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I-TASSER results for job id Rv2970A

[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
10.32 64 2wzmA NA7 Rep, Mult 14,16,17,18,22,25,26
20.22 46 4dbsB 0HV Rep, Mult 52,53,54
30.17 36 3r8gA IZP Rep, Mult 52
40.06 12 3cmfA PDN Rep, Mult 53,55,56
50.05 9 2pq3A ZN Rep, Mult 35,38
60.01 2 1s2cA FLF Rep, Mult 7,10,11,30
70.00 1 4ck2A NVU Rep, Mult 1,4,29
80.00 1 1xjbA ACT Rep, Mult 30
90.00 1 3hk7A CO3 Rep, Mult 45,46

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
10.0601q13A0.8681.270.1961.0001.1.1.189,1.1.1.149NA
20.0601vp5A0.8211.410.2501.0001.1.1.274NA
30.0603b3dA0.8591.110.2681.0001.-.-.-NA
40.0602p5nA0.8691.270.1961.0001.1.1.-NA
50.0601keuA0.5712.750.1110.9464.2.1.46NA
60.0601vbjA0.8950.950.3041.0001.1.1.188NA
70.0601afsA0.8441.390.1611.0001.1.1.213,1.1.1.50NA
80.0602clpA0.7151.830.1320.9461.-.-.-NA
90.0603h7rA0.7771.380.2590.9641.1.1.-NA
100.0601np3A0.5722.610.1020.8391.1.1.86NA
110.0601gveB0.6891.860.1130.9461.-.-.-NA
120.0601og6C0.7011.250.1350.8391.-.-.-17
130.0602d0tB0.5533.000.0570.9461.13.11.5234,39
140.0602fvlA0.8671.310.2141.0001.1.1.225,1.1.1.50NA
150.0601k8cB0.7761.380.2550.9821.1.1.21NA
160.0601mzrB0.8591.110.3931.0001.1.1.274NA
170.0603e08A0.5582.570.0600.8751.13.11.11NA
180.0601gveA0.6981.870.1130.9461.-.-.-NA
190.0603h7uA0.7771.440.2780.9641.1.1.-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
00.220.8821.010.321.004gieA GO:0000166 GO:0001516 GO:0005737 GO:0006629 GO:0006631 GO:0006633 GO:0006693 GO:0016491 GO:0036131 GO:0047017 GO:0055114
10.220.8791.030.361.004otkA GO:0005618 GO:0005886 GO:0016491 GO:0040007 GO:0055114
20.210.8571.110.200.983cv6A GO:0004032 GO:0004033 GO:0005737 GO:0005829 GO:0006629 GO:0006694 GO:0008202 GO:0016491 GO:0016655 GO:0018636 GO:0031406 GO:0032052 GO:0033764 GO:0047023 GO:0047042 GO:0047086 GO:0047115 GO:0055114 GO:0070062
30.210.8711.420.211.004zfcB GO:0000060 GO:0001523 GO:0001758 GO:0004032 GO:0004033 GO:0004745 GO:0005622 GO:0005634 GO:0005737 GO:0005829 GO:0006693 GO:0007186 GO:0007584 GO:0008202 GO:0008284 GO:0008584 GO:0009267 GO:0010942 GO:0016488 GO:0016491 GO:0016655 GO:0018636 GO:0019371 GO:0030216 GO:0034614 GO:0035410 GO:0036130 GO:0036131 GO:0042448 GO:0042572 GO:0042574 GO:0044259 GO:0044597 GO:0044598 GO:0045550 GO:0045703 GO:0047017 GO:0047020 GO:0047023 GO:0047035 GO:0047045 GO:0047086 GO:0047115 GO:0047718 GO:0047787 GO:0048385 GO:0051897 GO:0052650 GO:0055114 GO:0061370 GO:0070062 GO:0070293 GO:0071276 GO:0071277 GO:0071379 GO:0071384 GO:0071395 GO:0071799 GO:1900053 GO:2000224 GO:2000353 GO:2000379
40.210.8671.310.211.002fvlA GO:0001523 GO:0001758 GO:0004033 GO:0005737 GO:0005829 GO:0006699 GO:0008202 GO:0008209 GO:0009055 GO:0015125 GO:0015721 GO:0016491 GO:0016655 GO:0044597 GO:0044598 GO:0047023 GO:0047743 GO:0055114 GO:0070062 GO:0071395
50.200.8741.290.231.004l1wA GO:0004032 GO:0005737 GO:0006629 GO:0006693 GO:0007186 GO:0007586 GO:0008202 GO:0008284 GO:0016491 GO:0016655 GO:0018636 GO:0030855 GO:0031406 GO:0032052 GO:0042448 GO:0044597 GO:0044598 GO:0047086 GO:0047115 GO:0051897 GO:0055114 GO:0071395 GO:0071799
60.200.8561.100.360.983rx2A GO:0001894 GO:0004032 GO:0004033 GO:0005615 GO:0005654 GO:0005737 GO:0005829 GO:0005975 GO:0005996 GO:0006061 GO:0006700 GO:0006950 GO:0009055 GO:0009414 GO:0010033 GO:0016491 GO:0018931 GO:0031098 GO:0032838 GO:0033010 GO:0042415 GO:0042629 GO:0043220 GO:0043795 GO:0044597 GO:0044598 GO:0046370 GO:0046427 GO:0048471 GO:0048661 GO:0055114 GO:0060135 GO:0070062 GO:0070301 GO:0072061 GO:0097066 GO:0097238 GO:0097454 GO:1901653
70.200.8681.270.201.001q13A GO:0001516 GO:0005737 GO:0006629 GO:0006631 GO:0006633 GO:0006693 GO:0016491 GO:0047006 GO:0050221 GO:0055114
80.200.8501.470.391.004gq0A GO:0001523 GO:0001758 GO:0004033 GO:0005576 GO:0005764 GO:0005829 GO:0006081 GO:0007586 GO:0008202 GO:0016488 GO:0016491 GO:0044597 GO:0044598 GO:0045550 GO:0047718 GO:0055114 GO:0070062
90.200.8950.950.301.001vbjA GO:0000166 GO:0001516 GO:0004033 GO:0005737 GO:0006629 GO:0006631 GO:0006633 GO:0006693 GO:0016491 GO:0019571 GO:0036131 GO:0045290 GO:0047017 GO:0055114
100.190.8870.980.291.003f7jA GO:0016491 GO:0043892 GO:0055114
110.190.8940.950.301.004g5dA GO:0000166 GO:0001516 GO:0005737 GO:0006629 GO:0006631 GO:0006633 GO:0006693 GO:0016491 GO:0036131 GO:0047017 GO:0055114
120.190.8441.390.161.001afsA GO:0005737 GO:0008202 GO:0016229 GO:0016491 GO:0021766 GO:0047023 GO:0047042 GO:0055114
130.190.8581.140.381.003wbwA GO:0000166 GO:0016491 GO:0055114
140.190.8591.110.271.003b3dA GO:0016491 GO:0055114
150.190.8241.540.341.003fx4A GO:0008106 GO:0016491 GO:0055114
160.190.8401.400.321.003burA GO:0004033 GO:0005496 GO:0005737 GO:0005829 GO:0006629 GO:0006699 GO:0006707 GO:0007586 GO:0008202 GO:0008207 GO:0008209 GO:0016042 GO:0016491 GO:0030573 GO:0047787 GO:0055114 GO:0070062
170.180.8021.500.341.003wczA GO:0006629 GO:0008202 GO:0016491 GO:0055114
180.180.8471.330.271.003up8A GO:0016491 GO:0050580 GO:0055114


