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I-TASSER results for job id Rv3850

[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
10.05 3 3rdhA 3RD Rep, Mult 64,121,122,170,173
20.04 2 5d8pG FE2 Rep, Mult 205,208
30.04 2 1f59A III Rep, Mult 118,121,122,125,126,174,177,181
40.04 2 3obvB SUC Rep, Mult 55,92,93,96,97,100
50.04 2 1o6oA III Rep, Mult 121,124,125,129,181,182
60.02 1 1o6pA III Rep, Mult 25,28,29,79,82,85,86
70.02 1 1vstA GTP Rep, Mult 33,37
80.02 1 1yb1A AE2 Rep, Mult 157,211,214
90.02 1 1na0B IPT Rep, Mult 46,102,105,106,150
100.02 1 1vf5S III Rep, Mult 211,212
110.02 1 3nozX PLL Rep, Mult 71,83,87,90
120.02 1 3c9iC XE Rep, Mult 182,185
130.02 1 3scxA CA Rep, Mult 10,14
140.02 1 2a69F MG Rep, Mult 216,217
150.02 1 1bjyA CTC Rep, Mult 178,182
160.02 1 4dwqA PO4 Rep, Mult 118,122,135
170.02 1 3prqX CLA Rep, Mult 89,96
180.02 1 2bptA III Rep, Mult 35,38,39,42,43,92,95
190.02 1 3o8iA M1T Rep, Mult 61,64,170
200.02 1 1dxoB DQN Rep, Mult 124,187

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
10.0732fbnA0.4733.970.0270.6385.2.1.865,73,127
20.0601dceA0.4844.520.0580.7062.5.1.60141
30.0601y7910.4815.070.0590.7433.4.15.5NA
40.0601l2aE0.4975.490.0630.8073.2.1.4NA
50.0601gaiA0.4985.370.0630.8033.2.1.3NA
60.0601qd1B0.3366.040.0600.6062.1.2.5,4.3.1.4NA
70.0603c5wA0.5343.700.0730.7113.1.3.16105
80.0602pfdB0.5154.590.0660.7572.1.2.5,4.3.1.4NA
90.0603dsxA0.4554.540.0380.6702.5.1.6021
100.0601j0mA0.5474.890.0720.8174.2.2.12182
110.0602q1fA0.5225.060.0860.8074.2.2.21NA
120.0601ho8A0.5553.910.0810.7663.6.3.14NA
130.0601dl2A0.5294.590.0680.8033.2.1.113NA
140.0602qnoA0.4925.160.0590.7753.2.1.4NA
150.0601f1sA0.5774.750.0690.8584.2.2.1NA
160.0601rw9A0.5554.760.0440.8304.2.2.5NA
170.0601h54B0.5045.530.0590.8032.4.1.8NA
180.0602vn7A0.5065.240.0480.8073.2.1.3138,140
190.0602vn4A0.5035.280.0430.8033.2.1.3156
200.0601ug9A0.4825.110.1000.7393.2.1.7069

