67 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
Pden_0111  CDS  NC_008686  102697  103602  906  hypothetical protein  YP_913924  unclonable  2.53104e-11  decreased coverage  0.00222502  Paracoccus denitrificans PD1222  Bacteria 
 
 
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Pden_0112  CDS  NC_008686  103599  105035  1437  hypothetical protein  YP_913925  decreased coverage  2.24966e-07  decreased coverage  0.000517302  Paracoccus denitrificans PD1222  Bacteria 
 
 
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Pden_0429  CDS  NC_008686  400357  401133  777  AzlC family protein  YP_914239  decreased coverage  0.000397006  normal  Paracoccus denitrificans PD1222  Bacteria 
 
 
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Pden_0610  CDS  NC_008686  586652  587821  1170  amidohydrolase  YP_914418  decreased coverage  0.00962709  normal  0.632979  Paracoccus denitrificans PD1222  Bacteria 
 
 
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Pden_0744  CDS  NC_008686  725499  726200  702  50S ribosomal protein L1  YP_914552  normal  decreased coverage  0.00583178  Paracoccus denitrificans PD1222  Bacteria 
 
 
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Pden_0745  CDS  NC_008686  726682  727197  516  50S ribosomal protein L10  YP_914553  normal  decreased coverage  0.00501407  Paracoccus denitrificans PD1222  Bacteria 
 
 
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Pden_0746  CDS  NC_008686  727265  727639  375  50S ribosomal protein L7/L12  YP_914554  normal  decreased coverage  0.00478946  Paracoccus denitrificans PD1222  Bacteria 
 
 
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Pden_0747  CDS  NC_008686  727881  732029  4149  DNA-directed RNA polymerase subunit beta  YP_914555  normal  0.712795  decreased coverage  0.00979449  Paracoccus denitrificans PD1222  Bacteria 
 
 
-
 
Pden_0882  CDS  NC_008686  867833  868792  960  ribokinase-like domain-containing protein  YP_914689  decreased coverage  0.00379836  normal  Paracoccus denitrificans PD1222  Bacteria 
 
 
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Pden_0883  CDS  NC_008686  868792  869199  408  hypothetical protein  YP_914690  decreased coverage  0.00210212  normal  Paracoccus denitrificans PD1222  Bacteria 
 
 
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Pden_0896  CDS  NC_008686  879393  880181  789  hypothetical protein  YP_914703  decreased coverage  0.0019435  normal  0.509637  Paracoccus denitrificans PD1222  Bacteria 
 
 
-
 
Pden_0897  CDS  NC_008686  880185  881033  849  dimethyladenosine transferase  YP_914704  decreased coverage  0.00367265  normal  0.802625  Paracoccus denitrificans PD1222  Bacteria 
 
 
-
 
Pden_0946  CDS  NC_008686  928843  929733  891  binding-protein-dependent transport systems inner membrane component  YP_914753  decreased coverage  0.00558212  normal  Paracoccus denitrificans PD1222  Bacteria 
 
 
-
 
Pden_1235  CDS  NC_008686  1198949  1199602  654  ABC transporter related  YP_915036  decreased coverage  0.000953894  normal  0.730254  Paracoccus denitrificans PD1222  Bacteria 
 
 
-
 
Pden_1562  CDS  NC_008686  1535665  1536129  465  transcriptional regulator NrdR  YP_915358  decreased coverage  0.000599658  normal  0.0421133  Paracoccus denitrificans PD1222  Bacteria 
 
 
-
 
Pden_1583  CDS  NC_008686  1560447  1562045  1599  glucan biosynthesis protein G  YP_915379  normal  decreased coverage  0.00561497  Paracoccus denitrificans PD1222  Bacteria 
 
 
-
 
Pden_1589  CDS  NC_008686  1568656  1568943  288  hypothetical protein  YP_915385  normal  0.427706  decreased coverage  0.00475251  Paracoccus denitrificans PD1222  Bacteria 
 
