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I-TASSER results for job id Rv1958c

[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 1jj2N NUC Rep, Mult 46,47,66,67,70,75,76,79,86,87,97,99,100,103,104,120,122,123,124,125,142,143,144,169,170,171,172,173,174,177
20.05 3 1iw7F MG Rep, Mult 68,72
30.05 3 3ooyA TDP Rep, Mult 2,3,76,79
40.03 2 1w8qC CO Rep, Mult 35,39
50.03 2 2wghA DTP Rep, Mult 15,16,18,24,37
60.03 2 3hndA TTP Rep, Mult 5,11,13,14,15
70.03 2 2faqA MN Rep, Mult 136,138,188,192
80.03 2 1xhbA CA Rep, Mult 64,65
90.02 1 2zyqB TAR Rep, Mult 51,52
100.02 1 3d5bD MG Rep, Mult 180,187
110.02 1 3hnfB TTP Rep, Mult 79,85,86,88
120.02 1 3hnfA TTP Rep, Mult 11,15,16,19,20
130.02 1 2b0qA MG Rep, Mult 144,163
140.02 1 4q0pA Z6J Rep, Mult 59,62
150.02 1 2faqA MN Rep, Mult 136,138
160.02 1 2nvqB DUT Rep, Mult 93,94

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
10.0602wghB0.4245.570.0490.7401.17.4.1NA
20.0603n58A0.4025.660.0380.6963.3.1.193
30.0602vjyA0.4095.620.0520.7014.1.1.1NA
40.0601yirC0.4045.400.0470.6622.4.2.11158
50.0601kbpA0.4025.250.0590.6623.1.3.2NA
60.0602ji6A0.4055.340.0270.6764.1.1.8NA
70.0603ctzA0.4045.730.0230.7113.4.11.9NA
80.0601hwxA0.4115.590.0600.7161.4.1.3NA
90.0601itzB0.4265.350.0690.7112.2.1.1NA
100.0601ybeA0.4125.710.0430.6962.4.2.11NA
110.0603etdA0.4105.700.0430.7161.4.1.35,79,104
120.0601djnA0.4075.730.0680.7261.5.8.2,1.5.99.7NA
130.0602panA0.4205.580.0570.7064.1.1.47NA
140.0604kbpA0.4025.240.0480.6623.1.3.2NA
150.0602vk1A0.3406.080.0620.6324.1.1.1NA
160.0603komA0.4035.270.0710.6722.2.1.1NA
170.0601pg3B0.4145.850.0390.7456.2.1.114,103
180.0601z01A0.4095.630.0580.6911.14.13.61NA
190.0605r1rA0.4136.100.0470.7741.17.4.1NA

