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I-TASSER results for job id Rv0978c

[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
10.14 8 3ur4A 0BW Rep, Mult 46,47,68,93,94,95,136,178,195,306,322
20.07 4 2xl2A III Rep, Mult 184,227,228,230,254,267,269,290
30.05 3 2z2pA III Rep, Mult 46,68,95,136,151,176,178,221,236,261,263,279,305,322
40.03 2 3p4fA III Rep, Mult 45,47,68,93,110,136,152,322
50.02 1 2z2pA MHT Rep, Mult 236,237,259,261,280
60.02 1 2z2pA MHT Rep, Mult 184,227
70.02 1 3odtA CA Rep, Mult 44,322,325
80.02 1 1dbnB NAG Rep, Mult 294,312
90.02 1 1jmxB HEC Rep, Mult 282,283,284,285
100.02 1 1vyh4 III Rep, Mult 68,93,152,178,218,236,260,261,279,303,304
110.02 1 1kj4B III Rep, Mult 305,327
120.02 1 2winE UUU Rep, Mult 246,278
130.02 1 2z2pA III Rep, Mult 183,225,227,267,271
140.02 1 2z2pA DOL Rep, Mult 314,331
150.02 1 2z2pA UUU Rep, Mult 227,267,269,310,314
160.02 1 2z2pA DOL Rep, Mult 69,279,303,305,324

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
10.2221v04A0.6084.110.0880.7703.1.1.2,3.1.8.1221
20.1921rwlA0.5913.410.2100.7192.7.11.1232,267,310
30.1822fpcA0.5934.020.0900.7554.3.3.2NA
40.0852gc7A0.6744.340.0960.8821.4.99.3223,228,243,269,272
50.0842h47H0.6913.720.1040.8491.4.99.4226,232,243,312
60.0741madH0.6744.280.0980.8761.4.99.3224,228,244,289
70.0671pjxA0.5993.930.1090.7673.1.8.2NA
80.0672f10A0.6213.690.0620.7823.2.1.18NA
90.0671simA0.5924.100.0780.7733.2.1.18273
100.0662uvkB0.5754.290.0720.7585.1.3.-224,232,259,267,276,282
110.0662ht8A0.5874.580.0710.7983.2.1.18NA
120.0662htrA0.5684.830.0640.7883.2.1.18NA
130.0662xcyA0.5884.060.0800.7643.2.1.18281
140.0601fwxA0.6364.070.0560.7881.7.99.6NA
150.0601k32A0.6304.090.0710.8163.4.21.-NA
160.0601w6sC0.6914.070.0900.8851.1.99.8NA
170.0601lrwC0.6714.390.0710.8881.1.99.8227,290
180.0601k3iA0.7793.560.0810.9581.1.3.9NA
190.0602d0vA0.7093.900.0710.8881.1.99.8219
200.0601kitA0.6314.830.0730.8703.2.1.18NA
210.0602madH0.6774.290.0800.8821.4.99.3223,228,269
220.0602agsA0.6154.050.0780.7953.2.1.18NA
230.0602vk6A0.6064.030.0770.7823.2.1.18229
240.0603elqB0.6094.510.0750.8132.8.2.22227,269,309
250.0603fw0A0.6323.750.0900.7854.3.2.5229,267,312
260.0603dr2A0.6113.860.0920.7613.1.1.17NA
270.0603c75J0.6814.190.0870.8791.4.99.3223,228,243,246,269
280.0601ri6A0.7293.050.1220.8433.1.1.31221
290.0601vcuB0.6263.740.0760.7913.2.1.18NA
300.0601gjqA0.6523.730.0800.8131.7.99.1,1.7.2.1NA
310.0601cvmA0.6113.820.0860.7733.1.3.8NA
320.0602bixA0.6504.040.0610.8401.14.99.-48