 
-
 
Pden_1590  CDS  NC_008686  1569043  1569678  636  cobyrinic acid a,c-diamide synthase  YP_915386  normal  0.950784  decreased coverage  0.00512965  Paracoccus denitrificans PD1222  Bacteria 
 
 
-
 
Pden_1698  CDS  NC_008686  1681881  1682960  1080  fructose-1,6-bisphosphate aldolase  YP_915491  decreased coverage  0.0076037  normal  Paracoccus denitrificans PD1222  Bacteria 
 
 
-
 
Pden_1757  CDS  NC_008686  1743278  1744984  1707  Serine-type D-Ala-D-Ala carboxypeptidase  YP_915550  decreased coverage  2.93147e-08  normal  0.187754  Paracoccus denitrificans PD1222  Bacteria 
 
 
-
 
Pden_1783  CDS  NC_008686  1776681  1778087  1407  integral membrane sensor signal transduction histidine kinase  YP_915576  decreased coverage  0.0029863  normal  Paracoccus denitrificans PD1222  Bacteria 
 
 
-
 
Pden_1812  CDS  NC_008686  1806435  1807340  906  ribokinase-like domain-containing protein  YP_915605  normal  0.0916129  decreased coverage  0.00793411  Paracoccus denitrificans PD1222  Bacteria 
 
 
-
 
Pden_1813  CDS  NC_008686  1807328  1808242  915  indigoidine synthase A family protein  YP_915606  normal  0.114344  decreased coverage  0.0086217  Paracoccus denitrificans PD1222  Bacteria 
 
 
-
 
Pden_1862  CDS  NC_008686  1862142  1862417  276  hypothetical protein  YP_915655  decreased coverage  0.00332482  normal  0.539982  Paracoccus denitrificans PD1222  Bacteria 
 
 
-
 
Pden_1866  CDS  NC_008686  1865120  1865785  666  putative transcriptional regulator  YP_915659  decreased coverage  0.00902439  normal  0.534464  Paracoccus denitrificans PD1222  Bacteria 
 
 
-
 
Pden_1867  CDS  NC_008686  1865782  1866636  855  chromosome segregation and condensation protein ScpA  YP_915660  decreased coverage  0.00662232  normal  0.558522  Paracoccus denitrificans PD1222  Bacteria 
 
 
-
 
Pden_1930    NC_008686  1924860  1925046  187      normal  0.220954  decreased coverage  0.00936635  Paracoccus denitrificans PD1222  Bacteria 
 
 
-
 
Pden_1936  CDS  NC_008686  1935600  1936256  657  lipoyltransferase  YP_915725  normal  decreased coverage  0.00922586  Paracoccus denitrificans PD1222  Bacteria 
 
 
-
 
Pden_1937  CDS  NC_008686  1936399  1936866  468  cytochrome c, class I  YP_915726  normal  decreased coverage  0.00818219  Paracoccus denitrificans PD1222  Bacteria 
 
 
-
 
Pden_1941  CDS  NC_008686  1942478  1943488  1011  glyoxylate reductase  YP_915730  normal  0.0819733  decreased coverage  0.00730231  Paracoccus denitrificans PD1222  Bacteria 
 
 
-
 
Pden_1942  CDS  NC_008686  1943580  1944182  603  hypothetical protein  YP_915731  normal  0.0398084  decreased coverage  0.00719314  Paracoccus denitrificans PD1222  Bacteria 
 
 
-
 
Pden_1943  CDS  NC_008686  1944200  1945057  858  hypothetical protein  YP_915732  normal  0.0650141  decreased coverage  0.00812028  Paracoccus denitrificans PD1222  Bacteria 
 
 
-
 
Pden_1945  CDS  NC_008686  1947281  1948333  1053  UBA/THIF-type NAD/FAD binding protein  YP_915734  normal  0.0410103  decreased coverage  0.00836902  Paracoccus denitrificans PD1222  Bacteria 
 
 
-
 
Pden_1996  CDS  NC_008686  2002568  2004139  1572  hypothetical protein  YP_915784  decreased coverage  0.00622478  normal  Paracoccus denitrificans PD1222  Bacteria 
 
 
-
 
Pden_2054  CDS  NC_008686  2061405  2062328  924  hypothetical protein  YP_915842  decreased coverage  1.3578e-07  unclonable  2.42077e-05  Paracoccus denitrificans PD1222  Bacteria 
 
 
-
 
Pden_2307  CDS  NC_008686  2305820  2307172  1353  cytochrome c1  YP_916094  normal  0.334325  decreased coverage  0.0079978  Paracoccus denitrificans PD1222  Bacteria 
 
 
-
 
Pden_2436  CDS  NC_008686  2438382  2439323  942  hypothetical protein  YP_916219  decreased coverage  0.000505512  normal  0.51938  Paracoccus denitrificans PD1222  Bacteria 
 
 
-
 
Pden_2448  CDS  NC_008686  2454104  2455141  1038  hypothetical protein  YP_916231  decreased coverage  0.00427442  normal  Paracoccus denitrificans PD1222  Bacteria 
 
 
-
 
Pden_2642  CDS  NC_008686  2653148  2653450  303  hypothetical protein  YP_916425  decreased coverage  6.73245e-07  normal  Paracoccus denitrificans PD1222  Bacteria 
 
 
-
 
Pden_2759  CDS  NC_008686  2777503  2779713  2211  polynucleotide phosphorylase/polyadenylase  YP_916539  decreased coverage  0.00521923  normal  Paracoccus denitrificans PD1222  Bacteria 
 
 
-
 
Pden_2947  CDS  NC_008687  115042  116349  1308  hypothetical protein  YP_916727  decreased coverage  0.00388563  normal  Paracoccus denitrificans PD1222  Bacteria 
 
 
-
 
Pden_2996  CDS  NC_008687  170234  170545  312  methanol dehydrogenase, beta subunit  YP_916775  decreased coverage  0.0052543  normal  Paracoccus denitrificans PD1222  Bacteria 
 
 
-
 
Pden_3297  CDS  NC_008687  462189  464129  1941  heavy metal translocating P-type ATPase  YP_917071  decreased coverage  0.00745206  normal  0.534464  Paracoccus denitrificans PD1222  Bacteria 
 
 
-
 
Pden_3554  CDS  NC_008687  702466  704322  1857  hypothetical protein  YP_917320  decreased coverage  0.00291608  normal  0.487552  Paracoccus denitrificans PD1222  Bacteria 
 
 
-
 
Pden_3626  CDS  NC_008687  778453  778971  519  AsnC family transcriptional regulator  YP_917389  decreased coverage  0.00949051  normal  Paracoccus denitrificans PD1222  Bacteria 
 
 
-
 
Pden_3644  CDS  NC_008687  794966  795748  783  hypothetical protein  YP_917407  decreased coverage  0.00251577  normal  0.378344  Paracoccus denitrificans PD1222  Bacteria 
 
 
-
 
Pden_3672  CDS  NC_008687  821309  822499  1191  hypothetical protein  YP_917435  decreased coverage  0.00326083  normal  Paracoccus denitrificans PD1222  Bacteria 
 
 
-
 
Pden_3737  CDS  NC_008687  880555  880806  252  hypothetical protein  YP_917500  decreased coverage  0.00728994  normal  0.292015  Paracoccus denitrificans PD1222  Bacteria 
 
 
-
 
Pden_3738  CDS  NC_008687  880905  881876  972  Fis family transcriptional regulator  YP_917501  decreased coverage  0.00315119  normal  0.324352  Paracoccus denitrificans PD1222  Bacteria 
 
 
-
 
Pden_3775  CDS  NC_008687  912308  913123  816  hypothetical protein  YP_917537  decreased coverage  3.61227e-10  hitchhiker  0.000220505  Paracoccus denitrificans PD1222  Bacteria 
 
 
-
 
Pden_3964  CDS  NC_008687  1102409  1103935  1527  cysteine desulfurase activator complex subunit SufB  YP_917726  decreased coverage  0.00244471  normal  Paracoccus denitrificans PD1222  Bacteria 
 
 
-
 
Pden_4118  CDS  NC_008687  1270064  1271038  975  LysR family transcriptional regulator  YP_917878  decreased coverage  0.00686854  normal  Paracoccus denitrificans PD1222  Bacteria 
 
 
-
 
Pden_4182  CDS  NC_008687  1339157  1339621  465  7-cyano-7-deazaguanine reductase  YP_917942  decreased coverage  1.04861e-05  normal  0.570077  Paracoccus denitrificans PD1222  Bacteria 
 
 
-
 
Pden_4402  CDS  NC_008687  1598266  1599774  1509  hypothetical protein  YP_918162  decreased coverage  0.00944962  normal  0.211367  Paracoccus denitrificans PD1222  Bacteria 
 
 
-
 
Pden_4442  CDS  NC_008687  1650089  1651366  1278  extracellular solute-binding protein  YP_918202  decreased coverage  0.00539632  normal  Paracoccus denitrificans PD1222  Bacteria 
 
 
-
 
Pden_4634  CDS  NC_008688  121265  122743  1479  leucyl aminopeptidase  YP_918393  decreased coverage  0.00269371  normal  Paracoccus denitrificans PD1222  Bacteria 
 
 
-
 
Pden_4636  CDS  NC_008688  124022  125368  1347  carbohydrate-selective porin OprB  YP_918395  decreased coverage  0.00387478  normal  Paracoccus denitrificans PD1222  Bacteria 
 
 
-
 
Pden_4640    NC_008688  127450  127990  541      decreased coverage  0.00517155  normal  Paracoccus denitrificans PD1222  Bacteria 
 
 
-
 
Pden_4676  CDS  NC_008688  168892  169983  1092  FMN-dependent alpha-hydroxy acid dehydrogenase  YP_918433  decreased coverage  0.00322368  normal  Paracoccus denitrificans PD1222  Bacteria 
 
 
-
 
Pden_4711  CDS  NC_008688  200737  201006  270  cell division topological specificity factor MinE  YP_918468  normal  0.274995  decreased coverage  0.00834487  Paracoccus denitrificans PD1222  Bacteria 
 
 
-
 
Pden_4712  CDS  NC_008688  201008  201745  738  septum site-determining protein MinD  YP_918469  normal  0.233951  decreased coverage  0.00864523  Paracoccus denitrificans PD1222  Bacteria 
 
 
-
 
Pden_4713  CDS  NC_008688  201853  202599  747  septum site-determining protein MinC  YP_918470  normal  0.0342769  decreased coverage  0.00921136  Paracoccus denitrificans PD1222  Bacteria 
 
 
-
 
Pden_4714  CDS  NC_008688  202820  203488  669  phosphoribosyltransferase  YP_918471  normal  0.120595  decreased coverage  0.00895414  Paracoccus denitrificans PD1222  Bacteria 
 
 
-
 
Pden_4715  CDS  NC_008688  203601  204569  969  TRAP dicarboxylate transporter, DctP subunit  YP_918472  normal  0.517095  decreased coverage  0.00914415  Paracoccus denitrificans PD1222  Bacteria 
 
 
-
 
Pden_5104  CDS  NC_008688  618213  618905  693  Surfeit locus 1 family protein  YP_918860  decreased coverage  0.009439  normal  Paracoccus denitrificans PD1222  Bacteria 
 
 
-
 
Pden_R0036  tRNA  NC_008686  1931540  1931626  87  tRNA-Leu    normal  0.247967  decreased coverage  0.00943738  Paracoccus denitrificans PD1222  Bacteria 
 
 
-
 
Pden_r2  rRNA  NC_008687  144166  146983  2818  23S ribosomal RNA    decreased coverage  0.00999234  normal  0.528087  Paracoccus denitrificans PD1222  Bacteria 
 
 
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