008134 GO:0009791 GO:0030054 GO:0031076 GO:0035264 GO:0042633 GO:0042802 GO:0045171 GO:0045597 GO:0048871 GO:0060048 GO:0098609 GO:0098641 GO:1901796
20.060.1793.510.020.251agsA GO:0004364 GO:0005737 GO:0005829 GO:0006749 GO:0008152 GO:0016740 GO:0030855 GO:0070062 GO:1901687
30.060.1704.270.000.244a63B GO:0002039 GO:0005070 GO:0005634 GO:0005654 GO:0005737 GO:0005739 GO:0006915 GO:0007049 GO:0007165 GO:0017124 GO:0042802 GO:0042981 GO:0045786 GO:0048471 GO:0051059 GO:0072332 GO:1900119 GO:1900740 GO:1901216 GO:1901796
40.060.1344.410.090.212jt4A GO:0000147 GO:0003779 GO:0005634 GO:0005737 GO:0005768 GO:0005856 GO:0005886 GO:0005938 GO:0006897 GO:0008092 GO:0010008 GO:0016020 GO:0030041 GO:0030479 GO:0030674 GO:0042802 GO:0043130
50.060.1583.820.030.234igzA GO:0005200 GO:0005634 GO:0005737 GO:0005886 GO:0005925 GO:0007015 GO:0007155 GO:0008093 GO:0008307 GO:0015629 GO:0016020 GO:0016324 GO:0016477 GO:0030018 GO:0030027 GO:0030054 GO:0042995 GO:0044822 GO:0046872 GO:0048471 GO:0061049
60.060.1554.590.050.261griA GO:0000165 GO:0005070 GO:0005088 GO:0005154 GO:0005168 GO:0005634 GO:0005654 GO:0005730 GO:0005737 GO:0005768 GO:0005794 GO:0005829 GO:0005886 GO:0005911 GO:0007173 GO:0007265 GO:0007267 GO:0007411 GO:0008180 GO:0008286 GO:0008543 GO:0009967 GO:0012506 GO:0014066 GO:0016020 GO:0016032 GO:0016303 GO:0017124 GO:0019901 GO:0019903 GO:0019904 GO:0030154 GO:0030838 GO:0031295 GO:0031623 GO:0036092 GO:0038095 GO:0038096 GO:0038128 GO:0042059 GO:0042770 GO:0042802 GO:0043408 GO:0043547 GO:0043560 GO:0044822 GO:0046854 GO:0046875 GO:0046934 GO:0048015 GO:0048646 GO:0050900 GO:0060670 GO:0070062 GO:0070436 GO:0071479 GO:2000379
70.060.1464.540.090.231uffA GO:0005070 GO:0005089 GO:0005509 GO:0005737 GO:0005813 GO:0006897 GO:0009967 GO:0030154 GO:0035023 GO:0043547 GO:0046872 GO:0070062 GO:1903861
80.060.1374.390.090.224esrA GO:0001738 GO:0001947 GO:0002092 GO:0005737 GO:0005813 GO:0005814 GO:0005829 GO:0005856 GO:0005911 GO:0005912 GO:0005929 GO:0007169 GO:0007417 GO:0010842 GO:0016192 GO:0030030 GO:0030054 GO:0030862 GO:0030902 GO:0031513 GO:0034613 GO:0035844 GO:0035845 GO:0036038 GO:0036064 GO:0039008 GO:0039023 GO:0042384 GO:0042802 GO:0042995 GO:0043066 GO:0045944 GO:0050795 GO:0060271 GO:0065001 GO:0070121 GO:0070986 GO:0071599 GO:0072372
90.060.1403.970.090.212kbtA GO:0005576 GO:0005618 GO:0009405 GO:0016020 GO:0019864
100.060.1343.220.020.182yuoA GO:0005096 GO:0005622 GO:0005737 GO:0005829 GO:0005921 GO:0006886 GO:0007049 GO:0007050 GO:0012505 GO:0017137 GO:0030695 GO:0031338 GO:0032483 GO:0032486 GO:0045732 GO:0048227 GO:0090630