(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
00.070.4953.870.090.664v6wCQ GO:0000022 GO:0003723 GO:0003735 GO:0005622 GO:0005737 GO:0005840 GO:0006412 GO:0007052 GO:0022625 GO:0030529
10.070.5083.850.140.684v6xCQ GO:0000184 GO:0003723 GO:0003735 GO:0005622 GO:0005634 GO:0005730 GO:0005737 GO:0005829 GO:0005840 GO:0005925 GO:0006364 GO:0006412 GO:0006413 GO:0006614 GO:0016020 GO:0019083 GO:0022625 GO:0030529
20.070.4984.070.090.674v8mBI GO:0003723 GO:0003735 GO:0005622 GO:0005737 GO:0005840 GO:0006412 GO:0022625 GO:0030529
30.070.5033.930.080.694v3pLR GO:0003735 GO:0005622 GO:0005840 GO:0006412
40.070.5044.020.100.673j79S GO:0003723 GO:0003735 GO:0005622 GO:0005840 GO:0006412 GO:0022625
50.070.4994.030.140.685apnQ GO:0002181 GO:0003723 GO:0003735 GO:0005622 GO:0005737 GO:0005840 GO:0006412 GO:0022625 GO:0030529
60.070.4993.960.110.674v8pBN GO:0003735 GO:0005622 GO:0005737 GO:0005840 GO:0006412 GO:0030529
70.060.3284.580.060.494b3fX GO:0000049 GO:0000166 GO:0003676 GO:0003677 GO:0003678 GO:0003697 GO:0003723 GO:0004386 GO:0005524 GO:0005634 GO:0005737 GO:0006260 GO:0006281 GO:0006310 GO:0006351 GO:0006355 GO:0006357 GO:0006412 GO:0008026 GO:0008094 GO:0008134 GO:0008186 GO:0008270 GO:0016020 GO:0016787 GO:0030424 GO:0030426 GO:0030529 GO:0032508 GO:0032575 GO:0032797 GO:0042995 GO:0043022 GO:0043141 GO:0046872 GO:0051260
80.060.4253.230.110.544adxO GO:0003723 GO:0003735 GO:0005622 GO:0005840 GO:0006412 GO:0019843 GO:0030529
90.060.4575.430.030.784pj3A GO:0000398 GO:0003723 GO:0005634 GO:0005654 GO:0005681 GO:0006283 GO:0006397 GO:0008380 GO:0016020 GO:0044822 GO:0071013
100.060.3435.300.040.562xzlA GO:0000166 GO:0000184 GO:0000956 GO:0003677 GO:0004004 GO:0004386 GO:0005524 GO:0005634 GO:0005737 GO:0005739 GO:0005844 GO:0006310 GO:0006449 GO:0006452 GO:0008270 GO:0008298 GO:0016567 GO:0016787 GO:0016887 GO:0030466 GO:0043024 GO:0046872 GO:0070478
110.060.3195.960.030.585ffjA GO:0000166 GO:0003676 GO:0003677 GO:0004518 GO:0004519 GO:0005524 GO:0006306 GO:0008168 GO:0008170 GO:0016787 GO:0032259 GO:0090305
120.060.4215.580.040.715eanA GO:0000076 GO:0000166 GO:0000723 GO:0000729 GO:0000784 GO:0003677 GO:0003678 GO:0003824 GO:0004386 GO:0004518 GO:0004519 GO:0005524 GO:0005634 GO:0005739 GO:0005760 GO:0006260 GO:0006264 GO:0006281 GO:0006284 GO:0006974 GO:0008152 GO:0016787 GO:0016890 GO:0017108 GO:0032508 GO:0033567 GO:0042645 GO:0043137 GO:0043139 GO:0043142 GO:0043504 GO:0045740 GO:0046872 GO:0051536 GO:0051539 GO:0090305 GO:1902990
130.060.2996.370.030.594krhA GO:0008152 GO:0008168 GO:0032259 GO:0046872 GO:0051536 GO:0051539
140.060.3196.120.070.584bjpA GO:0008658 GO:0008955 GO:0016020 GO:0016021 GO:0016740 GO:0016757
150.060.3265.740.040.564ohwA GO:0000166 GO:0005524 GO:0005634 GO:0005849 GO:0006378 GO:0006379 GO:0006388 GO:0006397 GO:0031124 GO:0046939 GO:0051736
160.060.3195.660.060.585a5bM GO:0000166 GO:0000502 GO:0005524 GO:0005634 GO:0005737 GO:0006511 GO:0008540 GO:0016787 GO:0016887 GO:0017025 GO:0030163 GO:0030433 GO:0031595 GO:0031597 GO:0036402 GO:0045899 GO:0070682 GO:1901800
170.060.2766.100.050.502iy3A GO:0000166 GO:0003723 GO:0003924 GO:0005525 GO:0005737 GO:0006612 GO:0006614 GO:0008312 GO:0030529 GO:0048500
180.060.3465.510.050.571d2mA GO:0000166 GO:0003677 GO:0004386 GO:0004518 GO:0005524 GO:0005737 GO:0006281 GO:0006289 GO:0006974 GO:0009381 GO:0009432 GO:0016787 GO:0090305


Consensus prediction of GO terms
 
Molecular Function GO:0005198 GO:0003676
GO-Score 0.58 0.48
Biological Processes GO:0044267 GO:0034645 GO:0043043 GO:0010467
GO-Score 0.58 0.58 0.58 0.58
Cellular Component GO:0022626 GO:0015934
GO-Score 0.48 0.48

(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.