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I-TASSER results for job id Rv1396c

[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 2 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
10.20 11 3smrB NP7 Rep, Mult 138,139,180,181,182,197,219,251,253,269,379,395
20.06 3 2quaA CA Rep, Mult 511,512,513,514,516,537,538,539,542
30.04 2 2h6kB III Rep, Mult 138,181,197,219,269,270,291,292,336
40.02 1 1sqj0 III Rep, Mult 260,276,282,319,320,321,322,323
50.02 1 3lsmA SO3 Rep, Mult 238,463
60.02 1 1jtdB CA Rep, Mult 507,508
70.02 1 2wieC CVM Rep, Mult 54,59
80.02 1 4a0pA CA Rep, Mult 310,313,332
90.02 1 1ft6A SO3 Rep, Mult 140,199
100.02 1 1af0A CA Rep, Mult 491,492,493,495,502,503,504,507
110.02 1 2xzmR NUC Rep, Mult 172,173,175,176,202,210,484,487,488
120.02 1 3odtA CA Rep, Mult 395,401
130.02 1 3a6zA CA Rep, Mult 404,405,406,408,410,423,426,427,430
140.02 1 2wieD CVM Rep, Mult 51,54

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
10.0602jkbA0.3796.010.0350.5193.2.1.18,4.2.2.15NA
20.0601yr2A0.4365.950.0600.5943.4.21.26NA
30.0601kv9A0.3825.270.0630.4901.1.99.-NA
40.0601g72A0.3785.070.0830.4811.1.99.8NA
50.0601kitA0.3706.590.0530.5293.2.1.18NA
60.0601gjqA0.4075.100.0520.5191.7.99.1,1.7.2.1NA
70.0601ofdA0.4077.720.0310.6671.4.7.1NA
80.0603fsnB0.3895.040.0370.4935.2.1.7257,347
90.0601t3tA0.3797.680.0610.6096.3.5.3196
100.0602madH0.4014.060.0830.4761.4.99.3261
110.0601llwA0.4037.760.0430.6611.4.7.1NA
120.0601orvA0.3866.350.0260.5363.4.14.5466
130.0601k3iA0.4465.420.0680.5801.1.3.9NA
140.0601aomB0.4124.960.0580.5191.7.99.1,1.7.2.1NA
150.0602ecfA0.4257.020.0780.6343.4.14.5466
160.0602w68C0.1644.900.0730.2083.2.1.18NA
170.0601yrzA0.3896.460.0770.5563.2.1.37NA
180.0601yifA0.3895.880.0710.5283.2.1.37NA
190.0601k32A0.4315.030.0380.5473.4.21.-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
00.140.5544.870.080.672ymuA GO:0016020 GO:0016021
10.100.6465.030.040.813j2tA GO:0000166 GO:0001666 GO:0001843 GO:0005524 GO:0005634 GO:0005737 GO:0005829 GO:0006915 GO:0006919 GO:0007275 GO:0007399 GO:0007420 GO:0007568 GO:0007584 GO:0008635 GO:0008656 GO:0010659 GO:0030154 GO:0030900 GO:0031072 GO:0034349 GO:0042802 GO:0042981 GO:0043065 GO:0043293 GO:0043531 GO:0051260 GO:0051402 GO:0070059 GO:0070062 GO:0071560 GO:0072432 GO:0097190 GO:0097193 GO:1902510 GO:2001235
20.080.5404.890.090.661nr0A GO:0003779 GO:0005737 GO:0005856 GO:0016528 GO:0030016 GO:0030240 GO:0030836 GO:0030837 GO:0040011 GO:0040012 GO:0042643 GO:0051015 GO:0071689
30.070.5715.030.050.714nsxA GO:0005634 GO:0005654 GO:0005730 GO:0006364 GO:0030529 GO:0031167 GO:0032040 GO:0034388 GO:0042254 GO:0042274
40.070.5435.600.070.714ci8A GO:0000226 GO:0002244 GO:0005509 GO:0005737 GO:0005829 GO:0005856 GO:0005874 GO:0005875 GO:0007052 GO:0007405 GO:0007420 GO:0008017 GO:0015631 GO:0048471 GO:0097431 GO:1990023
50.070.5495.340.040.723sfzA GO:0000166 GO:0001666 GO:0001843 GO:0005524 GO:0005634 GO:0005737 GO:0005829 GO:0006915 GO:0006919 GO:0007275 GO:0007420 GO:0007568 GO:0007584 GO:0008635 GO:0008656 GO:0010659 GO:0030154 GO:0030900 GO:0031072 GO:0034349 GO:0042802 GO:0042981 GO:0043293 GO:0043531 GO:0051260 GO:0051402 GO:0070059 GO:0070062 GO:0071560 GO:0097190 GO:1902510 GO:2001235
60.070.5274.960.080.651pguB GO:0003779 GO:0005737 GO:0005856 GO:0005884 GO:0006970 GO:0030042 GO:0030479 GO:0032466 GO:0051016
70.070.5394.850.060.664xfvA GO:0002098 GO:0005634 GO:0005654 GO:0005737 GO:0006351 GO:0006355 GO:0006357 GO:0006810 GO:0008017 GO:0015031 GO:0032447 GO:0033588
