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I-TASSER results for job id Rv1194c

[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
10.12 9 1t01A III Rep, Mult 38,45,46,49,52,53,56,59,60,227,247,251,254,258,261,262,265
20.06 4 2vicA MN Rep, Mult 364,366
30.04 3 2aiyB IPH Rep, Mult 342,345
40.03 2 1ijdD BCL Rep, Mult 252,255
50.03 2 1i5bA MN Rep, Mult 366,367,368
60.03 2 4rkuB CLA Rep, Mult 270,276,393,396,397
70.03 2 3rfrG III Rep, Mult 345,349,380,388
80.01 1 3ak1B EDO Rep, Mult 328,349
90.01 1 3cisB MG Rep, Mult 310,394
100.01 1 1ibk2 III Rep, Mult 170,171,173,174,178
110.01 1 2gwwA III Rep, Mult 282,286,287,290,293,294,313,316,317,320,323,324,327,331,377,380,394,397
120.01 1 2eikC CD Rep, Mult 102,104,174,178
130.01 1 5jqhB CLR Rep, Mult 133,148,149
140.01 1 1hnz4 III Rep, Mult 386,399,401,403,413,414
150.01 1 1z8qA OXY Rep, Mult 119,123
160.01 1 4o6mB MPG Rep, Mult 21,22
170.01 1 1rke1 III Rep, Mult 108,109,112,150,153,156,157,160,161,163,176,179,182,183,186,190
180.01 1 2yu91 III Rep, Mult 269,347,348,349,352,353,354
190.01 1 1ow8A III Rep, Mult 88,92,98,99,102,182,185,189,192

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
10.0602vdcA0.3427.350.0470.5911.4.1.13NA
20.0602vvnA0.2997.690.0420.5443.2.1.52NA
30.0602uv8G0.3247.480.0220.5702.3.1.86NA
40.0603b8eC0.3417.000.0640.5583.6.3.9283,289,324
50.0601rqgA0.3375.670.0320.4736.1.1.10388
60.0601pn0C0.3326.990.0300.5371.14.13.7NA
70.0601rs0A0.2537.440.0420.4373.4.21.47345,348,351
80.0603eqlM0.3837.060.0500.6222.7.7.6NA
90.0602ivfA0.3217.150.0450.5391.17.99.2317
100.0602cseW0.3267.750.0550.5823.6.4.13NA
110.0602g8eA0.2026.710.0430.3253.4.22.52NA
120.0601reqA0.2597.330.0340.4395.4.99.2NA
130.0602aryA0.2046.770.0480.3283.4.22.52NA
140.0601qxpB0.3356.950.0380.5443.4.22.53,3.4.22.52401
150.0603hkzJ0.3416.600.0580.5442.7.7.6290
160.0601rtkA0.2447.100.0470.4043.4.21.47324
170.0601mo7A0.1415.990.0260.2113.6.3.9353
180.0603gtgB0.3777.120.0370.6222.7.7.6310
190.0601w27A0.3456.650.0560.5444.3.1.24NA