(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
00.190.5864.600.080.884uvkA GO:0000755 GO:0003682 GO:0005634 GO:0005829 GO:0006473 GO:0007064 GO:0009847 GO:0031505 GO:0031618 GO:0031934 GO:0034990 GO:1990707
10.080.3695.480.050.622y4uA GO:0004860 GO:0005737 GO:0005783 GO:0005788 GO:0005790 GO:0005829 GO:0006417 GO:0006986 GO:0016020 GO:0019901 GO:0031205 GO:0036494 GO:0036498 GO:0043066 GO:0051087 GO:0051603 GO:0051607 GO:0051787 GO:0070062 GO:0070417 GO:1903561 GO:1903912 GO:1904030
20.070.6774.080.070.935hb4B GO:0005634 GO:0005643 GO:0006810 GO:0015031 GO:0051028
30.070.5994.680.050.894knhB GO:0005634 GO:0005643 GO:0006810 GO:0015031 GO:0051028
40.070.6164.450.060.894knhA GO:0005634 GO:0005643 GO:0006810 GO:0015031 GO:0051028
50.070.5595.090.030.884ifqA GO:0000059 GO:0005634 GO:0005643 GO:0006810 GO:0006999 GO:0015031 GO:0017056 GO:0044611 GO:0046822 GO:0051028
60.070.5654.850.050.865ijnD GO:0000059 GO:0005634 GO:0005635 GO:0005643 GO:0005654 GO:0005737 GO:0006406 GO:0006409 GO:0006810 GO:0006913 GO:0007077 GO:0010827 GO:0015031 GO:0016020 GO:0016032 GO:0016925 GO:0017056 GO:0019083 GO:0031047 GO:0031965 GO:0034399 GO:0044611 GO:0051028 GO:0051292 GO:0075733 GO:1900034
70.060.4225.280.060.673l0oA GO:0000166 GO:0003676 GO:0003723 GO:0004386 GO:0005524 GO:0006351 GO:0006353 GO:0006355 GO:0008186 GO:0016787
80.060.4145.540.030.673renA GO:0003824 GO:0004553 GO:0005975 GO:0016020 GO:0016021 GO:0016787
90.060.3175.680.040.531bagA GO:0003824 GO:0004556 GO:0005576 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0043169 GO:0046872
100.060.3475.400.060.564dwjB GO:0000166 GO:0004798 GO:0005524 GO:0006233 GO:0006235 GO:0009165 GO:0016301 GO:0016310 GO:0016740 GO:0046939
110.060.3384.570.050.501n0rA
120.060.2756.340.030.512cuzA GO:0000049 GO:0000166 GO:0004812 GO:0004818 GO:0005524 GO:0005737 GO:0006412 GO:0006418 GO:0006424 GO:0016874 GO:0016876 GO:0043039
130.060.3345.800.060.581w62A GO:0005576 GO:0005737 GO:0007275 GO:0016020 GO:0016853 GO:0018112
140.060.3315.340.050.554p7kA GO:0000287 GO:0005737 GO:0005739 GO:0005829 GO:0005886 GO:0006584 GO:0007565 GO:0007612 GO:0007614 GO:0008168 GO:0008171 GO:0008210 GO:0009712 GO:0014070 GO:0016020 GO:0016021 GO:0016036 GO:0016206 GO:0016740 GO:0030424 GO:0030425 GO:0032259 GO:0032496 GO:0032502 GO:0035814 GO:0042135 GO:0042417 GO:0042420 GO:0042493 GO:0043197 GO:0044297 GO:0045211 GO:0045963 GO:0046498 GO:0046500 GO:0046872 GO:0048265 GO:0048609 GO:0048662 GO:0050668 GO:0051930 GO:0070062
150.060.3235.040.070.514hs7A GO:0005363 GO:0015768
160.060.2946.680.080.583wwpA GO:0016829 GO:0046872
170.060.3045.940.030.513wxeA GO:0004843 GO:0005829 GO:0006511 GO:0007346 GO:0016579 GO:0021551 GO:0032088 GO:0036459 GO:0061578 GO:0070266 GO:0070536 GO:1990108 GO:2001238 GO:2001242
180.060.2915.870.010.521uamA GO:0005737 GO:0006400 GO:0008033 GO:0008168 GO:0008685 GO:0009019 GO:0016740 GO:0030488 GO:0032259 GO:0052906


Consensus prediction of GO terms
 
Molecular Function GO:0044877
GO-Score 0.39
Biological Processes GO:0071852 GO:0032502 GO:0022413 GO:0071555 GO:0043543 GO:0000070 GO:0007062 GO:0000747 GO:0045184 GO:0050658
GO-Score 0.39 0.39 0.39 0.39 0.39 0.39 0.39 0.39 0.37 0.37
Cellular Component GO:0044444 GO:0000798 GO:0005720 GO:1990421 GO:0005721 GO:0030892 GO:0005635
GO-Score 0.52 0.39 0.39 0.39 0.39 0.39 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.