80.070.4684.080.040.535cvlA GO:0000724 GO:0005634 GO:0005737 GO:0005764 GO:0005768 GO:0005770 GO:0006974 GO:0007283 GO:0007338 GO:0008584 GO:0016032 GO:0016579 GO:0035264 GO:0043588 GO:0048568 GO:0048705 GO:0048872 GO:0050679 GO:0072520 GO:1902525
90.060.3765.720.060.503dm0A GO:0004871 GO:0005078 GO:0005215 GO:0005363 GO:0005634 GO:0005737 GO:0005829 GO:0006417 GO:0006810 GO:0006974 GO:0007165 GO:0008643 GO:0009507 GO:0009739 GO:0009749 GO:0009845 GO:0009967 GO:0010228 GO:0010476 GO:0015768 GO:0022626 GO:0030288 GO:0032947 GO:0034289 GO:0042254 GO:0042597 GO:0042956 GO:0043190 GO:0046686 GO:0055052 GO:0060326 GO:0071215 GO:1901982 GO:1990060
100.060.3812.910.060.414ui9R GO:0005634 GO:0005654 GO:0005680 GO:0005737 GO:0005829 GO:0006281 GO:0006974 GO:0007049 GO:0007067 GO:0008284 GO:0010997 GO:0016567 GO:0031145 GO:0031572 GO:0031965 GO:0040020 GO:0042787 GO:0045732 GO:0051301 GO:0051436 GO:0051437 GO:0051439 GO:0070306 GO:0070979 GO:0090344 GO:0097027 GO:1904668
110.060.4162.560.040.453cfvB GO:0000122 GO:0003723 GO:0004407 GO:0005634 GO:0005654 GO:0006260 GO:0006351 GO:0006355 GO:0007275 GO:0008283 GO:0016568 GO:0016575 GO:0016581 GO:0030308 GO:0034080 GO:0035098 GO:0045814 GO:0045892 GO:0048545 GO:0070370 GO:1901796
120.060.3822.620.050.415g04R GO:0000922 GO:0005634 GO:0005654 GO:0005680 GO:0005737 GO:0005813 GO:0005815 GO:0005819 GO:0005829 GO:0005856 GO:0007049 GO:0007062 GO:0007067 GO:0007399 GO:0008022 GO:0008284 GO:0010997 GO:0016567 GO:0019899 GO:0030154 GO:0031145 GO:0031915 GO:0040020 GO:0042787 GO:0042826 GO:0043161 GO:0043234 GO:0048471 GO:0050773 GO:0051301 GO:0051436 GO:0051437 GO:0051439 GO:0090129 GO:0097027 GO:1904668
130.060.3632.670.070.395emkB GO:0000387 GO:0005634 GO:0005654 GO:0005737 GO:0005794 GO:0005829 GO:0006357 GO:0008284 GO:0008285 GO:0008327 GO:0016274 GO:0030374 GO:0034709 GO:0035246 GO:0060528 GO:0060770
140.060.4192.340.060.453jcrL GO:0000375 GO:0000398 GO:0005634 GO:0005654 GO:0005681 GO:0006396 GO:0006397 GO:0008380 GO:0015030 GO:0016607 GO:0017070 GO:0030621 GO:0046540 GO:0071001 GO:0097525
150.060.3612.220.060.384lg8A GO:0000209 GO:0000244 GO:0000245 GO:0000398 GO:0000974 GO:0001833 GO:0004842 GO:0005634 GO:0005654 GO:0005662 GO:0005681 GO:0005737 GO:0005811 GO:0005819 GO:0005856 GO:0006281 GO:0006283 GO:0006303 GO:0006397 GO:0006974 GO:0008380 GO:0008610 GO:0010498 GO:0016020 GO:0016567 GO:0016607 GO:0016874 GO:0034450 GO:0034613 GO:0035861 GO:0042802 GO:0045665 GO:0048026 GO:0048711 GO:0061630 GO:0070534 GO:0071013 GO:0072422
160.060.3414.150.050.404e54B GO:0000209 GO:0000715 GO:0000717 GO:0003677 GO:0003684 GO:0004842 GO:0005634 GO:0005654 GO:0006281 GO:0006289 GO:0006290 GO:0006293 GO:0006294 GO:0006295 GO:0006296 GO:0006974 GO:0009411 GO:0016567 GO:0030054 GO:0031465 GO:0033683 GO:0035518 GO:0043234 GO:0051865 GO:0070911 GO:0070914 GO:0080008
170.060.4192.240.070.444v6wAg GO:0000398 GO:0005080 GO:0005737 GO:0005776 GO:0005829 GO:0005875 GO:0007626 GO:0009267 GO:0016243 GO:0018991 GO:0035220 GO:0042335 GO:0044829 GO:0045725 GO:0046716 GO:0048477 GO:0071011 GO:0071013 GO:0075522
180.060.4152.970.070.454l9oA GO:0005634 GO:0005643 GO:0005783 GO:0005789 GO:0006810 GO:0012507 GO:0015031 GO:0016020 GO:0016192 GO:0031410 GO:0051028


Consensus prediction of GO terms
 
Molecular Function GO:0031072 GO:0042802 GO:0005524 GO:0008656 GO:0043531 GO:0051015 GO:0005509 GO:0008017
GO-Score 0.10 0.10 0.10 0.10 0.10 0.08 0.07 0.07
Biological Processes GO:0007417 GO:0048513 GO:0060322
GO-Score 0.33 0.33 0.33
Cellular Component GO:0043231 GO:0044444
GO-Score 0.33 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.