58 decreased-coverage genes were found for selected organism/s



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Locus tag

Gene type

Replicon accession

From

To

Strand

Gene Length

Product

Protein accession

Plasmid clonability

Plasmid unclonability p-value

Fosmid clonability

Fosmid unclonability p-value

Organism name

Kingdom

Coverage Plot

PanDaTox homologs

Experimental validation
TM1040_0015  CDS  NC_008044  16023  16916  894  UDP-glucose pyrophosphorylase  YP_612010  decreased coverage  6.37346e-05  normal  Ruegeria sp. TM1040  Bacteria 
 
 
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TM1040_0021  CDS  NC_008044  23420  23884  465  PTS IIA-like nitrogen-regulatory protein PtsN  YP_612016  decreased coverage  0.00251551  normal  0.584916  Ruegeria sp. TM1040  Bacteria 
 
 
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TM1040_0022  CDS  NC_008044  23940  24503  564  SSU ribosomal protein S30P / sigma 54 modulation protein  YP_612017  decreased coverage  0.00266512  normal  0.613644  Ruegeria sp. TM1040  Bacteria 
 
 
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TM1040_0137  CDS  NC_008044  151103  152278  1176  histidine kinase  YP_612132  decreased coverage  0.00141334  normal  0.983928  Ruegeria sp. TM1040  Bacteria 
 
 
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TM1040_0143  CDS  NC_008044  156335  156646  312  ETC complex I subunit region  YP_612138  decreased coverage  7.05205e-06  normal  Ruegeria sp. TM1040  Bacteria 
 
 
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TM1040_0145  CDS  NC_008044  159057  160424  1368  deoxyguanosinetriphosphate triphosphohydrolase  YP_612140  decreased coverage  0.000232928  normal  Ruegeria sp. TM1040  Bacteria 
 
 
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TM1040_0413  CDS  NC_008044  423335  424114  780  hypothetical protein  YP_612408  decreased coverage  0.00475452  normal  0.256697  Ruegeria sp. TM1040  Bacteria 
 
 
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TM1040_0421  CDS  NC_008044  431975  432754  780  mannosyl-3-phosphoglycerate phosphatase  YP_612416  decreased coverage  0.00171889  normal  0.264679  Ruegeria sp. TM1040  Bacteria 
 
 
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TM1040_0491  CDS  NC_008044  513650  514654  1005  aldo/keto reductase  YP_612486  decreased coverage  0.00588566  normal  0.160086  Ruegeria sp. TM1040  Bacteria 
 
 
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TM1040_0686  CDS  NC_008044  734517  735437  921  D-alanine--D-alanine ligase  YP_612681  normal  0.280639  decreased coverage  0.000224556  Ruegeria sp. TM1040  Bacteria 
 
 
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TM1040_0687  CDS  NC_008044  735425  736324  900  cell division protein FtsQ  YP_612682  normal  0.0983299  decreased coverage  0.000241  Ruegeria sp. TM1040  Bacteria 
 
 
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TM1040_0688  CDS  NC_008044  736308  737660  1353  cell division protein FtsA  YP_612683  normal  0.0260143  decreased coverage  0.000277221  Ruegeria sp. TM1040  Bacteria 
 
 
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TM1040_0689  CDS  NC_008044  738085  739758  1674  cell division protein FtsZ  YP_612684  unclonable  1.08594e-08  decreased coverage  0.000313873  Ruegeria sp. TM1040  Bacteria 
 
 
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TM1040_0690  CDS  NC_008044  739957  740904  948  UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase  YP_612685  normal  0.0379633  decreased coverage  0.000248661  Ruegeria sp. TM1040  Bacteria 
 
 
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TM1040_0691  CDS  NC_008044  741250  742101  852  competence lipoprotein ComL, putative  YP_612686  normal  0.0174924  decreased coverage  0.000229911  Ruegeria sp. TM1040  Bacteria 
 
 
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TM1040_0692  CDS  NC_008044  742178  743827  1650  DNA repair protein RecN  YP_612687  normal  0.0261152  decreased coverage  0.000301908  Ruegeria sp. TM1040  Bacteria 
 
 
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TM1040_0796  CDS  NC_008044  845629  846108  480  single-strand binding protein  YP_612791  normal  decreased coverage  6.62422e-07  Ruegeria sp. TM1040  Bacteria 
 
 
-
 
TM1040_0797  CDS  NC_008044  846108  846362  255  hypothetical protein  YP_612792  normal  decreased coverage  5.68593e-07  Ruegeria sp. TM1040  Bacteria 
 