Consensus prediction of GO terms
 
Molecular Function GO:0016655 GO:0047023 GO:1901265 GO:0036094 GO:0033293 GO:0005496 GO:0035671 GO:0005319 GO:1901618 GO:0008028 GO:0047017 GO:0036131 GO:0047115 GO:0004032 GO:0047086 GO:0018636 GO:0001758
GO-Score 0.51 0.51 0.45 0.45 0.42 0.42 0.42 0.42 0.42 0.42 0.39 0.39 0.38 0.38 0.38 0.38 0.38
Biological Processes GO:0055114 GO:0046457 GO:0009913 GO:0034599 GO:2000377 GO:0044236 GO:1901617 GO:1900052 GO:0043588 GO:0008406 GO:0006606 GO:0016487 GO:0051592 GO:0016107 GO:0048384 GO:0031960 GO:0000302 GO:0046137 GO:0031325 GO:0071383 GO:0050810 GO:1904037 GO:0006081 GO:0031669 GO:0046686 GO:0010566 GO:2000351 GO:0042127 GO:0043170 GO:0019369 GO:0051055 GO:0051896 GO:1902533 GO:0046546 GO:0032351 GO:0003014 GO:0034310 GO:0071798 GO:0031327 GO:0045827 GO:0008207 GO:0071248 GO:0042594 GO:0016095 GO:0008206 GO:0015849 GO:0015718 GO:0006869 GO:0015850 GO:0006693 GO:0044597 GO:0044598 GO:0071395
GO-Score 0.70 0.45 0.42 0.42 0.42 0.42 0.42 0.42 0.42 0.42 0.42 0.42 0.42 0.42 0.42 0.42 0.42 0.42 0.42 0.42 0.42 0.42 0.42 0.42 0.42 0.42 0.42 0.42 0.42 0.42 0.42 0.42 0.42 0.42 0.42 0.42 0.42 0.42 0.42 0.42 0.42 0.42 0.42 0.42 0.42 0.42 0.42 0.42 0.42 0.39 0.38 0.38 0.38
Cellular Component GO:0005829 GO:0070062 GO:0030312 GO:0043231 GO:0016020
GO-Score 0.51 0.51 0.44 0.42 0.33

(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.