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I-TASSER results for job id Rv0465c

[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 5 3s8qB NUC Rep, Mult 14,20,21,33,36,40,46
20.04 2 4n0gA MG Rep, Mult 93,96
30.04 2 3rovB III Rep, Mult 24,25
40.04 2 1fbmA RTL Rep, Mult 104,111,114
50.04 2 1dubD CAA Rep, Mult 57,64
60.02 1 2q5dB III Rep, Mult 49,52,117
70.02 1 3ak1B EDO Rep, Mult 265,287
80.02 1 1dl2A UUU Rep, Mult 11,14,15,19,62,63
90.02 1 1vdfB CL Rep, Mult 111,114
100.02 1 1o6oA III Rep, Mult 18,21,22,26,70,71,74,75
110.02 1 4wrqA III Rep, Mult 77,155,162,163,194,195,197,223,227,230
120.02 1 2vywA OXY Rep, Mult 268,342
130.02 1 3s8qA NUC Rep, Mult 30,31,33,34,43,44,45,46,49
140.02 1 1o6pA III Rep, Mult 293,354,358
150.02 1 4acqA UUU Rep, Mult 15,16
160.02 1 3a6pA III Rep, Mult 17,53,60
170.02 1 1u6g0 III Rep, Mult 231,235,266,267,268
180.02 1 3lszA GSH Rep, Mult 259,293
190.02 1 3dtkA ZN Rep, Mult 233,236
200.02 1 1g6iA UUU Rep, Mult 65,66,146,148,152

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
10.0603ecqB0.3797.580.0510.6413.2.1.97NA
20.0601fmiA0.3786.170.0640.5553.2.1.113NA
30.0602vn4A0.3756.310.0500.5633.2.1.3292
40.0601js4A0.3836.300.0380.5593.2.1.4NA
50.0601w6jA0.4096.560.0460.6225.4.99.7405
60.0601ayxA0.3826.360.0390.5783.2.1.3165
70.0601hcuB0.3806.220.0720.5613.2.1.113NA
80.0602gtqA0.3837.390.0490.6413.4.11.2NA
90.0601gaiA0.3766.450.0610.5723.2.1.3181
100.0601ho8A0.3775.990.0700.5463.6.3.1412
110.0603ebgA0.4117.160.0440.6623.4.11.-NA
120.0601dl2A0.3976.390.0410.5973.2.1.113NA
130.0602zuwC0.3797.320.0360.6222.4.1.211288,295
140.0603c5wA0.2985.300.0670.4053.1.3.16NA
150.0601g87B0.3836.320.0720.5613.2.1.4NA
160.0601nxcA0.3746.260.0390.5593.2.1.113NA
170.0601kktA0.3786.220.0810.5613.2.1.113NA
180.0601ug9A0.3907.220.0600.6293.2.1.70216
190.0601f1sA0.3886.330.0570.5824.2.2.140

