Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   107020
Name   oriT_pKHM-1 in_silico
Organism   Citrobacter freundii strain KHM 243
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_AP014939 (47424..47574 [+], 151 nt)
oriT length   151 nt
IRs (inverted repeats)      61..67, 73..79  (ATGCTCA..TGAGCAT)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 151 nt

>oriT_pKHM-1
TGGTCGATGTGAACCCTTTTGACCGGGTTATGAATGAATTGAAAAATCGTGGCCGCAAAAATGCTCATATCCTGAGCATCCTTCAATTCGATTGGCCTGCATCAGAGGTCATCATCGAGAAGCTGAGCTGCTACATCACAGACGGTATTAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   4629 GenBank   WP_176453579
Name   mobH_HXF95_RS00340_pKHM-1 insolico UniProt ID   _
Length   989 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 989 a.a.        Molecular weight: 109277.46 Da        Isoelectric Point: 4.7510

>WP_176453579.1 MULTISPECIES: MobH family relaxase [Enterobacteriaceae]
MLKALNKLFGGRSGVIEATPSARVLPLKDVEDEEIPRYPPFAKGLPVAPLDKILATQAELIEKVRNSLGF
TVDDFNRLVLPVIQRYAAFVHLLPASESHHHRGAGGLFRHGLEVAFWATQASESVIFSIEGTPRERRDNE
PRWRLASCFSGLLHDVGKPLSDVSITDKDGSITWNPYSESLHDWAHRHGIERYFIRWRDKRHKRHEQFSL
LAWHRIIPAETQEFLSKSGPSIIEAMLEAISGTTVNQPVTRLMLRADQESVSRDLRQSRLDVDEFSYGVP
VERYVFDAIRRLVKTGKWKVNEPGAKVWHLNQGVFIAWKQLGDLYDLISQDKIPGIPRDPDTLADILIER
GFAVPNTVQEKGERAYYRYWEVLPEMLQEATGSLKILMLRLESNDLVFTNEPPSAVAAEVVGDVEDAEIE
FVDPDESDDDQDEGGVSLNDDMLAAEQEAEKALAGLGFGDAMEMLKSTSTEPEDTPAQGAAETKDSPKAT
SATTPSKGKQVKAKPKKDTEEQTEKPEAKEELSPQDIAKNAPPLANDNPLQALKDVGGGLGDIDFPFDAF
NASTDACIADEESLKNSNEAELEQPKPDFVPEEQNSLQDDDFPMFSGSDEPPSWAIEPLPMLAVESEEAS
ATTEMSQANIPNQQEKDAKTLLSEMLAGYGEASALLEQAIMPVLEGKKTLGEVLCLMKGQAVILYPEGAR
SLGAPSEVLSKLSHANAIVPDPIMPGRKVRDFSGVKAIVLAQQLSDAVVAAIKEVEASMGGYQDVFELVS
PPDSDVRKSKSAPKQQSQPMQKKNQQQKSDAGSGQAAPAKDTKGKAAQKPQKEKKGDTSSVVAGHESKPI
EEKQNVARLPKREAQPEAVVVTKVEREKELGHIEVREREEQEVREFEPPKAKTNPKDIKDEDFLPPGVTP
EKAILILKDMIQKRSGRWLVTPVLEEDGCLVTSDKAFDMIAGENIGINKHILCGMLSRAQKRPLLKKRQG
KLYLEVDET

  Protein domains


Predicted by InterproScan.

Putative helicase (TraI_2)

(51-357)


  Protein structure



No available structure.




