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I-TASSER results for job id Rv1134

[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
10.16 8 3pciA IHB Rep, Mult 28,45,46,47
20.08 4 4ryoA MPG Rep, Mult 12,15,62
30.08 4 1xk0A NO Rep, Mult 14,18
40.04 2 2ydoA SOG Rep, Mult 56,57,58,59,62
50.02 1 3pcaO DHB Rep, Mult 21,36
60.02 1 4plrA CA Rep, Mult 17,18
70.02 1 2ih9A 5AX Rep, Mult 31,34,37
80.02 1 4unpA TXW Rep, Mult 7,11,62,66
90.02 1 3zbyF BCD Rep, Mult 1,32
100.02 1 4ro2B GLY Rep, Mult 7,8
110.02 1 4m9vC MPD Rep, Mult 11,14

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
10.0601cg2A0.4733.600.0300.8213.4.17.1148
20.0603k1dA0.4873.840.0750.8332.4.1.18NA
30.0602zdoD0.4843.900.0450.8461.14.99.316,32,49,52,74
40.0601biqB0.5433.790.0390.9231.17.4.17
50.0601i19A0.5023.410.0290.8721.1.3.6NA
60.0602fgeA0.5023.760.0950.9103.4.24.-NA
70.0602d0tB0.4903.840.0410.9101.13.11.5210
80.0601jtnA0.4173.660.0310.7053.2.1.1753
90.0602pnrF0.4174.000.0560.8332.7.11.2NA
100.0601ad3A0.4943.170.0790.7951.2.1.5NA
110.0603bxvA0.2714.510.0000.5771.13.11.5530
120.0603d2rB0.4983.630.0540.8592.7.11.210
130.0603cskA0.4853.640.0310.8213.4.14.457
140.0601r0sA0.4923.760.0530.9103.2.2.5NA
150.0602gv9B0.4734.090.0790.9232.7.7.753,55
160.0601cfrA0.4723.350.0480.7563.1.21.4NA
170.0601jk0A0.4983.930.0530.9361.17.4.1NA
180.0602pnrB0.4194.000.0560.8332.7.11.210
190.0602rccA0.4774.120.0410.9101.17.4.1NA