(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
00.160.8113.200.100.914um2A GO:0000184 GO:0000333 GO:0000723 GO:0000781 GO:0003677 GO:0004518 GO:0004519 GO:0004521 GO:0005634 GO:0005694 GO:0005697 GO:0005730 GO:0005737 GO:0005829 GO:0006406 GO:0016787 GO:0032210 GO:0035145 GO:0035303 GO:0042162 GO:0043021 GO:0046872 GO:0070034 GO:0070182 GO:0090305 GO:0090502 GO:1904354
10.110.2766.640.030.431w3bA GO:0000123 GO:0000791 GO:0001933 GO:0001934 GO:0005547 GO:0005634 GO:0005654 GO:0005737 GO:0005739 GO:0005829 GO:0005886 GO:0006041 GO:0006110 GO:0006486 GO:0006493 GO:0006915 GO:0007165 GO:0007584 GO:0008047 GO:0008134 GO:0008289 GO:0008375 GO:0010628 GO:0010801 GO:0016020 GO:0016262 GO:0016568 GO:0016740 GO:0016757 GO:0019904 GO:0030854 GO:0030900 GO:0031397 GO:0032868 GO:0032869 GO:0032922 GO:0033137 GO:0035020 GO:0042277 GO:0042588 GO:0043005 GO:0043025 GO:0043085 GO:0043981 GO:0043982 GO:0043984 GO:0043995 GO:0043996 GO:0045793 GO:0045862 GO:0045944 GO:0046626 GO:0046972 GO:0048015 GO:0048029 GO:0048312 GO:0048511 GO:0051571 GO:0060548 GO:0061087 GO:0070207 GO:0070208 GO:0070688 GO:0071222 GO:0071300 GO:0071333 GO:0080182 GO:0090315 GO:0090526 GO:0097237 GO:0097363 GO:1900038 GO:1900182 GO:1903428
20.100.6783.650.050.801ya0B GO:0000184 GO:0005634 GO:0005737 GO:0005829 GO:0006406 GO:0035303 GO:0042162 GO:0045111 GO:0051721
30.070.5654.370.060.713zheB GO:0000184 GO:0005634 GO:0005737
40.070.5474.340.060.683zheA GO:0000184 GO:0004540 GO:0005634 GO:0005737 GO:0008601 GO:0016246 GO:0017151 GO:0030538 GO:0034047 GO:0034660 GO:0051721 GO:0090501
50.060.3406.670.050.535a31J GO:0005634 GO:0005654 GO:0005680 GO:0005737 GO:0005813 GO:0005815 GO:0005819 GO:0005829 GO:0005856 GO:0005876 GO:0007049 GO:0007067 GO:0007088 GO:0008283 GO:0016567 GO:0031145 GO:0042787 GO:0043161 GO:0051301 GO:0051436 GO:0051437 GO:0051439 GO:0070979
60.060.2834.270.060.352gw1A GO:0005739 GO:0005741 GO:0005742 GO:0006626 GO:0006886 GO:0015266 GO:0015450 GO:0016020 GO:0016021 GO:0030150 GO:0030943 GO:0031307 GO:0045039
70.060.2946.200.070.425a5tE GO:0000184 GO:0001731 GO:0003743 GO:0005634 GO:0005737 GO:0005852 GO:0006412 GO:0006413 GO:0006446 GO:0016020 GO:0016282 GO:0016605 GO:0033290 GO:0044822 GO:0047485 GO:0070062
80.060.2955.540.110.402c0mC GO:0000268 GO:0005052 GO:0005622 GO:0005737 GO:0005777 GO:0005778 GO:0005782 GO:0005829 GO:0006625 GO:0006810 GO:0008022 GO:0015031 GO:0016020 GO:0016558 GO:0016560 GO:0016561 GO:0019899 GO:0031267 GO:0043234 GO:0045046 GO:0047485 GO:0051262 GO:1901094
90.060.2714.550.070.341w3bB GO:0000123 GO:0000791 GO:0001933 GO:0001934 GO:0005547 GO:0005634 GO:0005654 GO:0005737 GO:0005739 GO:0005829 GO:0005886 GO:0006041 GO:0006110 GO:0006486 GO:0006493 GO:0006915 GO:0007165 GO:0007584 GO:0008047 GO:0008134 GO:0008289 GO:0008375 GO:0010628 GO:0010801 GO:0016020 GO:0016262 GO:0016568 GO:0016740 GO:0016757 GO:0019904 GO:0030854 GO:0030900 GO:0031397 GO:0032868 GO:0032869 GO:0032922 GO:0033137 GO:0035020 GO:0042277 GO:0042588 GO:0043005 GO:0043025 GO:0043085 GO:0043981 GO:0043982 GO:0043984 GO:0043995 GO:0043996 GO:0045793 GO:0045862 GO:0045944 GO:0046626 GO:0046972 GO:0048015 GO:0048029 GO:0048312 GO:0048511 GO:0051571 GO:0060548 GO:0061087 GO:0070207 GO:0070208 GO:0070688 GO:0071222 GO:0071300 GO:0071333 GO:0080182 GO:0090315 GO:0090526 GO:0097237 GO:0097363 GO:1900038 GO:1900182 GO:1903428
100.060.2347.670.050.403mznA GO:0003824 GO:0008152 GO:0008872 GO:0016829 GO:0046872
110.060.2886.760.040.453sqiA GO:0000022 GO:0000780 GO:0000921 GO:0005819 GO:0007059 GO:0008301 GO:0019237 GO:0031518 GO:0051233
120.060.2935.020.080.383cv0A GO:0005052 GO:0005778 GO:0005829 GO:0016560
130.060.2776.840.020.422vkdA GO:0000166 GO:0009405 GO:0016757 GO:0046872
140.060.2825.100.070.374eqfA GO:0000268 GO:0005052 GO:0005737 GO:0005778 GO:0005829 GO:0016020 GO:0016560 GO:0030425 GO:0031267 GO:0042391 GO:0043235 GO:0043949 GO:0045185
150.060.2496.370.060.373acwA GO:0009058 GO:0016117 GO:0016740 GO:0016765
160.060.2355.810.050.332b2cA GO:0003824 GO:0004766 GO:0006595 GO:0016740
170.060.2103.420.090.242vyiA GO:0005737 GO:0005829 GO:0016020 GO:0016032 GO:1903071 GO:1904288
180.060.2193.450.090.262fo7A


Consensus prediction of GO terms
 
Molecular Function GO:0043565 GO:0003723 GO:0004540 GO:0004519 GO:0044877 GO:0043169 GO:0019903
GO-Score 0.47 0.31 0.31 0.31 0.31 0.31 0.31
Biological Processes GO:0016311 GO:0051028 GO:0019220 GO:0006405 GO:0010467 GO:0071427 GO:0000184 GO:0090501 GO:1904356 GO:0032205 GO:1904353 GO:0007004 GO:2000278
GO-Score 0.47 0.47 0.47 0.47 0.47 0.47 0.33 0.31 0.31 0.31 0.31 0.31 0.31
Cellular Component GO:0005829 GO:0030529 GO:0043234 GO:0031981 GO:0098687
GO-Score 0.32 0.31 0.31 0.31 0.31

(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.