T4CP

ID   4726 GenBank   WP_022635536
Name   traD_HXF95_RS00345_pKHM-1 insolico UniProt ID   _
Length   621 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 621 a.a.        Molecular weight: 69430.92 Da        Isoelectric Point: 7.1173

>WP_022635536.1 MULTISPECIES: conjugative transfer system coupling protein TraD [Gammaproteobacteria]
MTMSYDPLAYEMPWRPNYEKNAVAGWLAASGAALAVEQVSTMPPEPFYWMTGICGVMAMARLPKAIKLHL
LQKHLRGRDLEFISITELQKYIKDTPEDMWLGSGFLWENRHAQRVFEILKRDWTSIVGKESTVKKVVRKI
QGKRKELPIGQPWIHGVEPKEEKLMQPLKHTEGHTLIVGTTGSGKTRMFDILISQAILRGEAVIIIDPKG
DKEMRDNARRACEAMGQPERFVSFHPAFPEESVRIDPLRNFTRVTEIASRLAALIPSEAGADPFKSFGWQ
ALNNIAQGLVITHDRPNLTKLRRFLEGGAAGLVIRAVQAYSERVRPDWEAEAAPFLEKVKNGSREKIAFA
LMRFYYEIIQPEHPNSDLEGLLSMFQHDQTHFSKMVANLLPIMNMLTSGELGPLLSPDSTDLSDERQITD
SAKIINNAQVAYLGLDSLTDNMVGSAMGSIFLSDLTAVAGDRYNYGVNNRPVNIFVDEAAEVINDPFIQL
LNKGRGAKLRLFVATQTFADFAARLGSKDKALQVLGNINNTFALRIVDGETQEYIADNLPKTRLKYVMRT
QGQNSDGKEPIMHGGNQGERLMEEEADLFPAQLLGMLPNLEYIAKISGGTIVKGRLPILTQ

  Protein domains


Predicted by InterproScan.

TraM recognition site of TraD and TraG (TraG-D_C)

(471-598)

Type IV secretion-system coupling protein DNA-binding domain (TrwB_AAD_bind)

(170-292)

  Protein structure



No available structure.



ID   4727 GenBank   WP_176453583
Name   traC_HXF95_RS00430_pKHM-1 insolico UniProt ID   _
Length   814 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 814 a.a.        Molecular weight: 92319.49 Da        Isoelectric Point: 6.0244

>WP_176453583.1 type IV secretion system protein TraC [Citrobacter freundii]
MIVTIKKKLQETLIPEHLRAAGIIPVLAYDEDDHVFLMDDHSVGFGFMCEPLCGADEKVQERMNGFLNQE
FPSKTTLQFVLFRSPDINQEMYRMMGLRDGFRHELLTSVIKERINFLQHHTTDRISAKTNKGTYDNGLIQ
DLKLFVTCKVPINNNNPSESELQNLAQLRTKVESSLQTVGLRPRTMTAVNYIRIMSTILNWGPDASWRHD
AVDWEMDKPICEQIFDYGTDVEVSKNGLRLGDYHAKVMSAKKLPDVFYFGDALTYAGDLSGGNSSIKENY
MVVTNVFFPEAESTKNTLERKRQFTVNQAYGPMLKFVPVLADKKESFDTLYESMKEGAKPVKISYSVVLF
APTKERVEAAAMAARNIWRESRFELMEDKFVALPMFLNCLPFCTDRDAVRDLFRYKTMTTEQAAVVLPVF
GEWKGTGTYHAALISRNGQLMSLSLHDSNTNKNLVIAAESGSGKSFLTNELIFSYLSEGAQVWVIDAGKS
YQKLSEMLNGDFVHFEEGTHVCLNPFELIQNYEDEEDAIVSLVCAMASAKGLLDEWQISALKQVLSRLWD
EKGKEMKVDDIAERCLEGEDMRLRDIGQQLYAFTSQGSYGKYFSRKNNVSFQNQFTVLELDELQGRKHLR
QVVLLQLIYQIQQEVFLGERNRKKVVIVDEAWDLLKEGEVSTFMEHAYRKFRKYGGSVVIATQSINDLYE
NAVGRAIAENSASMYLLGQTEETVESVKRSGRLTLSEGGFHTLKTVHTIQGVYSEIFIKSKSGMGVGRLI
VGDFQKLLYSTDPVDVNAIDQFVKQGMSIPEAIKAVMRNRKQAA

  Protein domains


Predicted by InterproScan.