(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
00.070.3734.140.010.643kz1A GO:0000910 GO:0001558 GO:0001664 GO:0005085 GO:0005089 GO:0005096 GO:0005622 GO:0005737 GO:0005829 GO:0006928 GO:0006941 GO:0007186 GO:0007266 GO:0016020 GO:0030010 GO:0030036 GO:0035023 GO:0043065 GO:0043547 GO:0045893 GO:0051056
10.070.4204.060.040.792pz1A GO:0005085 GO:0005089 GO:0005737 GO:0005829 GO:0005886 GO:0016020 GO:0019904 GO:0030032 GO:0030676 GO:0032587 GO:0035023 GO:0035556 GO:0042995 GO:0043065 GO:0043547 GO:0046847 GO:0051056
20.070.4343.900.060.774bmqA GO:0004748 GO:0005971 GO:0006260 GO:0009186 GO:0009263 GO:0016020 GO:0016021 GO:0016491 GO:0046872 GO:0055114
30.070.3513.610.040.604m1hB GO:0004748 GO:0005971 GO:0006260 GO:0009186 GO:0009263 GO:0016491 GO:0046872 GO:0055114
40.070.4704.060.040.833gf9A 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
50.070.4174.260.030.783odxB GO:0005085 GO:0005089 GO:0005096 GO:0005737 GO:0005829 GO:0005886 GO:0007266 GO:0008283 GO:0016020 GO:0035023 GO:0043547 GO:0044822 GO:0050771
60.070.4923.820.070.884n83A GO:0004748 GO:0005971 GO:0006260 GO:0009186 GO:0009263 GO:0016491 GO:0046872 GO:0055114
70.070.4934.070.070.904dr0B GO:0004748 GO:0005971 GO:0006260 GO:0009186 GO:0009263 GO:0016491 GO:0046872 GO:0055114
80.070.4045.030.040.822bq1I GO:0004748 GO:0005971 GO:0006260 GO:0009186 GO:0009263 GO:0016491 GO:0046872 GO:0055114
90.070.4324.070.010.824yonA GO:0005085 GO:0005089 GO:0005096 GO:0005543 GO:0005737 GO:0005829 GO:0005886 GO:0006801 GO:0007186 GO:0016020 GO:0019899 GO:0030041 GO:0030217 GO:0030426 GO:0030593 GO:0030833 GO:0035023 GO:0035556 GO:0042119 GO:0043198 GO:0043231 GO:0043547 GO:0045785 GO:0048471 GO:0050773 GO:0072593 GO:1900026
100.070.4113.760.010.724ac8A GO:0004748 GO:0005506 GO:0005829 GO:0005971 GO:0009186 GO:0009263 GO:0016491 GO:0030145 GO:0046872 GO:0055114
110.070.5093.440.100.903jv3A GO:0005085 GO:0005089 GO:0005509 GO:0005829 GO:0005886 GO:0005905 GO:0006897 GO:0007264 GO:0012505 GO:0016020 GO:0019209 GO:0030027 GO:0030054 GO:0030139 GO:0032947 GO:0035023 GO:0035556 GO:0042327 GO:0042995 GO:0043005 GO:0043524 GO:0043547 GO:0045202 GO:0046872 GO:0048013 GO:0051897 GO:0070064
120.070.4474.080.050.911uzrB GO:0004748 GO:0005971 GO:0006260 GO:0009186 GO:0009263 GO:0016491 GO:0040007 GO:0046872 GO:0055114
130.070.3644.040.000.674d0nB GO:0004691 GO:0004871 GO:0005078 GO:0005085 GO:0005089 GO:0005634 GO:0005737 GO:0005829 GO:0005938 GO:0006468 GO:0007186 GO:0007507 GO:0010611 GO:0016020 GO:0017048 GO:0030864 GO:0032947 GO:0035023 GO:0035025 GO:0035556 GO:0043065 GO:0043123 GO:0043547 GO:0045859 GO:0046872 GO:0048471 GO:0051018 GO:0051056 GO:0051168 GO:0055007 GO:0060297 GO:0060348 GO:0071875 GO:0086023 GO:1900169
140.070.4953.960.100.941x86A GO:0001664 GO:0005085 GO:0005089 GO:0005096 GO:0005737 GO:0005829 GO:0007186 GO:0016020 GO:0035023 GO:0035556 GO:0043065 GO:0043547 GO:0051056 GO:0070062
150.070.4204.410.030.792rccA GO:0004748 GO:0006260 GO:0009186 GO:0016491 GO:0046872 GO:0055114
160.070.4973.940.120.921x86E GO:0001664 GO:0005085 GO:0005089 GO:0005096 GO:0005737 GO:0005829 GO:0007186 GO:0016020 GO:0035023 GO:0035556 GO:0043065 GO:0043547 GO:0051056 GO:0070062
170.070.5543.780.040.925cnvH GO:0004748 GO:0005506 GO:0005737 GO:0005829 GO:0005971 GO:0006260 GO:0009186 GO:0009263 GO:0015949 GO:0016491 GO:0042802 GO:0046872 GO:0055114
180.070.5063.710.030.881f5xA GO:0005085 GO:0005089 GO:0005829 GO:0005911 GO:0006909 GO:0006955 GO:0007186 GO:0007229 GO:0007264 GO:0008361 GO:0030168 GO:0030217 GO:0030593 GO:0030676 GO:0035023 GO:0035556 GO:0042110 GO:0043087 GO:0043547 GO:0045785 GO:0045954 GO:0046872 GO:0048010 GO:0072593


Consensus prediction of GO terms
 
Molecular Function GO:0005088 GO:0043169
GO-Score 0.37 0.37
Biological Processes GO:0046578 GO:0043087 GO:0051345 GO:0007266
GO-Score 0.37 0.37 0.37 0.37
Cellular Component GO:0044424
GO-Score 0.37

(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.