 
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TM1040_0798  CDS  NC_008044  846385  846966  582  hypothetical protein  YP_612793  normal  decreased coverage  6.25591e-07  Ruegeria sp. TM1040  Bacteria 
 
 
-
 
TM1040_0813  CDS  NC_008044  857163  857633  471  hypothetical protein  YP_612808  decreased coverage  0.00956825  hitchhiker  0.00183494  Ruegeria sp. TM1040  Bacteria 
 
 
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TM1040_0826  CDS  NC_008044  867997  868806  810  hypothetical protein  YP_612821  decreased coverage  0.000568663  normal  0.254553  Ruegeria sp. TM1040  Bacteria 
 
 
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TM1040_0863  CDS  NC_008044  917168  917932  765  DSBA oxidoreductase  YP_612858  decreased coverage  0.00216121  normal  Ruegeria sp. TM1040  Bacteria 
 
 
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TM1040_1017  CDS  NC_008044  1088369  1089136  768  hypothetical protein  YP_613012  decreased coverage  0.00283953  normal  Ruegeria sp. TM1040  Bacteria 
 
 
-
 
TM1040_1078  CDS  NC_008044  1153751  1155127  1377  pyruvate dehydrogenase subunit beta  YP_613073  decreased coverage  0.00798693  normal  0.879524  Ruegeria sp. TM1040  Bacteria 
 
 
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TM1040_1160  CDS  NC_008044  1250605  1250919  315  cupin 2, barrel  YP_613155  normal  0.677962  decreased coverage  0.00806774  Ruegeria sp. TM1040  Bacteria 
 
 
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TM1040_1161  CDS  NC_008044  1250925  1251590  666  ribosomal large subunit pseudouridine synthase E  YP_613156  normal  decreased coverage  0.00928122  Ruegeria sp. TM1040  Bacteria 
 
 
-
 
TM1040_1162  CDS  NC_008044  1251838  1252422  585  HNH endonuclease  YP_613157  normal  decreased coverage  0.00934225  Ruegeria sp. TM1040  Bacteria 
 
 
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TM1040_1163  CDS  NC_008044  1252474  1253520  1047  ornithine cyclodeaminase  YP_613158  normal  0.833995  decreased coverage  0.00431249  Ruegeria sp. TM1040  Bacteria 
 
 
-
 
TM1040_1177  CDS  NC_008044  1266814  1269228  2415  hypothetical protein  YP_613172  decreased coverage  0.00247698  normal  0.649292  Ruegeria sp. TM1040  Bacteria 
 
 
-
 
TM1040_1223  CDS  NC_008044  1313953  1315497  1545  protein of unknown function DUF853, NPT hydrolase putative  YP_613218  decreased coverage  0.00822087  normal  Ruegeria sp. TM1040  Bacteria 
 
 
-
 
TM1040_1481  CDS  NC_008044  1582635  1583594  960  NAD-dependent epimerase/dehydratase  YP_613476  decreased coverage  0.00831994  normal  Ruegeria sp. TM1040  Bacteria 
 
 
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TM1040_1548  CDS  NC_008044  1654635  1656215  1581  5'-nucleotidase-like  YP_613543  decreased coverage  0.00999704  normal  0.364034  Ruegeria sp. TM1040  Bacteria 
 
 
-
 
TM1040_1625  CDS  NC_008044  1732375  1734075  1701  phage terminase  YP_613620  decreased coverage  0.000276041  normal  0.989877  Ruegeria sp. TM1040  Bacteria 
 
 
-
 
TM1040_1740  CDS  NC_008044  1834669  1836678  2010  DNA topoisomerase IV subunit B  YP_613735  decreased coverage  0.00895559  normal  Ruegeria sp. TM1040  Bacteria 
 
 
-
 
TM1040_1798  CDS  NC_008044  1890558  1890881  324  hypothetical protein  YP_613793  decreased coverage  0.00123437  normal  0.0181915  Ruegeria sp. TM1040  Bacteria 
 
 
-
 
TM1040_1799  CDS  NC_008044  1890915  1891604  690  helix-turn-helix, type 11  YP_613794  decreased coverage  0.000591723  normal  0.0198726  Ruegeria sp. TM1040  Bacteria 
 
 
-
 
TM1040_2269  CDS  NC_008044  2383855  2384532  678  lipolytic enzyme, G-D-S-L  YP_614263  decreased coverage  0.00077116  normal  0.478679  Ruegeria sp. TM1040  Bacteria 
 
 
-
 
TM1040_2686  CDS  NC_008044  2825147  2826733  1587  extracellular solute-binding protein  YP_614680  decreased coverage  3.82125e-05  normal  0.980281  Ruegeria sp. TM1040  Bacteria 
 