(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
00.290.9581.360.080.985ic0A GO:0001726 GO:0003779 GO:0005178 GO:0005200 GO:0005737 GO:0005815 GO:0005856 GO:0005886 GO:0005925 GO:0007016 GO:0007044 GO:0007155 GO:0009986 GO:0016020 GO:0017166 GO:0030054 GO:0030274 GO:0030866 GO:0032403 GO:0032587 GO:0042995 GO:0051015 GO:0070062 GO:0070527
10.060.3495.120.070.474p9tA GO:0005198 GO:0005634 GO:0005737 GO:0005856 GO:0005886 GO:0005912 GO:0005913 GO:0007155 GO:0007275 GO:0007409 GO:0015629 GO:0016020 GO:0016323 GO:0016337 GO:0021942 GO:0030027 GO:0030054 GO:0030154 GO:0030424 GO:0042995 GO:0045296 GO:0048813 GO:0048854 GO:0051015 GO:0051823 GO:0060134 GO:0097481
20.060.3965.690.060.561st6A GO:0001725 GO:0002009 GO:0002162 GO:0003779 GO:0005198 GO:0005623 GO:0005737 GO:0005743 GO:0005856 GO:0005886 GO:0005903 GO:0005911 GO:0005912 GO:0005913 GO:0005915 GO:0005916 GO:0005925 GO:0005927 GO:0007155 GO:0008013 GO:0015629 GO:0016020 GO:0017166 GO:0030018 GO:0030032 GO:0030054 GO:0030334 GO:0030486 GO:0031594 GO:0031625 GO:0034333 GO:0034394 GO:0042383 GO:0042803 GO:0043034 GO:0043234 GO:0043297 GO:0045121 GO:0045294 GO:0045296 GO:0048675 GO:0051015 GO:0051371 GO:0051393 GO:0070062 GO:0070527 GO:0090136 GO:0090636 GO:0090637 GO:0097110 GO:0098723 GO:1903561 GO:1990357
30.060.3095.050.050.414k1nA GO:0001541 GO:0001669 GO:0005198 GO:0005737 GO:0005794 GO:0005829 GO:0005856 GO:0005886 GO:0005911 GO:0005912 GO:0005913 GO:0005915 GO:0005925 GO:0007015 GO:0007155 GO:0007163 GO:0007406 GO:0007568 GO:0008013 GO:0008584 GO:0014070 GO:0014704 GO:0015629 GO:0016020 GO:0016264 GO:0016342 GO:0016600 GO:0017166 GO:0030027 GO:0030054 GO:0031103 GO:0034613 GO:0042127 GO:0042475 GO:0043066 GO:0043231 GO:0043297 GO:0043627 GO:0044822 GO:0045295 GO:0045296 GO:0045880 GO:0046982 GO:0051015 GO:0051291 GO:0071681 GO:0090136 GO:2000146 GO:2001045 GO:2001240 GO:2001241
40.060.3272.390.090.352l7nA GO:0001726 GO:0003779 GO:0005178 GO:0005200 GO:0005737 GO:0005815 GO:0005856 GO:0005886 GO:0005925 GO:0007016 GO:0007044 GO:0007155 GO:0009986 GO:0016020 GO:0017166 GO:0030054 GO:0030274 GO:0030866 GO:0032403 GO:0032587 GO:0042995 GO:0051015 GO:0070062 GO:0070527
50.060.2982.980.130.331sj8A GO:0001726 GO:0003779 GO:0005178 GO:0005200 GO:0005737 GO:0005815 GO:0005856 GO:0005886 GO:0005925 GO:0007016 GO:0007044 GO:0007155 GO:0009986 GO:0016020 GO:0017166 GO:0030054 GO:0030274 GO:0030866 GO:0032403 GO:0032587 GO:0042995 GO:0051015 GO:0070062 GO:0070527
60.060.3001.820.100.323fyqA GO:0001726 GO:0003779 GO:0005158 GO:0005178 GO:0005200 GO:0005856 GO:0005925 GO:0006909 GO:0007016 GO:0007155 GO:0007298 GO:0007390 GO:0007430 GO:0007475 GO:0007526 GO:0008360 GO:0016203 GO:0033627 GO:0035160 GO:0045214 GO:0045892 GO:0051015 GO:0060439 GO:0086042
70.060.4135.980.050.574iggB GO:0001541 GO:0001669 GO:0005198 GO:0005737 GO:0005794 GO:0005829 GO:0005856 GO:0005886 GO:0005911 GO:0005912 GO:0005913 GO:0005915 GO:0005925 GO:0007015 GO:0007155 GO:0007163 GO:0007406 GO:0007568 GO:0008013 GO:0008584 GO:0014070 GO:0014704 GO:0015629 GO:0016020 GO:0016264 GO:0016342 GO:0016600 GO:0017166 GO:0030027 GO:0030054 GO:0031103 GO:0034332 GO:0034613 GO:0042127 GO:0042475 GO:0043066 GO:0043231 GO:0043297 GO:0043627 GO:0044822 GO:0045295 GO:0045296 GO:0045880 GO:0051015 GO:0051149 GO:0051291 GO:0071681 GO:0090136 GO:0098641 GO:2000146 GO:2001045 GO:2001240 GO:2001241
