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I-TASSER results for job id Rv1473A

[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
10.24 25 4on0A NUC Rep, Mult 9,12,35,37,38,41,42,45
20.07 8 2e1cA NUC Rep, Mult 24,25,26,36,37,40
30.06 7 3dk4A GSH Rep, Mult 15,18,19
40.04 5 2h27A NUC Rep, Mult 19,24,25,40,44,45,47
50.03 3 3foeA NUC Rep, Mult 11,32,34,35,38
60.03 4 2ve9B NUC Rep, Mult 24,25,26,36
70.03 3 1zt9A TRP Rep, Mult 12,15,38,42,47
80.01 1 3bdnB NUC Rep, Mult 34,35,37,51,52,53,54,57
90.01 1 1smyF MG Rep, Mult 51,55
100.01 1 2xquA CVM Rep, Mult 8,12
110.01 1 3v2cM MG Rep, Mult 53,54
120.01 1 3x01A AMP Rep, Mult 10,14
130.01 1 5gm1A SAH Rep, Mult 19,20

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
10.0602ewnA0.6162.380.1640.8576.3.4.15NA
20.0602ip2A0.5662.860.1900.8572.1.1.-NA
30.0603dbmA0.4413.640.0830.7464.2.1.92NA
40.0603hxxA0.5662.540.1150.8096.1.1.726
50.0601l3sA0.5703.160.0950.8572.7.7.7NA
60.0602q2eA0.5813.320.1610.9365.99.1.3NA
70.0601mj9A0.6332.920.0950.9842.3.1.4810
80.0602wuzA0.5093.010.0370.8411.14.13.70NA
90.0603l4dB0.4973.000.0330.8251.14.13.70NA
100.0601d8yA0.5892.690.0750.7942.7.7.714
110.0602gaiA0.5623.080.0670.9525.99.1.2NA
120.0601cyfA0.5663.810.0630.9521.11.1.5NA
130.0601leaA0.5922.450.1020.8733.4.21.8814,26,29
140.0603ilwA0.5753.540.1290.9685.99.1.3NA
150.0603c46B0.5822.870.0890.8092.7.7.617
160.0602zo4A0.6432.630.1360.9363.-.-.-NA
170.0602e18B0.5792.480.1150.7466.3.1.516,22,59
180.0602rc4A0.5582.990.0350.9052.3.1.48,NA
190.0603k9fA0.6193.290.1130.9685.99.1.-NA

(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
00.210.5822.180.100.731fseB GO:0003677 GO:0006351 GO:0006355
10.210.5603.250.100.985k1yB GO:0003700 GO:0006355
20.140.7062.310.150.941j5yA GO:0003677 GO:0006351 GO:0006355 GO:0036094 GO:0046872
30.110.6892.360.150.955furG GO:0000166 GO:0002039 GO:0003677 GO:0003713 GO:0004402 GO:0004674 GO:0005524 GO:0005634 GO:0005654 GO:0005669 GO:0006351 GO:0006352 GO:0006355 GO:0006366 GO:0006367 GO:0006368 GO:0006974 GO:0007049 GO:0008134 GO:0016032 GO:0016301 GO:0016310 GO:0016573 GO:0016740 GO:0016746 GO:0017025 GO:0018105 GO:0018107 GO:0032436 GO:0043565 GO:0044212 GO:0045944 GO:0046777 GO:0051123 GO:0060261 GO:0070577 GO:0071339 GO:1901796
40.100.7042.880.050.973iuoB GO:0000166 GO:0003676 GO:0003824 GO:0004003 GO:0004386 GO:0005524 GO:0005622 GO:0006260 GO:0006281 GO:0006310 GO:0008026 GO:0009432 GO:0032508 GO:0043140 GO:0044237
50.090.6812.720.050.951fokA GO:0003677 GO:0004518 GO:0004519 GO:0004536 GO:0009036 GO:0009307 GO:0016787 GO:0090305
60.080.6302.950.100.921ufmA GO:0000338 GO:0005634 GO:0005654 GO:0005737 GO:0005829 GO:0008021 GO:0008180 GO:0010388 GO:0019784 GO:0030054 GO:0031410 GO:0045202 GO:0070062
70.080.6332.960.080.974d10C GO:0000715 GO:0001701 GO:0005634 GO:0005654 GO:0005737 GO:0006283 GO:0006511 GO:0007165 GO:0008180 GO:0009416 GO:0010388
80.070.5753.220.080.953txmA GO:0000502 GO:0005838 GO:0005875 GO:0008541 GO:0043161
90.070.5802.510.050.864pdxA GO:0016787 GO:0018741 GO:0030288 GO:0046983
100.070.5823.190.080.953jcoP GO:0000502 GO:0006511 GO:0008180 GO:0008541 GO:0010388 GO:0031595 GO:0034515 GO:0043161
110.070.5312.350.190.732l4aA GO:0003677 GO:0003700 GO:0005622 GO:0005829 GO:0006351 GO:0006355 GO:0009098 GO:0042802 GO:0043201 GO:0043565
120.070.5722.620.120.904oy2A GO:0001075 GO:0003682 GO:0004402 GO:0005634 GO:0005669 GO:0005829 GO:0006351 GO:0006355 GO:0006366 GO:0016568 GO:0016573 GO:0016740 GO:0016746 GO:0017025 GO:0032947 GO:0051123
130.070.6302.880.100.973jckF GO:0000502 GO:0005198 GO:0005634 GO:0005829 GO:0006511 GO:0008541 GO:0034515 GO:0043248
140.070.5383.320.050.901q1hA GO:0003677 GO:0006351 GO:0006352 GO:0006355 GO:0006367 GO:0043565
150.070.5802.980.070.944d10D GO:0000338 GO:0000715 GO:0005634 GO:0005654 GO:0005737 GO:0005829 GO:0006283 GO:0008021 GO:0008180 GO:0010388 GO:0019784 GO:0030054 GO:0031410 GO:0045202 GO:0070062
160.070.5153.400.060.944rb3C GO:0003677 GO:0003700 GO:0006355 GO:0046872
170.070.4183.150.040.733hjzA GO:0003824 GO:0004801 GO:0005737 GO:0005975 GO:0006098 GO:0016740
180.070.4334.060.070.794r0vA GO:0016491 GO:0046872 GO:0051536 GO:0051539 GO:0055114
190.070.4493.390.050.814flbA GO:0005654 GO:0016591 GO:0042795
200.070.4332.910.060.674ijcA GO:0005737 GO:0005829 GO:0016491 GO:0044262 GO:0045290 GO:0055114
210.060.4223.490.050.834wvyA GO:0000166 GO:0003678 GO:0004386 GO:0005524 GO:0005634 GO:0006281 GO:0006351 GO:0006355 GO:0006974 GO:0016568 GO:0016787 GO:0032508 GO:0043141


Consensus prediction of GO terms
 
Molecular Function GO:0001071 GO:0003677 GO:0032550 GO:0035639 GO:0032559
GO-Score 0.41 0.40 0.40 0.40 0.40
Biological Processes GO:0006355
GO-Score 0.52
Cellular Component GO:0071339 GO:0005669
GO-Score 0.11 0.11

(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.