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I-TASSER results for job id Rv3217c

[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
10.08 4 3s8gA OLC Rep, Mult 79,115,116,117
20.08 4 4tt0A IOD Rep, Mult 19,22
30.06 3 2xqtE CVM Rep, Mult 31,32,35
40.04 2 1vdfB CL Rep, Mult 24,27
50.04 2 4zzcA XE Rep, Mult 23,51,54
60.04 2 3mk4A III Rep, Mult 50,54,109,110,122
70.02 1 3ap2B PO4 Rep, Mult 70,143
80.02 1 1uo4B PIH Rep, Mult 43,47
90.02 1 3mk7A CA Rep, Mult 62,66,73
100.02 1 3d1lA MPR Rep, Mult 115,140
110.02 1 1y66A DIO Rep, Mult 78,82
120.02 1 4zzcA XE Rep, Mult 12,16,59,62
130.02 1 2ljcB RIM Rep, Mult 9,12
140.02 1 2p1cA GG3 Rep, Mult 81,84
150.02 1 2jstA HLT Rep, Mult 72,108

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
10.0601m56A0.5154.580.0510.8321.9.3.1NA
20.0601w27A0.5154.370.0770.8254.3.1.24NA
30.0602v8tA0.5114.840.0700.8671.11.1.6NA
40.0603fedA0.5133.970.0600.7693.4.17.21NA
50.0601mo7A0.2875.280.0250.5243.6.3.958
60.0601h0nA0.5274.060.0800.7691.17.4.1NA
70.0601z8lA0.5234.000.0610.7833.4.17.21NA
80.0601qleA0.5764.140.1010.8741.9.3.1NA
90.0601sojL0.5253.890.0500.7693.1.4.17NA
100.0601xmeA0.5744.440.1170.9231.9.3.1122
110.0601zklA0.5293.650.0490.7413.1.4.1716,19
120.0601occA0.5724.550.1200.9301.9.3.1NA
130.0602bl2A0.5543.600.1060.8113.6.3.1421,54
140.0602qymA0.5253.870.0170.7483.1.4.17121
150.0601tazA0.5223.680.0730.7553.1.4.1763
160.0603b8eA0.5394.130.0580.8183.6.3.9NA
170.0602qb0B0.3524.680.0860.5943.2.1.17NA
180.0603ecnB0.5283.700.0420.7623.1.4.178,60
190.0601mhsA0.5154.660.1040.8323.6.3.6NA