110.060.1323.630.040.192oi3A GO:0000166 GO:0002376 GO:0002522 GO:0002758 GO:0004672 GO:0004713 GO:0004715 GO:0005102 GO:0005524 GO:0005634 GO:0005737 GO:0005764 GO:0005794 GO:0005829 GO:0005856 GO:0005884 GO:0005886 GO:0005901 GO:0005925 GO:0006468 GO:0006887 GO:0006909 GO:0006954 GO:0007155 GO:0007169 GO:0007229 GO:0007498 GO:0008284 GO:0008360 GO:0016020 GO:0016023 GO:0016032 GO:0016301 GO:0016310 GO:0016740 GO:0018108 GO:0019221 GO:0030054 GO:0030133 GO:0030154 GO:0030838 GO:0031234 GO:0031410 GO:0031663 GO:0038083 GO:0038096 GO:0042995 GO:0043066 GO:0043299 GO:0045087 GO:0045728 GO:0046777 GO:0050690 GO:0050727 GO:0050764 GO:0051090 GO:0060333 GO:0071801 GO:2000251
120.060.1425.310.070.281x2qA GO:0005654 GO:0005737 GO:0005768 GO:0005829 GO:0006810 GO:0006886 GO:0006914 GO:0015031 GO:0016020 GO:0016197 GO:0031901 GO:0033565 GO:0036258 GO:0042059 GO:0043231
130.060.1193.480.000.172ed0A GO:0003677 GO:0005737 GO:0005829 GO:0005856 GO:0006928 GO:0007010 GO:0008093 GO:0008154 GO:0016032 GO:0016477 GO:0016601 GO:0017124 GO:0018108 GO:0019900 GO:0030027 GO:0030175 GO:0031209 GO:0031625 GO:0032403 GO:0042995 GO:0048365 GO:0070064 GO:2000601
140.060.1303.410.000.192i0nA GO:0000166 GO:0000902 GO:0001891 GO:0003774 GO:0003779 GO:0005524 GO:0005737 GO:0005829 GO:0005856 GO:0006909 GO:0008017 GO:0009847 GO:0016020 GO:0016459 GO:0030048 GO:0030175 GO:0030898 GO:0031252 GO:0031589 GO:0043621 GO:0046847 GO:0051015
150.060.1343.390.000.192drkA GO:0000166 GO:0003774 GO:0005524 GO:0016459
160.060.1264.640.110.212dl7A
170.060.1264.610.050.211pnjA GO:0001678 GO:0001953 GO:0005068 GO:0005158 GO:0005159 GO:0005168 GO:0005634 GO:0005737 GO:0005801 GO:0005829 GO:0005911 GO:0005942 GO:0005943 GO:0006468 GO:0006810 GO:0007162 GO:0007165 GO:0008134 GO:0008286 GO:0008625 GO:0008630 GO:0014065 GO:0015031 GO:0016020 GO:0019903 GO:0030183 GO:0030335 GO:0032760 GO:0032869 GO:0033120 GO:0034644 GO:0034976 GO:0035014 GO:0036312 GO:0042993 GO:0043066 GO:0043125 GO:0043548 GO:0043551 GO:0043559 GO:0043560 GO:0045671 GO:0045944 GO:0046326 GO:0046854 GO:0046935 GO:0046982 GO:0048009 GO:0050821 GO:0051492 GO:0051531 GO:0060396 GO:0090003 GO:0090004 GO:1900103 GO:1990578 GO:2001275
180.060.1284.200.000.202k9gA GO:0005737 GO:0005829 GO:0005856 GO:0005886 GO:0005911 GO:0005925 GO:0006897 GO:0006915 GO:0007010 GO:0007267 GO:0008360 GO:0016020 GO:0016477 GO:0017124 GO:0030054 GO:0030139 GO:0030659 GO:0031410 GO:0042059 GO:0043005 GO:0045202


Consensus prediction of GO terms
 
Molecular Function GO:0005515
GO-Score 0.46
Biological Processes GO:1901796 GO:0071156 GO:0048711 GO:0016032 GO:0045664 GO:0008283 GO:0030100 GO:0042692 GO:0060988 GO:0006997 GO:0006749 GO:0000147 GO:0098609 GO:0030041 GO:0035264 GO:1901216 GO:1901687 GO:0009791 GO:0003215 GO:0003229 GO:0000122 GO:0031076 GO:0060048 GO:1900119 GO:0030855 GO:1900740 GO:0042633 GO:0072332 GO:0048871
GO-Score 0.12 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 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 0.06
Cellular Component GO:0043231
GO-Score 0.46

(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.