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I-TASSER results for job id Rv0959

[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
10.11 6 3q3gI CA Rep, Mult 489,491,493,551,579
20.08 4 1shtX MG Rep, Mult 491,493,551
30.04 2 1o6pA III Rep, Mult 481,484,485,543,551,552
40.04 2 3q0gA COA Rep, Mult 224,227
50.02 1 4jyxC UNL Rep, Mult 222,226
60.02 1 4rfuB CA Rep, Mult 470,471
70.02 1 4d2eC 78M Rep, Mult 510,514
80.02 1 3n8nB N88 Rep, Mult 402,405
90.02 1 2rh1A CLR Rep, Mult 487,510
100.02 1 5klaA NUC Rep, Mult 124,129,157,160,161,196,198,199,202,244,286,290,322,323,325,326,365,366,368,369,372,402,404,405,408,455
110.02 1 2q5dB III Rep, Mult 448,451,508
120.02 1 2z66A UUU Rep, Mult 525,527,541
130.02 1 1r2rB DMS Rep, Mult 195,198,244,248
140.02 1 1f59A III Rep, Mult 269,272,273,276,277,304,308,312
150.02 1 1u6g0 III Rep, Mult 440,446,450,491,503
160.02 1 1jkjA COA Rep, Mult 218,221

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
10.0601d8dA0.3465.050.0880.4382.5.1.58NA
20.0602np0A0.3328.630.0320.5673.4.24.69612
30.0601fo4A0.3298.310.0510.5401.17.1.4NA
40.0601kc7A0.3358.170.0470.5482.7.9.1NA
50.0603btaA0.3388.340.0370.5593.4.24.69NA
60.0603dpyA0.3455.160.0740.4422.5.1.58,2.5.1.59487
70.0603c5wA0.2933.290.1130.3293.1.3.16488,547
80.0603b9jI0.1175.230.0500.1491.17.1.4,1.17.3.2NA
90.0602x0sA0.3358.430.0350.5542.7.9.1NA
100.0601slyA0.3247.140.0680.4854.2.2.-507
110.0601kblA0.3378.170.0430.5512.7.9.1NA
120.0601l5jA0.3447.790.0310.5394.2.1.3NA
130.0601z1wA0.3387.240.0390.4983.4.11.-NA
140.0603h09B0.3697.790.0480.5763.4.21.72NA
150.0602ckjA0.3288.250.0470.5341.17.1.4,1.17.3.2NA
160.0602pffD0.3198.760.0200.5522.3.1.86486,525
170.0601z0hB0.1637.720.0260.2523.4.24.69552
180.0603ecqB0.3768.600.0380.6353.2.1.97NA
190.0601ug9A0.2907.770.0370.4493.2.1.70NA

