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I-TASSER results for job id Rv1087

[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
10.14 7 1bl9A DHE Rep, Mult 450,484,485,487,500,529,530,543,569,570,571,608,690,691,737,752
20.04 2 2ce9A III Rep, Mult 126,128,169,171,203,225,227,260,276,302,345,366,394
30.02 1 4zoxA III Rep, Mult 435,451,453,481,482,504,527,608,650,688,690,707,737,752
40.02 1 1aomB DHE Rep, Mult 203,227,228,230,240,260,261,302,303,304,344
50.02 1 3gzrB UNL Rep, Mult 108,110
60.02 1 3kiwE MG Rep, Mult 718,719
70.02 1 2quaA CA Rep, Mult 506,507,508,509,511,523
80.02 1 2z8xA CA Rep, Mult 351,352,353,354,356,363,364,365
90.02 1 5jrkA BGC Rep, Mult 438,439,488,693,739,740
100.02 1 1ft6A SO3 Rep, Mult 144,208
110.02 1 2xqtB DCW Rep, Mult 55,62
120.02 1 2xqtE CVM Rep, Mult 62,65
130.02 1 1d4m1 MYR Rep, Mult 727,728
140.02 1 1srpA CA Rep, Mult 323,325,327,334,335,336
150.02 1 1sqj0 III Rep, Mult 491,512,517,518,521,551,552,557
160.02 1 3iurA III Rep, Mult 243,255,259
170.02 1 2wsc4 CLA Rep, Mult 128,132

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
10.0601orvA0.3667.440.0390.5273.4.14.5NA
20.0601gjqA0.3664.610.0560.4331.7.99.1,1.7.2.1NA
30.0601ea0A0.3598.450.0550.5841.4.1.13NA
40.0601w6sC0.3264.830.0670.3901.1.99.8NA
50.0601llwA0.3518.580.0650.5741.4.7.1NA
60.0602ecfA0.3807.270.0590.5483.4.14.5NA
70.0603b9jI0.1044.910.0260.1281.17.1.4,1.17.3.2300,306,314
80.0602ebsB0.5406.100.0840.7153.2.1.150445,462
90.0603ffzA0.3378.750.0520.5593.4.24.69NA
100.0601aomB0.3824.860.0530.4541.7.99.1,1.7.2.1NA
110.0602e1qA0.3348.480.0340.5401.17.3.2,1.17.1.4NA
120.0603g0bB0.3667.520.0410.5323.4.14.5320
130.0601yiqA0.3535.070.0620.4301.1.99.-NA
140.0603c75J0.3284.190.0750.3791.4.99.3NA
150.0601e5tA0.3657.050.0510.5153.4.21.26NA
160.0601lrwC0.3284.630.0640.3891.1.99.8NA
170.0603b9jC0.2278.300.0470.3581.17.3.2,1.17.1.4NA
180.0601ofdA0.3708.240.0690.5881.4.7.1NA
190.0601k32A0.4476.630.0560.6103.4.21.-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
00.150.6535.350.070.813j2tA 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
10.070.6135.390.070.773sfzA 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
20.070.5645.210.060.704nsxA GO:0005634 GO:0005654 GO:0005730 GO:0006364 GO:0030529 GO:0031167 GO:0032040 GO:0034388 GO:0042254 GO:0042274
30.070.5096.420.050.694xfvA GO:0002098 GO:0005634 GO:0005654 GO:0005737 GO:0006351 GO:0006355 GO:0006357 GO:0006810 GO:0008017 GO:0015031 GO:0032447 GO:0033588
40.070.4986.420.070.681nr0A 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
50.070.4975.640.070.644ci8A 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
60.070.4806.450.080.662ymuA GO:0016020 GO:0016021
70.070.4606.170.060.611pguB GO:0003779 GO:0005737 GO:0005856 GO:0005884 GO:0006970 GO:0030042 GO:0030479 GO:0032466 GO:0051016
80.060.4002.190.050.421r5mA GO:0003714 GO:0005634 GO:0006355 GO:0006357 GO:0016568 GO:0016575 GO:0031939 GO:0032874 GO:0034967 GO:0045835 GO:1903507
90.060.3826.520.060.513mkqA GO:0005198 GO:0006886 GO:0016192 GO:0030117
100.060.3805.390.070.473dm0A 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
110.060.3864.520.040.455cvlA 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
120.060.3946.130.050.515a1uD GO:0000139 GO:0005198 GO:0005737 GO:0005794 GO:0005829 GO:0006810 GO:0006886 GO:0006888 GO:0006890 GO:0006891 GO:0015031 GO:0016020 GO:0016192 GO:0030117 GO:0030126 GO:0030663 GO:0031410 GO:1901998
130.060.3227.780.050.495a1vK GO:0000139 GO:0005179 GO:0005198 GO:0005576 GO:0005615 GO:0005737 GO:0005794 GO:0006810 GO:0006886 GO:0006888 GO:0006890 GO:0006891 GO:0015031 GO:0016020 GO:0016192 GO:0030117 GO:0030126 GO:0030157 GO:0030663 GO:0031410 GO:0070062
140.060.3932.870.060.424lg9A 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
150.060.3413.860.060.393zwlD GO:0001731 GO:0002183 GO:0002188 GO:0003743 GO:0005737 GO:0005852 GO:0006412 GO:0006413 GO:0006446 GO:0016282 GO:0033290 GO:0043614
160.060.3394.020.050.393gfcA 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
170.060.3313.670.060.375ajaA GO:0000122 GO:0000166 GO:0004674 GO:0005524 GO:0005634 GO:0005730 GO:0005737 GO:0006351 GO:0006355 GO:0008180 GO:0016032 GO:0016301 GO:0016310 GO:0016567 GO:0016568 GO:0016740 GO:0030183 GO:0033151 GO:0035212 GO:1990244 GO:1990245
180.060.3242.240.070.345it9g GO:0000747 GO:0001403 GO:0001965 GO:0004871 GO:0005080 GO:0005092 GO:0005737 GO:0007186 GO:0010255 GO:0017148 GO:0022627 GO:0031139 GO:0031954 GO:0032995 GO:0034613 GO:0035556 GO:0043022 GO:0050790 GO:0060733


Consensus prediction of GO terms
 
Molecular Function GO:0032550 GO:0032559 GO:0043028 GO:0035639 GO:0005515 GO:0016505
GO-Score 0.42 0.42 0.42 0.42 0.42 0.42
Biological Processes GO:0060606 GO:0009967 GO:0097193 GO:1903624 GO:0048869 GO:0014020 GO:0010658 GO:0031667 GO:0006309 GO:0051128 GO:0070997 GO:0071559 GO:0071363 GO:0034976 GO:1900117 GO:0006919 GO:0036293 GO:2001233 GO:0007420 GO:0051259 GO:0072423 GO:0072414
GO-Score 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 0.31 0.31
Cellular Component GO:1903561 GO:0043234 GO:0031988 GO:0044445 GO:0005634
GO-Score 0.42 0.42 0.42 0.42 0.31

(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.