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I-TASSER results for job id Rv1670

[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
10.10 5 5f9hE GTP Rep, Mult 23,41,45,51,53,71,88,90
20.06 3 4a2xB NUC Rep, Mult 22,23,46,70,71,88,89,90
30.04 2 1yd4A MN Rep, Mult 5,96,98
40.04 2 2fu50 III Rep, Mult 29,31,36,37,40,56,58,59,60,65,66,67
50.02 1 3fegA MG Rep, Mult 55,68
60.02 1 2pe7A PDC Rep, Mult 75,76
70.02 1 3grbC ZN Rep, Mult 3,98
80.02 1 3zw2A FUC Rep, Mult 41,53,71
90.02 1 3i4zB BU2 Rep, Mult 25,27
100.02 1 3eqtA QNA Rep, Mult 21,23,46,49
110.02 1 3hchA RSM Rep, Mult 18,19,20
120.02 1 1w79A MG Rep, Mult 21,22,82,86
130.02 1 3g0gD NAG Rep, Mult 7,8,9,59,92
140.02 1 3sy9C C8E Rep, Mult 54,70
150.02 1 4xjwA DMS Rep, Mult 30,87,88,89
160.02 1 2q9pA MG Rep, Mult 34,38
170.02 1 3mmhB MG Rep, Mult 27,31

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
10.0601h54B0.4374.220.0950.7302.4.1.8NA
20.0602qttA0.4464.120.0730.7303.2.2.16NA
30.0601eiyA0.4614.080.0300.7396.1.1.20NA
40.0601j71A0.4394.960.0570.7743.4.23.24NA
50.0603iplA0.4383.400.0520.6616.2.1.2636
60.0603e0mC0.5333.550.0870.7741.8.4.11,1.8.4.12NA
70.0602gprA0.4393.890.0430.6962.7.1.69NA
80.0602h6sA0.4344.820.0380.7563.4.23.24NA
90.0601amuA0.4393.710.0430.6875.1.1.11NA
100.0601sk6C0.4483.990.0210.6964.6.1.125,71
110.0602k8dA0.4803.650.0790.7301.8.4.1211
120.0603cxkA0.5173.430.0820.7301.8.4.12NA
130.0602v7bA0.4343.890.0110.6966.2.1.2573
140.0601y0vD0.4494.200.0330.7134.6.1.111,13
150.0602rhsC0.4704.040.0300.7486.1.1.2019
160.0601zapA0.4394.810.0570.7653.4.23.24NA
170.0601xa8A0.4773.390.0590.7394.4.1.2252,73
180.0601spiA0.3765.310.0400.7653.1.3.11NA
190.0603eqtB0.5373.410.0590.7833.6.4.1310