(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
00.300.7763.160.070.902ybaB GO:0000122 GO:0000281 GO:0003682 GO:0005634 GO:0005667 GO:0005700 GO:0006281 GO:0006334 GO:0006335 GO:0006342 GO:0006351 GO:0006355 GO:0007307 GO:0007346 GO:0007379 GO:0007517 GO:0008284 GO:0016568 GO:0016571 GO:0016573 GO:0016581 GO:0016584 GO:0016589 GO:0016590 GO:0031491 GO:0031497 GO:0031523 GO:0033186 GO:0035035 GO:0035097 GO:0035098 GO:0042054 GO:0042393 GO:0042766 GO:0042803 GO:0042826 GO:0046974 GO:0046976 GO:0048666 GO:0048812 GO:0048813 GO:0051567 GO:0061085 GO:0070615 GO:0070734 GO:0070822
10.290.7772.420.120.863vgzC GO:0003677 GO:0030288
20.280.7793.210.100.914xyhA GO:0000070 GO:0000778 GO:0000790 GO:0005634 GO:0005829 GO:0051382 GO:0061638 GO:0061641 GO:0070317 GO:0098654
30.280.8492.650.120.963bwsA
40.280.7703.280.080.911erjC 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
50.260.7753.190.070.914pc0B GO:0000790 GO:0000978 GO:0000980 GO:0004407 GO:0005634 GO:0005654 GO:0006260 GO:0006335 GO:0006336 GO:0006338 GO:0006351 GO:0006355 GO:0007049 GO:0008094 GO:0008285 GO:0016568 GO:0016575 GO:0016580 GO:0016581 GO:0016589 GO:0031492 GO:0031497 GO:0033186 GO:0034080 GO:0035098 GO:0042393 GO:0042826 GO:0043044 GO:0043234 GO:0045814 GO:0051726 GO:1901796
60.190.7782.930.070.903gfcA GO:0000790 GO:0000978 GO:0000980 GO:0004407 GO:0005634 GO:0005654 GO:0006260 GO:0006335 GO:0006336 GO:0006338 GO:0006351 GO:0006355 GO:0007049 GO:0008094 GO:0008285 GO:0016568 GO:0016575 GO:0016580 GO:0016581 GO:0016589 GO:0031492 GO:0031497 GO:0033186 GO:0034080 GO:0035098 GO:0042393 GO:0042826 GO:0043044 GO:0043234 GO:0045814 GO:0051726 GO:1901796
70.160.7863.300.120.933dm0A 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
80.150.7683.250.070.904xfvA GO:0002098 GO:0005634 GO:0005654 GO:0005737 GO:0006351 GO:0006355 GO:0006357 GO:0006810 GO:0008017 GO:0015031 GO:0032447 GO:0033588
90.150.7753.330.070.923cfvB 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
100.150.7602.970.120.884btsAR GO:0005840
110.140.7373.170.170.851l0qA GO:0016020 GO:0016021
120.140.7632.820.110.872h9lA 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
130.140.7512.900.080.873jcrL 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
140.140.7572.970.090.884a11B 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
150.140.7652.790.080.873jcmB GO:0000398 GO:0005634 GO:0005681 GO:0006397 GO:0008380 GO:0017070 GO:0030621 GO:0034247 GO:0046540
160.140.7572.900.110.873ow8C 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
170.140.7612.660.070.863jb9K GO:0000974 GO:0005634 GO:0005662 GO:0005681 GO:0006397 GO:0008380 GO:0045292 GO:0071011 GO:0071013 GO:0080008
180.140.7572.830.110.874aezA 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
190.140.7493.110.130.872ymuA GO:0016020 GO:0016021
200.120.7372.870.070.854d0kA GO:0000288 GO:0000289 GO:0003676 GO:0004518 GO:0004527 GO:0004535 GO:0005737 GO:0006397 GO:0016787 GO:0031251 GO:0090305 GO:0090503
210.120.7323.420.090.884lg9A GO:0000118 GO:0000122 GO:0002021 GO:0003677 GO:0003714 GO:0005634 GO:0005654 GO:0005876 GO:0006351 GO:0006355 GO:0008013 GO:0010468 GO:0016042 GO:0016568 GO:0016575 GO:0017053 GO:0030814 GO:0035264 GO:0042393 GO:0043161 GO:0044212 GO:0044255 GO:0045892 GO:0045893 GO:0045944 GO:0047485 GO:0050872 GO:0060070 GO:0060612 GO:0060613 GO:0090207
220.120.7163.090.120.843fgbA GO:0005829 GO:0017057
230.110.6903.360.100.813dsmA
240.070.6913.900.100.874v7fq GO:0000027 GO:0005634 GO:0005730 GO:0042254
250.070.7213.680.100.893jctx GO:0000027 GO:0005634 GO:0005730 GO:0042254
260.070.7313.520.100.895fl8q GO:0000027 GO:0005634 GO:0005730 GO:0042254
270.070.6264.290.090.821jmxB
280.070.7583.390.090.891nr0A 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
290.070.6523.730.080.811gjqA GO:0009055 GO:0016491 GO:0020037 GO:0042597 GO:0046872 GO:0050418 GO:0050421 GO:0055114
300.070.7133.780.110.884nsxA GO:0005634 GO:0005654 GO:0005730 GO:0006364 GO:0030529 GO:0031167 GO:0032040 GO:0034388 GO:0042254 GO:0042274


Consensus prediction of GO terms
 
Molecular Function GO:0003676 GO:0043168 GO:0001076 GO:0042393 GO:0042826 GO:0070615 GO:0046976 GO:0031491 GO:0046974 GO:0042803 GO:0035035
GO-Score 0.57 0.55 0.55 0.50 0.50 0.30 0.30 0.30 0.30 0.30 0.30
Biological Processes GO:0070925 GO:0043623 GO:0000819 GO:0034508 GO:0010948 GO:0051383 GO:0070316 GO:0035953 GO:0100070 GO:0035952 GO:2000879 GO:0043044 GO:0000430 GO:0000437 GO:0045894 GO:0070784 GO:0045014 GO:0080135 GO:0001196 GO:0046021 GO:0007068 GO:0001403 GO:0016584 GO:0007346 GO:0008284 GO:0007379 GO:0016568 GO:0006335 GO:0042766 GO:0007307 GO:0016573 GO:0007517 GO:0051567 GO:0048813 GO:0061085 GO:0006281 GO:0000281 GO:0006342
GO-Score 0.56 0.56 0.56 0.56 0.56 0.56 0.56 0.55 0.55 0.55 0.55 0.55 0.55 0.55 0.55 0.55 0.55 0.55 0.55 0.55 0.55 0.55 0.50 0.30 0.30 0.30 0.30 0.30 0.30 0.30 0.30 0.30 0.30 0.30 0.30 0.30 0.30 0.30
Cellular Component GO:0030313 GO:0042597 GO:0044444 GO:0000777 GO:0000780 GO:0034506 GO:0031248 GO:0005667 GO:0033186 GO:0016590 GO:0005700 GO:0035098 GO:0031523 GO:0070822 GO:0016589 GO:0016581
GO-Score 0.57 0.57 0.56 0.56 0.56 0.56 0.55 0.30 0.30 0.30 0.30 0.30 0.30 0.30 0.30 0.30

(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.