(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
00.210.6902.920.090.872mgyA GO:0005497 GO:0005737 GO:0005739 GO:0005741 GO:0006694 GO:0006810 GO:0006811 GO:0006821 GO:0006869 GO:0007268 GO:0007568 GO:0008347 GO:0008503 GO:0010042 GO:0010266 GO:0010823 GO:0010940 GO:0014012 GO:0016020 GO:0016021 GO:0030325 GO:0031397 GO:0031965 GO:0031966 GO:0032570 GO:0032720 GO:0033574 GO:0042493 GO:0043065 GO:0043231 GO:0044325 GO:0045019 GO:0048265 GO:0048266 GO:0048678 GO:0050810 GO:0051901 GO:0051928 GO:0060242 GO:0060252 GO:0060253 GO:0070062 GO:0071222 GO:0071294 GO:0071476 GO:0072655 GO:0072656 GO:0098794 GO:0099565 GO:1903147 GO:1903579 GO:2000379
10.090.5533.950.080.854rymA GO:0005886 GO:0006810 GO:0016020 GO:0016021 GO:0033013 GO:0046906
20.090.6173.620.130.902jswA 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
30.080.5834.230.110.923o0rB GO:0004129 GO:0005506 GO:0005886 GO:0009055 GO:0009060 GO:0016020 GO:0016021 GO:0016491 GO:0016966 GO:0019333 GO:0020037 GO:0046872 GO:0055114 GO:0070469 GO:1902600
40.070.5644.430.080.895c6nA GO:0006855 GO:0015238 GO:0015297 GO:0016020 GO:0016021 GO:0055085
50.070.5494.390.080.933vvpA GO:0006855 GO:0015238 GO:0015297 GO:0016020 GO:0016021 GO:0055085
60.070.5814.120.080.922yevA GO:0004129 GO:0005506 GO:0005507 GO:0005886 GO:0006119 GO:0006810 GO:0006811 GO:0009055 GO:0009060 GO:0015002 GO:0015992 GO:0016020 GO:0016021 GO:0016491 GO:0020037 GO:0022900 GO:0022904 GO:0046872 GO:0055114 GO:0070469 GO:1902600
70.070.5904.450.050.934xydA GO:0004129 GO:0005506 GO:0009055 GO:0009060 GO:0016020 GO:0016021 GO:0016491 GO:0016966 GO:0020037 GO:0055114 GO:0070469 GO:1902600
80.070.5614.420.060.935djqA GO:0004129 GO:0005506 GO:0005507 GO:0005886 GO:0005887 GO:0006119 GO:0009055 GO:0009060 GO:0015078 GO:0015990 GO:0015992 GO:0016020 GO:0016021 GO:0016491 GO:0016705 GO:0019411 GO:0019646 GO:0019825 GO:0020037 GO:0045154 GO:0045278 GO:0046872 GO:0055114 GO:0070069 GO:0070469 GO:0070470 GO:1902600
90.070.5863.600.060.851r0dA GO:0003779 GO:0005543 GO:0005737 GO:0005856 GO:0005905 GO:0006897 GO:0006898 GO:0006915 GO:0012505 GO:0016020 GO:0030136 GO:0030276 GO:0030665 GO:0031410 GO:0035091 GO:0043231 GO:0048471 GO:0072583
100.070.5843.430.070.822wvoA GO:0005737 GO:0006915
110.070.5304.130.080.835duoA GO:0005886 GO:0006810 GO:0008289 GO:0016020 GO:0016021 GO:0033013 GO:0046906
120.070.6034.110.040.933mk4A GO:0002230 GO:0003333 GO:0005654 GO:0005777 GO:0005778 GO:0005779 GO:0005783 GO:0005829 GO:0007031 GO:0008289 GO:0015171 GO:0016020 GO:0016021 GO:0016557 GO:0032994 GO:0043231 GO:0043234 GO:0045046 GO:0046983 GO:0055085 GO:0098779 GO:0098792
130.070.5824.280.070.913ajbA GO:0002230 GO:0003333 GO:0005654 GO:0005777 GO:0005778 GO:0005779 GO:0005783 GO:0005829 GO:0007031 GO:0008289 GO:0015171 GO:0016020 GO:0016021 GO:0016557 GO:0032994 GO:0043231 GO:0043234 GO:0045046 GO:0046983 GO:0055085 GO:0098779 GO:0098792
140.070.5934.000.100.904mlbB GO:0006855 GO:0015238 GO:0015297 GO:0016020 GO:0016021 GO:0055085
150.070.5754.290.070.933ayfA GO:0004129 GO:0005506 GO:0009055 GO:0009060 GO:0016020 GO:0016021 GO:0020037 GO:0046872 GO:0055114 GO:1902600
160.060.4843.620.050.665ic0A 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
170.060.5694.070.080.854z3nA GO:0006855 GO:0015238 GO:0015297 GO:0016020 GO:0016021 GO:0055085
180.060.3325.300.080.592o18C GO:0005886 GO:0016020 GO:0016740 GO:0017013 GO:0046872


Consensus prediction of GO terms
 
Molecular Function GO:0042562 GO:0030594 GO:0005515
GO-Score 0.41 0.41 0.41
Biological Processes GO:0031396 GO:0070585 GO:1904406 GO:1903321 GO:0007268 GO:0031327 GO:0071470 GO:0015698 GO:0014015 GO:0045978 GO:1901701 GO:0048732 GO:0042981 GO:1903556 GO:0071702 GO:0032680 GO:1900543 GO:0051900 GO:1905114 GO:1903427 GO:0043068 GO:0010876 GO:0008284 GO:0071219 GO:0010043 GO:0043270 GO:0010507 GO:0045428 GO:1903146 GO:0048545 GO:0033273 GO:0033555 GO:0006971 GO:0072594 GO:0060251 GO:0051924 GO:1904181 GO:0016477 GO:0072595 GO:0010243 GO:0010939 GO:0051220 GO:0035270 GO:0071396 GO:0046890 GO:0014014 GO:0019218 GO:1901654 GO:0010639 GO:0044708 GO:0008285 GO:0031103 GO:0032496 GO:1903578 GO:1901362 GO:0071248 GO:0031325
GO-Score 0.41 0.41 0.41 0.41 0.41 0.41 0.41 0.41 0.41 0.41 0.41 0.41 0.41 0.41 0.41 0.41 0.41 0.41 0.41 0.41 0.41 0.41 0.41 0.41 0.41 0.41 0.41 0.41 0.41 0.41 0.41 0.41 0.41 0.41 0.41 0.41 0.41 0.41 0.41 0.41 0.41 0.41 0.41 0.41 0.41 0.41 0.41 0.41 0.41 0.41 0.41 0.41 0.41 0.41 0.41 0.41 0.41
Cellular Component GO:0031988 GO:1903561 GO:0071944 GO:0005635 GO:0031968 GO:0044456 GO:0031966 GO:0016021
GO-Score 0.55 0.55 0.47 0.41 0.41 0.41 0.41 0.38

(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.