 
-
 
TM1040_2750  CDS  NC_008044  2898076  2899119  1044  TRAP dicarboxylate transporter, DctP subunit  YP_614744  decreased coverage  0.000216568  normal  Ruegeria sp. TM1040  Bacteria 
 
 
-
 
TM1040_3144  CDS  NC_008043  123368  124948  1581  extracellular solute-binding protein  YP_611380  decreased coverage  0.000116165  normal  Ruegeria sp. TM1040  Bacteria 
 
 
-
 
TM1040_3151  CDS  NC_008043  131814  132701  888  ATPase, BadF/BadG/BcrA/BcrD type  YP_611387  decreased coverage  1.02812e-05  normal  Ruegeria sp. TM1040  Bacteria 
 
 
-
 
TM1040_3152  CDS  NC_008043  132916  133797  882  N-acetylmuramic acid-6-phosphate etherase  YP_611388  decreased coverage  2.49376e-06  normal  Ruegeria sp. TM1040  Bacteria 
 
 
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TM1040_3221  CDS  NC_008043  218070  218747  678  tripartite ATP-independent periplasmic transporter DctQ  YP_611457  decreased coverage  0.000218018  normal  Ruegeria sp. TM1040  Bacteria 
 
 
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TM1040_3222  CDS  NC_008043  218740  220140  1401  TRAP C4-dicarboxylate transport system permease DctM subunit  YP_611458  decreased coverage  0.00234978  normal  Ruegeria sp. TM1040  Bacteria 
 
 
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TM1040_3247  CDS  NC_008043  250042  250839  798  integrase catalytic subunit  YP_611483  decreased coverage  0.00558432  normal  Ruegeria sp. TM1040  Bacteria 
 
 
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TM1040_3254  CDS  NC_008043  255172  256242  1071  TMAO reductase system periplasmic protein TorT  YP_611490  decreased coverage  0.00636832  normal  Ruegeria sp. TM1040  Bacteria 
 
 
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TM1040_3312  CDS  NC_008043  321168  322187  1020  putative periplasmic solute-binding protein  YP_611546  decreased coverage  0.00706911  normal  Ruegeria sp. TM1040  Bacteria 
 
 
-
 
TM1040_3318  CDS  NC_008043  327007  327534  528  tripartite ATP-independent periplasmic transporter DctQ  YP_611552  decreased coverage  0.00300706  normal  0.60312  Ruegeria sp. TM1040  Bacteria 
 
 
-
 
TM1040_3573  CDS  NC_008043  613580  614725  1146  lytic murein transglycosylase  YP_611804  normal  0.161419  decreased coverage  0.00457991  Ruegeria sp. TM1040  Bacteria 
 
 
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TM1040_3580  CDS  NC_008043  629292  630824  1533  hypothetical protein  YP_611811  decreased coverage  0.00103089  normal  0.191716  Ruegeria sp. TM1040  Bacteria 
 
 
-
 
TM1040_3613  CDS  NC_008043  668225  669037  813  hypothetical protein  YP_611842  normal  decreased coverage  0.00635836  Ruegeria sp. TM1040  Bacteria 
 
 
-
 
TM1040_3619  CDS  NC_008043  675641  676090  450  putative thiol-disulphide oxidoreductase DCC  YP_611848  normal  0.204045  decreased coverage  0.00487281  Ruegeria sp. TM1040  Bacteria 
 
 
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TM1040_3620  CDS  NC_008043  676087  677670  1584  saccharopine dehydrogenase  YP_611849  normal  decreased coverage  0.00695172  Ruegeria sp. TM1040  Bacteria 
 
 
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TM1040_3792  CDS  NC_008042  40650  41243  594  hypothetical protein  YP_611186  decreased coverage  0.000356225  normal  Ruegeria sp. TM1040  Bacteria 
 
 
-
 
TM1040_3793  CDS  NC_008042  41230  43440  2211  relaxase/mobilization nuclease domain-containing protein  YP_611187  decreased coverage  0.00267002  normal  Ruegeria sp. TM1040  Bacteria 
 
 
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TM1040_R0002  rRNA  NC_008044  144962  146416  1455  16S ribosomal RNA    decreased coverage  0.0087575  normal  Ruegeria sp. TM1040  Bacteria 
 
 
-
 
TM1040_R0020  tRNA  NC_008044  1257137  1257222  86  tRNA-Leu    normal  decreased coverage  0.00905739  Ruegeria sp. TM1040  Bacteria 
 
 
-
 
TM1040_R0050  tRNA  NC_008044  2984654  2984740  87  tRNA-Leu    decreased coverage  0.0025278  normal  0.537231  Ruegeria sp. TM1040  Bacteria 
 
 
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