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I-TASSER results for job id Rv0124

[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
10.08 4 3smrB NP7 Rep, Mult 91,92,133,134,135,150,189,191,207,306,323
20.06 3 4hhoA CA Rep, Mult 91,232,273,274
30.04 2 3a6zA CA Rep, Mult 319,320,321,323,325,338,339,340,343
40.04 2 1qniA CUA Rep, Mult 181,183,185,189
50.02 1 4v0oF PB Rep, Mult 94,136,137,309
60.02 1 1jiwP CA Rep, Mult 258,259,260,261,263,289
70.02 1 4gm9B III Rep, Mult 89,91,130,133,134,150,274,323
80.02 1 1sqj0 III Rep, Mult 198,220,257,258,259,260,261
90.02 1 3sbrF IMD Rep, Mult 410,436,451,452
100.02 1 1jtdB CA Rep, Mult 275,276
110.02 1 3hbvP CA Rep, Mult 255,256,257,258,275,282
120.02 1 1aklA CA Rep, Mult 226,227,228,230,243,244,245,248
130.02 1 1srpA CA Rep, Mult 385,386,387,388,402,410
140.02 1 1af0A CA Rep, Mult 391,392,393,394,396,423
150.02 1 1tyeA CA Rep, Mult 246,271,273,275
160.02 1 3fbyB CA Rep, Mult 228,230,232,234,238
170.02 1 1srpA CA Rep, Mult 371,373,375,385,386,387,390
180.02 1 3odtA CA Rep, Mult 89,323,328

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
10.0601y4wA0.4016.440.0370.5813.2.1.80NA
20.0602bklB0.4195.580.0490.5673.4.21.26NA
30.0601ri6A0.3983.250.0710.4483.1.1.31NA
40.0601k3iA0.4155.370.0530.5461.1.3.9NA
50.0601kb0A0.4245.400.0610.5631.1.99.-230
60.0603fsnB0.3965.190.0590.5175.2.1.7424
70.0601yiqA0.4355.420.0610.5791.1.99.-NA
80.0602vk6A0.4024.800.0590.5153.2.1.18402
90.0601simA0.4044.660.0470.5113.2.1.18NA
100.0602madH0.4094.540.0550.5111.4.99.3354,356
110.0603g0bB0.4106.520.0410.6043.4.14.5251
120.0601ea0A0.4057.590.0490.6901.4.1.13NA
130.0602gbcA0.3975.970.0400.5633.4.14.5,3.4.15.5NA
140.0601yrzA0.4156.710.0550.6373.2.1.37382
150.0601vcuB0.3954.820.0560.5013.2.1.18NA
160.0601yr2A0.4615.210.0590.6063.4.21.26NA
170.0602f10A0.3944.700.0570.4953.2.1.1891
180.0603elqB0.4215.780.0640.5752.8.2.22261
190.0602ecfA0.4266.830.0530.6433.4.14.5NA

(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
00.140.5565.040.070.692ymuA GO:0016020 GO:0016021
10.110.5865.280.050.773j2tA 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
20.070.5585.130.050.724nsxA GO:0005634 GO:0005654 GO:0005730 GO:0006364 GO:0030529 GO:0031167 GO:0032040 GO:0034388 GO:0042254 GO:0042274
30.070.5435.100.070.704xfvA GO:0002098 GO:0005634 GO:0005654 GO:0005737 GO:0006351 GO:0006355 GO:0006357 GO:0006810 GO:0008017 GO:0015031 GO:0032447 GO:0033588
40.070.5425.220.070.704ci8A 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
50.070.5365.020.100.681nr0A 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
60.070.5375.950.060.773sfzA 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
70.070.5315.170.080.681pguB GO:0003779 GO:0005737 GO:0005856 GO:0005884 GO:0006970 GO:0030042 GO:0030479 GO:0032466 GO:0051016
80.070.4804.290.060.575cvlA 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
90.060.3903.410.070.444jxmA GO:0003723 GO:0005634 GO:0005654 GO:0005730 GO:0006364 GO:0030529 GO:0031428 GO:0032040 GO:0034511 GO:0044822
100.060.3913.410.070.442h9lA GO:0000123 GO:0001501 GO:0005622 GO:0005634 GO:0005654 GO:0005671 GO:0006351 GO:0006355 GO:0016568 GO:0018024 GO:0031175 GO:0035064 GO:0035097 GO:0035948 GO:0042800 GO:0043966 GO:0043981 GO:0043982 GO:0043984 GO:0043995 GO:0043996 GO:0044666 GO:0046972 GO:0048188 GO:0051568 GO:0071339
110.060.4353.380.060.494bujC GO:0000228 GO:0005634 GO:0005694 GO:0005737 GO:0006461 GO:0007131 GO:0034427 GO:0051321 GO:0051607 GO:0055087 GO:0065004 GO:0070478 GO:0070481
120.060.3713.830.070.435emkB 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
130.060.4283.430.080.494aezA GO:0000070 GO:0005634 GO:0007049 GO:0007067 GO:0010997 GO:0032153 GO:0033597 GO:0034613 GO:0044732 GO:0051301 GO:0072686 GO:0097027 GO:1904668
140.060.4293.010.060.484u7aA GO:0000463 GO:0000466 GO:0005634 GO:0005654 GO:0005730 GO:0006364 GO:0030687 GO:0042254 GO:0042273 GO:0043021 GO:0070180 GO:0070545
150.060.4323.210.060.483ow8C GO:0005634 GO:0005654 GO:0005737 GO:0006351 GO:0006355 GO:0016055 GO:0016593 GO:0032968 GO:0035327 GO:0045638 GO:0045944 GO:0051571 GO:0055087 GO:0080182 GO:2001162
160.060.4333.250.070.481erjC GO:0000122 GO:0000123 GO:0000433 GO:0001191 GO:0001198 GO:0005634 GO:0006351 GO:0006355 GO:0007070 GO:0008023 GO:0016584 GO:0017053 GO:0033588 GO:0035955 GO:0036033 GO:0042393 GO:0042826 GO:0043486 GO:0080025 GO:2000217 GO:2000531 GO:2001020
170.060.4313.090.080.483jcrL 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
180.060.4403.240.040.494a11B GO:0000109 GO:0000209 GO:0003678 GO:0004842 GO:0005634 GO:0005654 GO:0006281 GO:0006283 GO:0006289 GO:0006974 GO:0006979 GO:0008094 GO:0009411 GO:0010165 GO:0016363 GO:0016567 GO:0031464 GO:0032403 GO:0043161 GO:0043234 GO:0045739 GO:0051865


Consensus prediction of GO terms
 
Molecular Function GO:0008017 GO:0005524 GO:0031072 GO:0043531 GO:0008656 GO:0042802 GO:0005509
GO-Score 0.13 0.11 0.11 0.11 0.11 0.11 0.07
Biological Processes GO:0060322 GO:0007417 GO:0048513
GO-Score 0.33 0.33 0.33
Cellular Component GO:0043231 GO:0044444
GO-Score 0.44 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.