TraC protein (TraC_F_IV)

(21-255)

TraG P-loop domain (P-loop_TraG)

(449-808)

Family of unknown function (DUF5934) (DUF5934)

(284-434)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 45508..70711

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HXF95_RS00330 41542..41775 - 234 WP_176453578 hypothetical protein -
HXF95_RS00335 41757..42374 - 618 WP_071681756 hypothetical protein -
HXF95_RS00340 42542..45511 + 2970 WP_176453579 MobH family relaxase -
HXF95_RS00345 45508..47373 + 1866 WP_022635536 conjugative transfer system coupling protein TraD virb4
HXF95_RS00350 47423..47968 + 546 WP_023044870 hypothetical protein -
HXF95_RS00355 47925..48554 + 630 WP_022635537 DUF4400 domain-containing protein tfc7
HXF95_RS00360 48563..49009 + 447 WP_071681752 hypothetical protein -
HXF95_RS00365 49019..49396 + 378 WP_013141541 hypothetical protein -
HXF95_RS00370 49396..50058 + 663 WP_176453580 hypothetical protein -
HXF95_RS00375 50240..50383 + 144 WP_001275801 hypothetical protein -
HXF95_RS00380 50395..50757 + 363 WP_231897578 hypothetical protein -
HXF95_RS00385 50769..50936 + 168 WP_176453581 hypothetical protein -
HXF95_RS00390 50905..51186 + 282 WP_000805625 type IV conjugative transfer system protein TraL traL
HXF95_RS00395 51183..51809 + 627 WP_022635539 TraE/TraK family type IV conjugative transfer system protein traE
HXF95_RS00400 51793..52710 + 918 WP_022635540 type-F conjugative transfer system secretin TraK traK
HXF95_RS00405 52710..54029 + 1320 WP_071681777 TraB/VirB10 family protein traB
HXF95_RS00410 54026..54604 + 579 WP_010845916 type IV conjugative transfer system lipoprotein TraV traV
HXF95_RS00415 54617..55000 + 384 WP_089140452 TraA family conjugative transfer protein -
HXF95_RS00420 55204..60735 + 5532 WP_176453582 Ig-like domain-containing protein -
HXF95_RS00425 60884..61591 + 708 WP_089140450 DsbC family protein trbB
HXF95_RS00430 61588..64032 + 2445 WP_176453583 type IV secretion system protein TraC virb4
HXF95_RS00435 64047..64364 + 318 WP_013141553 hypothetical protein -
HXF95_RS00440 64361..64891 + 531 WP_022635546 S26 family signal peptidase -
HXF95_RS00445 64854..66119 + 1266 WP_089140448 TrbC family F-type conjugative pilus assembly protein traW
HXF95_RS00450 66116..66787 + 672 WP_071681744 EAL domain-containing protein -
HXF95_RS00455 66808..67791 + 984 WP_231398180 TraU family protein traU
HXF95_RS00460 67907..70711 + 2805 WP_071681742 conjugal transfer mating pair stabilization protein TraN traN
HXF95_RS00465 70749..71612 - 864 WP_022635550 hypothetical protein -
HXF95_RS00470 71734..72375 - 642 WP_041979271 hypothetical protein -
HXF95_RS00475 72669..72989 + 321 WP_013141561 hypothetical protein -
HXF95_RS00480 73294..73479 + 186 WP_231858731 hypothetical protein -
HXF95_RS00485 73701..74669 + 969 WP_113620223 AAA family ATPase -
HXF95_RS00490 74680..75585 + 906 WP_114822855 hypothetical protein -

Host bacterium

ID   7456 GenBank   NZ_AP014939
Plasmid name   pKHM-1 Incompatibility group   IncA/C2
Plasmid size   166258 bp Coordinate of oriT [Strand]   47424..47574 [+]
Host baterium   Citrobacter freundii strain KHM 243

Cargo genes

Drug resistance gene   aadA2, aac(6')-Iae, qacE, sul1, blaKHM-1
Virulence gene   -
Metal resistance gene   merA, merP, merT, merR
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -