88 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
SeD_A0044  CDS  NC_011205  48370  50409  2040  glycoside hydrolase, family 31  YP_002213996  normal  0.228548  decreased coverage  0.00512205  Salmonella enterica subsp. enterica serovar Dublin str. CT_02021853  Bacteria 
 
 
-
 
SeD_A0098  CDS  NC_011205  103679  103840  162  hypothetical protein  YP_002214046  decreased coverage  0.0000599323  normal  0.605992  Salmonella enterica subsp. enterica serovar Dublin str. CT_02021853  Bacteria 
 
 
-
 
SeD_A0141  CDS  NC_011205  149913  151175  1263  cell division protein FtsA  YP_002214084  decreased coverage  0.0011437  normal  0.628842  Salmonella enterica subsp. enterica serovar Dublin str. CT_02021853  Bacteria 
 
 
-
 
SeD_A0142  CDS  NC_011205  151236  152387  1152  cell division protein FtsZ  YP_002214085  decreased coverage  0.000809484  normal  0.893784  Salmonella enterica subsp. enterica serovar Dublin str. CT_02021853  Bacteria 
 
 
-
 
SeD_A0389  CDS  NC_011205  406724  408682  1959  type III restriction-modification system StyLTI enzyme mod  YP_002214310  normal  decreased coverage  1.57999e-20  Salmonella enterica subsp. enterica serovar Dublin str. CT_02021853  Bacteria 
 
 
-
 
SeD_A0584  CDS  NC_011205  601886  602380  495  peptidyl-prolyl cis-trans isomerase B (rotamase B)  YP_002214491  decreased coverage  0.00143281  normal  0.41238  Salmonella enterica subsp. enterica serovar Dublin str. CT_02021853  Bacteria 
 
 
-
 
SeD_A0618  CDS  NC_011205  625876  626073  198  hypothetical protein  YP_002214521  normal  0.374768  decreased coverage  0.000963461  Salmonella enterica subsp. enterica serovar Dublin str. CT_02021853  Bacteria 
 
 
-
 
SeD_A0619  CDS  NC_011205  626220  626429  210  hypothetical protein  YP_002214522  normal  0.570933  decreased coverage  0.000948316  Salmonella enterica subsp. enterica serovar Dublin str. CT_02021853  Bacteria 
 
 
-
 
SeD_A0620  CDS  NC_011205  626465  627388  924  hypothetical protein  YP_002214523  normal  decreased coverage  0.00146691  Salmonella enterica subsp. enterica serovar Dublin str. CT_02021853  Bacteria 
 
 
-
 
SeD_A0624  CDS  NC_011205  629058  629891  834  DNA replication protein gp18  YP_002214527  normal  decreased coverage  0.00127495  Salmonella enterica subsp. enterica serovar Dublin str. CT_02021853  Bacteria 
 
 
-
 
SeD_A0832  CDS  NC_011205  830844  832010  1167  succinyl-CoA synthetase subunit beta  YP_002214706  decreased coverage  0.00412785  normal  Salmonella enterica subsp. enterica serovar Dublin str. CT_02021853  Bacteria 
 
 
-
 
SeD_A1078  CDS  NC_011205  1081217  1084405  3189  gifsy-1 prophage RecE  YP_002214937  normal  0.673362  decreased coverage  0.00000173114  Salmonella enterica subsp. enterica serovar Dublin str. CT_02021853  Bacteria 
 
 
-
 
SeD_A1255  CDS  NC_011205  1250284  1250406  123  hypothetical protein  YP_002215100  decreased coverage  0.00474032  normal  0.887463  Salmonella enterica subsp. enterica serovar Dublin str. CT_02021853  Bacteria 
 
 
-
 
SeD_A1281  CDS  NC_011205  1267503  1267871  369  flagellar biosynthesis protein FliT  YP_002215125  decreased coverage  0.000909072  normal  0.322252  Salmonella enterica subsp. enterica serovar Dublin str. CT_02021853  Bacteria 
 
 
-
 
SeD_A1320  CDS  NC_011205  1296707  1297285  579  transcriptional activator FlhC  YP_002215158  unclonable  0.0000170782  decreased coverage  3.16651e-27  Salmonella enterica subsp. enterica serovar Dublin str. CT_02021853  Bacteria 
 
 
-
 
SeD_A1321  CDS  NC_011205  1297410  1298297  888  flagellar motor protein MotA  YP_002215159  normal  0.142338  decreased coverage  5.03142e-27  Salmonella enterica subsp. enterica serovar Dublin str. CT_02021853  Bacteria 
 
 
-
 
SeD_A1432  CDS  NC_011205  1399187  1400266  1080  integrase  YP_002215264  decreased coverage  0.00370653  normal  0.301971  Salmonella enterica subsp. enterica serovar Dublin str. CT_02021853  Bacteria 
 
 
-
 
SeD_A1468  CDS  NC_011205  1423221  1423718  498  GAF domain-containing protein  YP_002215294  decreased coverage  0.000132233  normal  0.144363  Salmonella enterica subsp. enterica serovar Dublin str. CT_02021853  Bacteria 
 
 
-
 
SeD_A1542  CDS  NC_011205  1490911  1491081  171  hypothetical protein  YP_002215364  decreased coverage  0.00491769  normal  0.0893384  Salmonella enterica subsp. enterica serovar Dublin str. CT_02021853  Bacteria 
 
 
-
 
SeD_A1543  CDS  NC_011205  1491078  1491926  849  4-diphosphocytidyl-2-C-methyl-D-erythritol kinase  YP_002215365  decreased coverage  0.00558855  normal  0.0908777  Salmonella enterica subsp. enterica serovar Dublin str. CT_02021853  Bacteria 
 
 
-
 
SeD_A1621  CDS  NC_011205  1565608  1565916  309  hypothetical protein  YP_002215434  decreased coverage  0.000478704  decreased coverage  6.99573e-22  Salmonella enterica subsp. enterica serovar Dublin str. CT_02021853  Bacteria 
 
 
-
 
SeD_A1622  CDS  NC_011205  1565923  1567092  1170  tetratricopeptide repeat protein  YP_002215435  decreased coverage  0.000649442  decreased coverage  2.66656e-22  Salmonella enterica subsp. enterica serovar Dublin str. CT_02021853  Bacteria 
 
 
-
 
SeD_A1624  CDS  NC_011205  1567142  1567267  126  hypothetical protein  YP_002215436  hitchhiker  0.0012329  decreased coverage  6.15545e-22  Salmonella enterica subsp. enterica serovar Dublin str. CT_02021853  Bacteria 
 
 
-
 
SeD_A1698  CDS  NC_011205  1633353  1637273  3921  ATP-dependent RNA helicase HrpA  YP_002215507  normal  0.615295  decreased coverage  0.00323043  Salmonella enterica subsp. enterica serovar Dublin str. CT_02021853  Bacteria 
 
 
-
 
SeD_A1827  CDS  NC_011205  1769427  1770113  687  GntR family transcriptional regulator  YP_002215627  decreased coverage  0.000849458  normal  Salmonella enterica subsp. enterica serovar Dublin str. CT_02021853  Bacteria 
 
 
-
 
SeD_A1872  CDS  NC_011205  1810414  1811715  1302  sensor protein RstB  YP_002215666  decreased coverage  0.00123019  normal  Salmonella enterica subsp. enterica serovar Dublin str. CT_02021853  Bacteria 
 
 
-
 
SeD_A1873  CDS  NC_011205  1811791  1812720  930  DNA replication terminus site-binding protein  YP_002215667  decreased coverage  0.00330018  normal  Salmonella enterica subsp. enterica serovar Dublin str. CT_02021853  Bacteria 
 
 
-
 
SeD_A1913  CDS  NC_011205  1849103  1850128  1026  DNA-binding transcriptional repressor PurR  YP_002215704  decreased coverage  0.000592501  normal  Salmonella enterica subsp. enterica serovar Dublin str. CT_02021853  Bacteria 
 
 
-
 
SeD_A1914  CDS  NC_011205  1850125  1851057  933  putative DNA-binding transcriptional regulator  YP_002215705  decreased coverage  0.000429246  normal  Salmonella enterica subsp. enterica serovar Dublin str. CT_02021853  Bacteria 
 
 
-
 
SeD_A1918  CDS  NC_011205  1854713  1856086  1374  multidrug efflux protein  YP_002215709  decreased coverage  0.00462926  normal  Salmonella enterica subsp. enterica serovar Dublin str. CT_02021853  Bacteria 
 
 
-
 
SeD_A1965  CDS  NC_011205  1898396  1898632  237  major outer membrane lipoprotein  YP_002215750  unclonable  0.00000537115  decreased coverage  0.000000000167771  Salmonella enterica subsp. enterica serovar Dublin str. CT_02021853  Bacteria 
 
 
-
 
SeD_A2094  CDS  NC_011205  2017510  2017698  189  hypothetical protein  YP_002215871  unclonable  0.00000279182  decreased coverage  0.0000000248657  Salmonella enterica subsp. enterica serovar Dublin str. CT_02021853  Bacteria 
 
 
-
 
SeD_A2171  CDS  NC_011205  2084391  2085200  810  4-amino-4-deoxychorismate lyase  YP_002215940  normal  0.216662  decreased coverage  0.000000000000025967  Salmonella enterica subsp. enterica serovar Dublin str. CT_02021853  Bacteria 
 
 
-
 
SeD_A2172  CDS  NC_011205  2085324  2086565  1242  3-oxoacyl-(acyl carrier protein) synthase II  YP_002215941  normal  0.0165662  decreased coverage  0.0000000000000469452  Salmonella enterica subsp. enterica serovar Dublin str. CT_02021853  Bacteria 
 
 
-
 
SeD_A2174  CDS  NC_011205  2087043  2087777  735  3-ketoacyl-(acyl-carrier-protein) reductase  YP_002215943  hitchhiker  0.000160421  decreased coverage  0.0000000000000218664  Salmonella enterica subsp. enterica serovar Dublin str. CT_02021853  Bacteria 
 
 
-
 
SeD_A2175  CDS  NC_011205  2087790  2088719  930  malonyl CoA-acyl carrier protein transacylase  YP_002215944  hitchhiker  0.00200572  decreased coverage  0.0000000000000303555  Salmonella enterica subsp. enterica serovar Dublin str. CT_02021853  Bacteria 
 
 
-
 
SeD_A2180  CDS  NC_011205  2091925  2092509  585  Maf-like protein  YP_002215949  decreased coverage  0.000292018  hitchhiker  0.00000000000623683  Salmonella enterica subsp. enterica serovar Dublin str. CT_02021853  Bacteria 
 
 
-
 
SeD_A2181  ncRNA  NC_011205  2091764  2091931  168  SraB RNA    decreased coverage  0.0000964894  hitchhiker  0.0000000000036206  Salmonella enterica subsp. enterica serovar Dublin str. CT_02021853  Bacteria 
 
 
-
 
SeD_A2182  CDS  NC_011205  2092580  2092804  225  hypothetical protein  YP_002215950  decreased coverage  0.000112944  hitchhiker  0.00000000000386488  Salmonella enterica subsp. enterica serovar Dublin str. CT_02021853  Bacteria 
 
 
-
 
SeD_A2184    NC_011205  2093007  2093767  761      decreased coverage  0.000429246  hitchhiker  0.00000000000725915  Salmonella enterica subsp. enterica serovar Dublin str. CT_02021853  Bacteria 
 
 
-
 
SeD_A2276  CDS  NC_011205  2169792  2170268  477  lysozyme  YP_002216036  decreased coverage  0.00766878  hitchhiker  1.42848e-18  Salmonella enterica subsp. enterica serovar Dublin str. CT_02021853  Bacteria 
 
 
-
 
SeD_A2279  CDS  NC_011205  2172048  2173043  996  hypothetical protein  YP_002216039  decreased coverage  0.00859838  hitchhiker  4.1808499999999996e-21  Salmonella enterica subsp. enterica serovar Dublin str. CT_02021853  Bacteria 
 
 
-
 
SeD_A2280  CDS  NC_011205  2173045  2173905  861  KilA-N domain-containing protein  YP_002216040  normal  0.0187873  decreased coverage  1.7596300000000002e-23  Salmonella enterica subsp. enterica serovar Dublin str. CT_02021853  Bacteria 
 
 
-
 
SeD_A2283  CDS  NC_011205  2175198  2175671  474  hypothetical protein  YP_002216043  normal  0.89521  decreased coverage  1.1409300000000001e-23  Salmonella enterica subsp. enterica serovar Dublin str. CT_02021853  Bacteria 
 
 
-
 
SeD_A2433    NC_011205  2305791  2306765  975      normal  decreased coverage  0.0000697737  Salmonella enterica subsp. enterica serovar Dublin str. CT_02021853  Bacteria 
 
 
-
 
SeD_A2434  CDS  NC_011205  2306771  2307319  549  dTDP-4-dehydrorhamnose 3,5-epimerase  YP_002216181  normal  decreased coverage  0.0000547292  Salmonella enterica subsp. enterica serovar Dublin str. CT_02021853  Bacteria 
 
 
-
 
SeD_A2436  CDS  NC_011205  2308249  2309148  900  dTDP-4-dehydrorhamnose reductase  YP_002216183  normal  decreased coverage  0.0000731521  Salmonella enterica subsp. enterica serovar Dublin str. CT_02021853  Bacteria 
 
 
-
 
SeD_A2557  CDS  NC_011205  2437901  2438032  132  hypothetical protein  YP_002216290  decreased coverage  0.00740006  hitchhiker  0.0000726871  Salmonella enterica subsp. enterica serovar Dublin str. CT_02021853  Bacteria 
 
 
-
 
SeD_A2562  CDS  NC_011205  2441250  2441822  573  elongation factor P  YP_002216295  normal  0.015045  decreased coverage  0.0000164335  Salmonella enterica subsp. enterica serovar Dublin str. CT_02021853  Bacteria 
 
 
-
 
SeD_A2563  CDS  NC_011205  2442035  2443021  987  cobalamin synthesis protein, P47K  YP_002216296  hitchhiker  0.00261863  decreased coverage  0.00000585707  Salmonella enterica subsp. enterica serovar Dublin str. CT_02021853  Bacteria 
 
 
-
 
SeD_A2564  CDS  NC_011205  2443024  2443770  747  inner membrane protein YeiU  YP_002216297  decreased coverage  0.00168101  hitchhiker  0.0000332566  Salmonella enterica subsp. enterica serovar Dublin str. CT_02021853  Bacteria 
 
 
-
 
SeD_A2652  CDS  NC_011205  2536023  2536781  759  acyl-CoA thioester hydrolase YfbB  YP_002216376  decreased coverage  0.00598559  normal  Salmonella enterica subsp. enterica serovar Dublin str. CT_02021853  Bacteria 
 
 
-
 
SeD_A2676  CDS  NC_011205  2561278  2562216  939  HTH-type transcriptional regulator PecT  YP_002216400  decreased coverage  0.00370653  normal  0.784227  Salmonella enterica subsp. enterica serovar Dublin str. CT_02021853  Bacteria 
 
 
-
 
SeD_A2697  CDS  NC_011205  2580182  2580733  552  phosphodiesterase  YP_002216419  decreased coverage  0.000161935  normal  Salmonella enterica subsp. enterica serovar Dublin str. CT_02021853  Bacteria 
 
 
-
 
SeD_A2745  CDS  NC_011205  2623560  2624867  1308  long-chain fatty acid outer membrane transporter  YP_002216462  decreased coverage  0.00852795  normal  Salmonella enterica subsp. enterica serovar Dublin str. CT_02021853  Bacteria 
 
 
-
 
SeD_A2780  tRNA  NC_011205  2657979  2658054  76  tRNA-Val    decreased coverage  0.000064612  normal  Salmonella enterica subsp. enterica serovar Dublin str. CT_02021853  Bacteria 
 
 
-
 
SeD_A2781  tRNA  NC_011205  2658099  2658176  78  tRNA-Val    decreased coverage  0.0000634028  normal  Salmonella enterica subsp. enterica serovar Dublin str. CT_02021853  Bacteria 
 
 
-
 
SeD_A2782  tRNA  NC_011205  2658216  2658293  78  tRNA-Val    decreased coverage  0.0000628066  normal  Salmonella enterica subsp. enterica serovar Dublin str. CT_02021853  Bacteria 
 
 
-
 
SeD_A2783  tRNA  NC_011205  2658297  2658372  76  tRNA-Lys    decreased coverage  0.0000664691  normal  Salmonella enterica subsp. enterica serovar Dublin str. CT_02021853  Bacteria 
 
 
-
 
SeD_A2933  CDS  NC_011205  2824172  2825716  1545  DNA-binding transcriptional activator CadC  YP_002216624  decreased coverage  0.00185207  normal  Salmonella enterica subsp. enterica serovar Dublin str. CT_02021853  Bacteria 
 
 
-
 
SeD_A3033  CDS  NC_011205  2930573  2932258  1686  tail fiber domain-containing protein  YP_002216709  normal  decreased coverage  0.000290271  Salmonella enterica subsp. enterica serovar Dublin str. CT_02021853  Bacteria 
 
 
-
 
SeD_A3034  CDS  NC_011205  2932255  2932860  606  phage tail protein I  YP_002216710  normal  0.8346  decreased coverage  0.00021132  Salmonella enterica subsp. enterica serovar Dublin str. CT_02021853  Bacteria 
 
 
-
 
SeD_A3035  CDS  NC_011205  2932853  2933761  909  baseplate assembly protein J  YP_002216711  normal  0.805786  decreased coverage  0.000161965  Salmonella enterica subsp. enterica serovar Dublin str. CT_02021853  Bacteria 
 
 
-
 
SeD_A3138  CDS  NC_011205  3019242  3020303  1062  recombinase A  YP_002216800  normal  decreased coverage  0.000383703  Salmonella enterica subsp. enterica serovar Dublin str. CT_02021853  Bacteria 
 
 
-
 
SeD_A3139  CDS  NC_011205  3020388  3020885  498  competence damage-inducible protein A  YP_002216801  normal  decreased coverage  0.000242069  Salmonella enterica subsp. enterica serovar Dublin str. CT_02021853  Bacteria 
 
 
-
 
SeD_A3147  CDS  NC_011205  3026793  3027758  966  D-arabinose 5-phosphate isomerase  YP_002216809  decreased coverage  0.00650637  normal  0.0214142  Salmonella enterica subsp. enterica serovar Dublin str. CT_02021853  Bacteria 
 
 
-
 
SeD_A3148  CDS  NC_011205  3027755  3029275  1521  anaerobic nitric oxide reductase transcription regulator  YP_002216810  decreased coverage  0.00147569  normal  0.0293519  Salmonella enterica subsp. enterica serovar Dublin str. CT_02021853  Bacteria 
 
 
-
 
SeD_A3308  ncRNA  NC_011205  3183064  3183210  147  GcvB RNA    decreased coverage  0.000406754  normal  Salmonella enterica subsp. enterica serovar Dublin str. CT_02021853  Bacteria 
 
 
-
 
SeD_A3309  CDS  NC_011205  3183283  3183510  228  putative lipoprotein  YP_002216959  decreased coverage  0.00054484  normal  Salmonella enterica subsp. enterica serovar Dublin str. CT_02021853  Bacteria 
 
 
-
 
SeD_A3330  CDS  NC_011205  3207656  3209902  2247  fused phosphoenolpyruvate-protein phosphotransferase PtsP/GAF domain  YP_002216976  normal  0.0459028  decreased coverage  0.00181307  Salmonella enterica subsp. enterica serovar Dublin str. CT_02021853  Bacteria 
 
 
-
 
SeD_A3427    NC_011205  3293821  3293937  117      normal  decreased coverage  0.000571641  Salmonella enterica subsp. enterica serovar Dublin str. CT_02021853  Bacteria 
 
 
-
 
SeD_A3428  CDS  NC_011205  3294154  3294903  750  Uxu operon transcriptional regulator  YP_002217060  normal  decreased coverage  0.000900091  Salmonella enterica subsp. enterica serovar Dublin str. CT_02021853  Bacteria 
 
 
-
 
SeD_A3430  CDS  NC_011205  3295984  3297882  1899  arginine decarboxylase  YP_002217062  normal  decreased coverage  0.000516135  Salmonella enterica subsp. enterica serovar Dublin str. CT_02021853  Bacteria 
 
 
-
 
SeD_A3436  CDS  NC_011205  3302463  3303170  708  endonuclease I  YP_002217068  decreased coverage  0.00127424  hitchhiker  0.00168464  Salmonella enterica subsp. enterica serovar Dublin str. CT_02021853  Bacteria 
 
 
-
 
SeD_A3662  CDS  NC_011205  3513334  3513591  258  50S ribosomal protein L27  YP_002217275  decreased coverage  0.0000324123  normal  0.0701159  Salmonella enterica subsp. enterica serovar Dublin str. CT_02021853  Bacteria 
 
 
-
 
SeD_A3664  CDS  NC_011205  3514039  3515151  1113  octaprenyl diphosphate synthase  YP_002217276  decreased coverage  0.000479372  normal  0.0578061  Salmonella enterica subsp. enterica serovar Dublin str. CT_02021853  Bacteria 
 
 
-
 
SeD_A3745  CDS  NC_011205  3596094  3597059  966  tRNA-dihydrouridine synthase B  YP_002217354  decreased coverage  0.000576344  normal  0.0689485  Salmonella enterica subsp. enterica serovar Dublin str. CT_02021853  Bacteria 
 
 
-
 
SeD_A3746  CDS  NC_011205  3597085  3597381  297  DNA-binding protein Fis  YP_002217355  decreased coverage  0.000657586  normal  0.0919555  Salmonella enterica subsp. enterica serovar Dublin str. CT_02021853  Bacteria 
 
 
-
 
SeD_A3747  CDS  NC_011205  3597467  3598351  885  putative methyltransferase  YP_002217356  decreased coverage  0.00189132  normal  0.187537  Salmonella enterica subsp. enterica serovar Dublin str. CT_02021853  Bacteria 
 
 
-
 
SeD_A3855  CDS  NC_011205  3682166  3682687  522  shikimate kinase I  YP_002217448  decreased coverage  0.0000716125  normal  Salmonella enterica subsp. enterica serovar Dublin str. CT_02021853  Bacteria 
 
 
-
 
SeD_A4302  CDS  NC_011205  4150420  4151901  1482  guanosine pentaphosphate phosphohydrolase  YP_002217851  decreased coverage  0.00653056  normal  Salmonella enterica subsp. enterica serovar Dublin str. CT_02021853  Bacteria 
 
 
-
 
SeD_A4556  CDS  NC_011205  4394420  4395124  705  50S ribosomal protein L1  YP_002218067  normal  0.103924  decreased coverage  0.00000000000032652  Salmonella enterica subsp. enterica serovar Dublin str. CT_02021853  Bacteria 
 
 
-
 
SeD_A4750  tRNA  NC_011205  4609165  4609240  76  tRNA-Gly    decreased coverage  0.000206378  normal  Salmonella enterica subsp. enterica serovar Dublin str. CT_02021853  Bacteria 
 
 
-
 
SeD_A4751  tRNA  NC_011205  4609397  4609472  76  tRNA-Gly    decreased coverage  0.000215477  normal  Salmonella enterica subsp. enterica serovar Dublin str. CT_02021853  Bacteria 
 
 
-
 
SeD_A4753  CDS  NC_011205  4609742  4610896  1155  putative iron-sulfur cluster binding protein  YP_002218239  decreased coverage  0.00412785  normal  Salmonella enterica subsp. enterica serovar Dublin str. CT_02021853  Bacteria 
 
 
-
 
SeD_A4791  CDS  NC_011205  4644649  4645575  927  hypothetical protein  YP_002218276  decreased coverage  0.00231071  normal  Salmonella enterica subsp. enterica serovar Dublin str. CT_02021853  Bacteria 
 
 
-
 
SeD_A4865  CDS  NC_011205  4715900  4716982  1083  inner membrane protein YjgQ  YP_002218343  decreased coverage  0.000705517  normal  0.203916  Salmonella enterica subsp. enterica serovar Dublin str. CT_02021853  Bacteria 
 
 
-
 
SeD_A4899  CDS  NC_011205  4739999  4741624  1626  putative SAM-dependent methyltransferase  YP_002218368  normal  decreased coverage  0.00310573  Salmonella enterica subsp. enterica serovar Dublin str. CT_02021853  Bacteria 
 
 
-
 
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