(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
00.070.5333.330.040.795jb2A GO:0003677 GO:0005524 GO:0016787 GO:0016817
10.070.5403.490.030.805f9fI GO:0000166 GO:0002230 GO:0002376 GO:0003676 GO:0003690 GO:0003723 GO:0003725 GO:0003727 GO:0004386 GO:0005524 GO:0005737 GO:0005829 GO:0005856 GO:0005886 GO:0005923 GO:0008270 GO:0009597 GO:0009615 GO:0010628 GO:0015629 GO:0016020 GO:0016032 GO:0016787 GO:0016817 GO:0030054 GO:0030334 GO:0032480 GO:0032587 GO:0032725 GO:0032727 GO:0032728 GO:0032755 GO:0032757 GO:0034344 GO:0039528 GO:0039529 GO:0042802 GO:0042993 GO:0042995 GO:0043330 GO:0045087 GO:0045944 GO:0046872 GO:0051091 GO:0051607
20.070.5383.560.030.805f9hG GO:0000166 GO:0002230 GO:0002376 GO:0003676 GO:0003690 GO:0003723 GO:0003725 GO:0003727 GO:0004386 GO:0005524 GO:0005737 GO:0005829 GO:0005856 GO:0005886 GO:0005923 GO:0008270 GO:0009597 GO:0009615 GO:0010628 GO:0015629 GO:0016020 GO:0016032 GO:0016787 GO:0016817 GO:0030054 GO:0030334 GO:0032480 GO:0032587 GO:0032725 GO:0032727 GO:0032728 GO:0032755 GO:0032757 GO:0034344 GO:0039528 GO:0039529 GO:0042802 GO:0042993 GO:0042995 GO:0043330 GO:0045087 GO:0045944 GO:0046872 GO:0051091 GO:0051607
30.070.5333.700.030.812ykgA GO:0000166 GO:0002230 GO:0002376 GO:0003676 GO:0003690 GO:0003723 GO:0003725 GO:0003727 GO:0004386 GO:0005524 GO:0005737 GO:0005829 GO:0005856 GO:0005886 GO:0005923 GO:0008270 GO:0009597 GO:0009615 GO:0010628 GO:0015629 GO:0016020 GO:0016032 GO:0016787 GO:0016817 GO:0030054 GO:0030334 GO:0032480 GO:0032587 GO:0032725 GO:0032727 GO:0032728 GO:0032755 GO:0032757 GO:0034344 GO:0039528 GO:0039529 GO:0042802 GO:0042993 GO:0042995 GO:0043330 GO:0045087 GO:0045944 GO:0046872 GO:0051091 GO:0051607
40.070.5573.550.050.834a2vA GO:0000166 GO:0003677 GO:0005524 GO:0005737 GO:0016787 GO:0016817 GO:0046872
50.070.5123.460.060.744tzcC GO:0004176 GO:0005634 GO:0005730 GO:0005737 GO:0006508 GO:0016020 GO:0016567 GO:0031464 GO:0032463 GO:0034766 GO:0043161 GO:0046872 GO:0090073
60.070.5373.410.060.783eqtB GO:0000166 GO:0002376 GO:0003677 GO:0003723 GO:0003725 GO:0003727 GO:0004386 GO:0005524 GO:0005737 GO:0008270 GO:0009615 GO:0016032 GO:0016787 GO:0016817 GO:0032480 GO:0032481 GO:0039534 GO:0039536 GO:0045087 GO:0045088 GO:0045824 GO:0046872 GO:0051607 GO:1900245 GO:1900246
70.070.5293.510.040.772rqbA GO:0000166 GO:0002376 GO:0003677 GO:0003723 GO:0003725 GO:0003727 GO:0004386 GO:0005524 GO:0005634 GO:0005737 GO:0005829 GO:0008270 GO:0009597 GO:0009615 GO:0016032 GO:0016787 GO:0016817 GO:0016925 GO:0032480 GO:0032727 GO:0032728 GO:0034344 GO:0039528 GO:0039530 GO:0043021 GO:0045087 GO:0046872 GO:0051607
80.070.2995.270.080.615jc7A GO:0003677 GO:0005524 GO:0016787 GO:0016817
90.060.4793.620.060.735jc3A GO:0003677 GO:0005524 GO:0016787 GO:0016817
100.060.3085.240.050.612fwrA GO:0000166 GO:0003677 GO:0005524 GO:0016787
110.060.3345.030.040.653e9dA GO:0003824 GO:0004083 GO:0004331 GO:0005634 GO:0005737 GO:0005739 GO:0005741 GO:0005829 GO:0006003 GO:0006914 GO:0006915 GO:0008152 GO:0016311 GO:0016787 GO:0030388
120.060.3014.130.030.503ld1A GO:0001172 GO:0003723 GO:0003968 GO:0004197 GO:0006508 GO:0008233 GO:0008234 GO:0008242 GO:0008270 GO:0016020 GO:0016021 GO:0016032 GO:0016740 GO:0016787 GO:0019079 GO:0019082 GO:0030430 GO:0033644 GO:0039520 GO:0044220 GO:0046872
130.060.3364.620.050.604w7sA GO:0000166 GO:0000384 GO:0000395 GO:0003676 GO:0003723 GO:0004004 GO:0004386 GO:0005524 GO:0005634 GO:0005682 GO:0005737 GO:0006397 GO:0006413 GO:0007059 GO:0008380 GO:0010468 GO:0010501 GO:0016787 GO:0036464
140.060.3305.320.030.664ovyA GO:0016787 GO:0046872
150.060.3554.620.040.642hoxB GO:0003824 GO:0005773 GO:0016829 GO:0016846 GO:0047654
160.060.2865.440.040.582p6nA GO:0000166 GO:0000398 GO:0003676 GO:0003677 GO:0003723 GO:0004004 GO:0004386 GO:0005524 GO:0005634 GO:0005681 GO:0005783 GO:0005829 GO:0006396 GO:0006397 GO:0006915 GO:0007275 GO:0008380 GO:0010501 GO:0016020 GO:0016787 GO:0032479 GO:0032481 GO:0035458 GO:0044822 GO:0045944 GO:0046872 GO:0051607 GO:0071013
170.060.2955.170.100.552zu6F GO:0000166 GO:0000289 GO:0000339 GO:0003676 GO:0003723 GO:0003725 GO:0003729 GO:0003743 GO:0004004 GO:0004386 GO:0005524 GO:0005634 GO:0005737 GO:0005829 GO:0006412 GO:0006413 GO:0006446 GO:0008135 GO:0010468 GO:0010501 GO:0016020 GO:0016032 GO:0016281 GO:0016787 GO:0016887 GO:0031012 GO:0031100 GO:0044822 GO:0070062
180.060.3064.790.070.582zj8A GO:0000166 GO:0003676 GO:0003677 GO:0004386 GO:0005524 GO:0006281 GO:0006974 GO:0016787 GO:0016818
190.060.3224.470.040.532eqnA GO:0001522 GO:0003723 GO:0005634 GO:0005732 GO:0005737 GO:0006364 GO:0030529 GO:0042254 GO:0044822 GO:0070034 GO:1904874


Consensus prediction of GO terms
 
Molecular Function GO:0032550 GO:0032559 GO:0035639 GO:0003723 GO:0005515 GO:0003677 GO:0017111 GO:0046914
GO-Score 0.58 0.58 0.58 0.37 0.37 0.37 0.37 0.37
Biological Processes GO:0032645 GO:0050691 GO:0043331 GO:0016477 GO:0002753 GO:0032481 GO:0032675 GO:0042307 GO:0032648 GO:0001818 GO:0045893 GO:0098586 GO:2000145 GO:0044093 GO:0051090 GO:0032647 GO:0006357 GO:0034343 GO:0042990 GO:0032677
GO-Score 0.37 0.37 0.37 0.37 0.37 0.37 0.37 0.37 0.37 0.37 0.37 0.37 0.37 0.37 0.37 0.37 0.37 0.37 0.37 0.37
Cellular Component GO:0031256 GO:0070160 GO:0044444 GO:0031253 GO:0043296 GO:0001726 GO:0005856
GO-Score 0.37 0.37 0.37 0.37 0.37 0.37 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.