80.060.2734.220.050.341dowA GO:0001541 GO:0001669 GO:0005198 GO:0005737 GO:0005794 GO:0005829 GO:0005856 GO:0005886 GO:0005911 GO:0005912 GO:0005913 GO:0005915 GO:0005925 GO:0007015 GO:0007155 GO:0007163 GO:0007406 GO:0007568 GO:0008013 GO:0008584 GO:0014070 GO:0014704 GO:0015629 GO:0016020 GO:0016264 GO:0016342 GO:0016600 GO:0017166 GO:0030027 GO:0030054 GO:0031103 GO:0034613 GO:0042127 GO:0042475 GO:0043066 GO:0043231 GO:0043297 GO:0043627 GO:0044822 GO:0045295 GO:0045296 GO:0045880 GO:0046982 GO:0051015 GO:0051291 GO:0071681 GO:0090136 GO:2000146 GO:2001045 GO:2001240 GO:2001241
90.060.3635.660.050.513dyjA GO:0001726 GO:0003779 GO:0005178 GO:0005200 GO:0005737 GO:0005815 GO:0005856 GO:0005886 GO:0005925 GO:0007016 GO:0007044 GO:0007155 GO:0009986 GO:0016020 GO:0017166 GO:0030054 GO:0030274 GO:0030866 GO:0032403 GO:0032587 GO:0042995 GO:0051015 GO:0070062 GO:0070527
100.060.3032.540.090.332l10A GO:0001726 GO:0003779 GO:0005178 GO:0005200 GO:0005737 GO:0005815 GO:0005856 GO:0005886 GO:0005925 GO:0007016 GO:0007044 GO:0007155 GO:0009986 GO:0016020 GO:0017166 GO:0030054 GO:0030274 GO:0030866 GO:0032403 GO:0032587 GO:0042995 GO:0051015 GO:0070062 GO:0070527
110.060.2733.920.100.334k1oA GO:0005198 GO:0005634 GO:0005737 GO:0005856 GO:0005886 GO:0005912 GO:0005913 GO:0007155 GO:0007275 GO:0007409 GO:0015629 GO:0016020 GO:0016323 GO:0016337 GO:0021942 GO:0030027 GO:0030054 GO:0030154 GO:0030424 GO:0042995 GO:0045296 GO:0048813 GO:0048854 GO:0051015 GO:0051823 GO:0060134 GO:0097481
120.060.2027.470.040.354l80B GO:0003824 GO:0015977 GO:0016829 GO:0043427 GO:0046872 GO:0047777 GO:0050083
130.060.1853.820.070.221rccA GO:0005623 GO:0006826 GO:0006879 GO:0008199 GO:0046872
140.060.2964.900.060.394onsC GO:0005198 GO:0005634 GO:0005737 GO:0005856 GO:0005886 GO:0005912 GO:0005913 GO:0007155 GO:0007275 GO:0007409 GO:0015629 GO:0016020 GO:0016323 GO:0016337 GO:0021942 GO:0030027 GO:0030054 GO:0030154 GO:0030424 GO:0042995 GO:0045296 GO:0048813 GO:0048854 GO:0051015 GO:0051823 GO:0060134 GO:0097481
150.060.2266.670.010.363owoA GO:0004022 GO:0016491 GO:0046872 GO:0055114
160.060.1986.260.050.305hbgA GO:0004124 GO:0006535 GO:0008652 GO:0016740 GO:0019344
170.060.1995.620.070.282hpvA GO:0008752 GO:0009055 GO:0010181 GO:0016491 GO:0016652 GO:0016661 GO:0055114
180.060.2083.420.060.242jswA GO:0001726 GO:0003779 GO:0005178 GO:0005200 GO:0005737 GO:0005815 GO:0005856 GO:0005886 GO:0005925 GO:0007016 GO:0007044 GO:0007155 GO:0009986 GO:0016020 GO:0017166 GO:0030054 GO:0030274 GO:0030866 GO:0032403 GO:0032587 GO:0042995 GO:0051015 GO:0070062 GO:0070527


Consensus prediction of GO terms
 
Molecular Function GO:0051015 GO:0017166 GO:0005200 GO:0030274 GO:0005178
GO-Score 0.45 0.42 0.34 0.34 0.34
Biological Processes GO:0070527 GO:0007044 GO:0030866 GO:0007016
GO-Score 0.38 0.34 0.34 0.34
Cellular Component GO:0005737 GO:0005925 GO:0070062 GO:0005911 GO:0005815 GO:0009986 GO:0032587
GO-Score 0.45 0.42 0.38 0.36 0.34 0.34 0.34

(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.