(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
00.180.8212.060.110.861b3uA GO:0000086 GO:0000159 GO:0000184 GO:0000188 GO:0000775 GO:0003823 GO:0004722 GO:0005634 GO:0005694 GO:0005737 GO:0005739 GO:0005829 GO:0006275 GO:0006355 GO:0006461 GO:0006470 GO:0006672 GO:0006915 GO:0007059 GO:0007084 GO:0007143 GO:0008380 GO:0008601 GO:0010033 GO:0015630 GO:0016020 GO:0019932 GO:0030111 GO:0030155 GO:0030308 GO:0034047 GO:0040008 GO:0042518 GO:0045595 GO:0046982 GO:0051232 GO:0051306 GO:0051754 GO:0070062 GO:0070262 GO:1903538 GO:2001241
10.070.6426.190.070.884v7oA6 GO:0000502 GO:0005634 GO:0005737 GO:0005839 GO:0006281 GO:0006974 GO:0010499 GO:0010952 GO:0016504 GO:0034515 GO:0043248 GO:0043486 GO:0061136 GO:0070577 GO:0070628 GO:1990236 GO:1990237
20.070.5875.240.070.754a0cA GO:0000151 GO:0005634 GO:0005654 GO:0005737 GO:0005794 GO:0010265 GO:0016020 GO:0016567 GO:0017025 GO:0030154 GO:0031461 GO:0043086 GO:0045893 GO:0045899 GO:0070062
30.070.5405.990.060.724xriA GO:0005622 GO:0006886 GO:0008536
40.070.5475.390.060.703nd2A GO:0000059 GO:0000060 GO:0000176 GO:0005087 GO:0005634 GO:0005643 GO:0005737 GO:0006606 GO:0006607 GO:0006610 GO:0006612 GO:0006656 GO:0006810 GO:0006886 GO:0008139 GO:0008536 GO:0008565 GO:0015031 GO:0031965 GO:0034399 GO:0043547 GO:0051028 GO:0051292 GO:0060188
50.070.5355.730.080.701qgkA GO:0000059 GO:0000060 GO:0005634 GO:0005635 GO:0005643 GO:0005654 GO:0005737 GO:0005829 GO:0006309 GO:0006606 GO:0006607 GO:0006610 GO:0006810 GO:0006886 GO:0007079 GO:0007080 GO:0008139 GO:0008270 GO:0008536 GO:0008565 GO:0015031 GO:0016020 GO:0016032 GO:0019054 GO:0019899 GO:0019904 GO:0030953 GO:0031291 GO:0031965 GO:0034399 GO:0040001 GO:0043234 GO:0044822 GO:0045184 GO:0051879 GO:0070062 GO:0071782 GO:0075733 GO:0090307
60.070.5296.290.060.722q5dB GO:0000059 GO:0000060 GO:0005634 GO:0005635 GO:0005643 GO:0005654 GO:0005737 GO:0005829 GO:0006309 GO:0006606 GO:0006607 GO:0006610 GO:0006810 GO:0006886 GO:0007079 GO:0007080 GO:0008139 GO:0008270 GO:0008536 GO:0008565 GO:0015031 GO:0016020 GO:0016032 GO:0019054 GO:0019899 GO:0019904 GO:0030953 GO:0031291 GO:0031965 GO:0034399 GO:0040001 GO:0043234 GO:0044822 GO:0045184 GO:0051879 GO:0070062 GO:0071782 GO:0075733 GO:0090307
70.060.3876.190.070.534uadA GO:0005634 GO:0005643 GO:0005654 GO:0005737 GO:0005829 GO:0006606 GO:0006607 GO:0006810 GO:0008139 GO:0008565 GO:0015031 GO:0016020 GO:0045944 GO:0060135
80.060.3746.130.070.524rxhB GO:0005634 GO:0005737 GO:0006606 GO:0006810 GO:0008565 GO:0015031
90.060.3696.300.070.524b8jA GO:0005634 GO:0005643 GO:0005654 GO:0005737 GO:0005829 GO:0006606 GO:0006607 GO:0006810 GO:0008139 GO:0008565 GO:0015031 GO:0016032 GO:0048471
100.060.3616.020.070.491wa5B GO:0000176 GO:0005634 GO:0005643 GO:0005654 GO:0005737 GO:0005829 GO:0006606 GO:0006607 GO:0006612 GO:0006810 GO:0008139 GO:0008565 GO:0015031 GO:0031144 GO:0048471
110.060.3293.940.070.381oyzA GO:0006974 GO:0046677
120.060.2943.350.120.334lacA GO:0000086 GO:0000159 GO:0000184 GO:0000188 GO:0000775 GO:0003823 GO:0004722 GO:0005634 GO:0005694 GO:0005737 GO:0005739 GO:0005829 GO:0006275 GO:0006355 GO:0006461 GO:0006470 GO:0006672 GO:0006915 GO:0007059 GO:0007084 GO:0007143 GO:0008380 GO:0008601 GO:0010033 GO:0015630 GO:0016020 GO:0019932 GO:0030111 GO:0030155 GO:0030308 GO:0034047 GO:0040008 GO:0042518 GO:0045595 GO:0046982 GO:0051232 GO:0051306 GO:0051754 GO:0070062 GO:0070262 GO:1903538 GO:2001241
130.060.2933.430.090.331lrvA
140.060.2734.720.060.333ebbA GO:0006644 GO:0006954 GO:0007165 GO:0016005 GO:0043085 GO:0070062
150.060.2774.260.080.334g3aB GO:0000022 GO:0000070 GO:0000775 GO:0000776 GO:0000922 GO:0005525 GO:0005634 GO:0005737 GO:0005813 GO:0005815 GO:0005819 GO:0005827 GO:0005856 GO:0005874 GO:0005875 GO:0005876 GO:0007049 GO:0007051 GO:0007052 GO:0007067 GO:0007275 GO:0007282 GO:0007411 GO:0008017 GO:0016325 GO:0019827 GO:0030154 GO:0030426 GO:0030723 GO:0031116 GO:0032154 GO:0035099 GO:0035371 GO:0040001 GO:0042995 GO:0045169 GO:0045172 GO:0046580 GO:0046602 GO:0048477 GO:0051225 GO:0051301 GO:0051315 GO:0090307
160.060.2554.730.100.324qmhA GO:0000022 GO:0000132 GO:0000922 GO:0005813 GO:0005875 GO:0007017 GO:0007029 GO:0007067 GO:0007143 GO:0007344 GO:0007411 GO:0008017 GO:0015631 GO:0016325 GO:0031122 GO:0035371 GO:0045196 GO:0045450 GO:0048477 GO:0090063
170.060.2463.720.100.283ltjA
180.060.2077.870.030.332ymwB GO:0005576 GO:0016491 GO:0031640 GO:0033736 GO:0042742 GO:0048038 GO:0055114 GO:1900191


Consensus prediction of GO terms
 
Molecular Function GO:0004721 GO:0019888 GO:0046983
GO-Score 0.36 0.36 0.36
Biological Processes GO:0001558 GO:0051304 GO:0007155 GO:0042221 GO:0051231 GO:0016055 GO:0043666 GO:1903506 GO:0042516 GO:0000070 GO:0006665 GO:0045926 GO:0051445 GO:0051052 GO:0031468 GO:0000956 GO:0043407 GO:0071822 GO:0070601 GO:1903537 GO:0065003 GO:2001239 GO:2001238 GO:0010468 GO:0000212 GO:2000112 GO:0070271 GO:0043603 GO:0051177 GO:0042532 GO:0044772 GO:0006351 GO:0044839 GO:0006260 GO:1900193 GO:0006396 GO:0010564
GO-Score 0.36 0.36 0.36 0.36 0.36 0.36 0.36 0.36 0.36 0.36 0.36 0.36 0.36 0.36 0.36 0.36 0.36 0.36 0.36 0.36 0.36 0.36 0.36 0.36 0.36 0.36 0.36 0.36 0.36 0.36 0.36 0.36 0.36 0.36 0.36 0.36 0.36
Cellular Component GO:0031988 GO:1903561 GO:0098687 GO:0008287 GO:0044444 GO:0005856 GO:0005634
GO-Score 0.47 0.47 0.36 0.36 0.36 0.36 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.