Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   103427
Name   oriT_pIB2020_IncA in_silico
Organism   Enterobacter kobei strain IB2020
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP059480 (26565..26715 [-], 151 nt)
oriT length   151 nt
IRs (inverted repeats)      12..17, 24..29  (AACCCG..CGGGTT)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 151 nt

>oriT_pIB2020_IncA
TGGTCGATGTGAACCCGTTTGACCGGGTTATGAATGAGTTGAAAAGTCGTGGCCGCAAGAACGCTCATATCCTGAGCATCCTTCAATTCGACTGGCCCGCATCGGAGGTCATCATCGAGAAGCTGAGCTGTTACATCACAGATGGGATTAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2554 GenBank   WP_058662807
Name   TraI_2_H1R18_RS00140_pIB2020_IncA insolico UniProt ID   A0A221KLA3
Length   987 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 987 a.a.        Molecular weight: 109306.91 Da        Isoelectric Point: 4.9372

>WP_058662807.1 MULTISPECIES: MobH family relaxase [Gammaproteobacteria]
MLKALHKLFGGRSGAIETAPSARVLPLKDVEDEEIPRYPPFAKGLPVAPLDKILATQAELIEKVRNSLGF
TVDDFNRLVLPVIQRYAAFVHLLPASESHHHRGAGGLFRHGLEVAFWATQASESVIFSIEGTPRERRDNE
PRWRLASCFSGLLHDVGKPLSDVSITDKDGSITWNPYSESLHDWAYRHGIDRYFIRWRDKRHKRHEQFSL
LAWHRIIPAETQEFLSKSGPSIIEAMLEAISGTSVNQPVTKLMLRADQESVSRDLRQSRLDVNEFSYGVP
VERYVFDAIRRLVKTGKWKVNEPGAKVWHLNQGVFIAWKQLGDLYDLISQDKIPGIPRDPDTLADILIER
GFAVPNTVQEKGERAYYRYWEVLPEMLQEAAGPVKILMLRLESNDLVFTTEPPAAVTGEVVGDVEDAEIE
FVDPEEADEDQAEGDAGLNNDMLAAELEAEKALAGLGFGDAMAMLKSTSDIAEEKPEQEDTESTELPKPD
ASKKGKQQSKPGKARAEKQPQKPEVKEDLSPQDIAKNAPPLANDDPLQALKDVGGGLGDIDFPFDVFNAS
AETACTDATNLAIPDITEPVKQEEQPKPDFVPQEQNSLQNGDFPIFSDSDEPPSWAIEPLPMLTDTPEQT
IPAPDMQHAGKPKELEKDAKTLLSEMLAGYGEASTLLEQAIMPVLEGKTTLGEVLCLMKGQAVILYPEGA
RSLGAPSEVLSKLSHANAIVPDPIMPGRKVRDFSGVKAIVLVDQLSDAVVAAIKDAEASMGGYQEAFELV
SPPGSGVSKNKSAPKQQSRKKTQQQKPEVDAGAGSEQKTKDKSLQQQPKEKQGNVASLVEEQKRKPVQDQ
EKQNVARLPKREAQPVASKPKVEHERELGHVEVRERDEPEVREFEPPKAKTNPKDINEEDFLPSGVTPEK
ALLMLKDMIQKRSGRWLVTPVLEEDGCLVTSVKAFDMIAGENVGISKHILYGLLSRAQRRPLLKKRQGKL
YLEVDKA

  Protein domains


Predicted by InterproScan.

Putative helicase (TraI_2)

(51-357)


  Protein structure


Source ID Structure
AlphaFold DB A0A221KLA3


T4CP

ID   2343 GenBank   WP_051479468
Name   traC_H1R18_RS00040_pIB2020_IncA insolico UniProt ID   _
Length   815 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 815 a.a.        Molecular weight: 92523.78 Da        Isoelectric Point: 5.9204

>WP_051479468.1 MULTISPECIES: type IV secretion system protein TraC [Gammaproteobacteria]
MIITIKKKLEETLIPEHLRAAGIIPVLAYDEDDHVFLMDDQSVGFGFMCEPLCGADEKVQERMNGFLNQE
FPSKTSLQFVLFRSPDINQEMYRMMGLRDGFRHELLTSVIKERINFLQHHTTDRIFAKTSKGIYDNGLIQ
DLKLFVTCKVPIKNNNPTESELQHLAQIRTKVESSLQTVGLRPRTMTAVNYIRIMSTILNWGPDASWRHD
SVDWEMDKPICEQIFDYGTDVEVSKNGIRLGDYHAKVMSAKKLPDVFYFGDALTYAGDLSGGNSSIKENY
MVVTNVFFPEAESTKNTLERKRQFTVNQAYGPMLKFVPVLADKKESFDTLYESMKEGAKPVKITYSVVLF
APTKERVEAAAMAARNIWRESRFELMEDKFVALPMFLNCLPFCTDRDAVRDLFRYKTMTTEQAAVVLPVF
GEWKGTGTYHAALISRNGQLMSLSLHDSNTNKNLVIAAESGSGKSFLTNELIFSYLSEGAQVWVIDAGKS
YQKLSEMLNGDFVHFEEGTHVCLNPFELIQNYDDEEDAIVSLVCAMASAKGLLDEWQISALKQVLSRLWE
EKGKEMKVDDIAERCLEEENDQRLKDIGQQLYAFTSKGSYGKYFSQKNNVSFQNQFTVLELDELQGRKHL
RQVVLLQLIYQIQQEVFLGERNRKKVVIVDEAWDLLKEGEVSTFMEHAYRKFRKYGGSVVIATQSINDLY
ENAVGRAIAENSASMYLLGQTEETVESVKRSGRLTLSDGGFHTLKTVHTIQGVYSEIFIKSKSGMGVGRL
IVGDFQKLLYSTDPVDVNAIDQFVKQGMSIPEAIKAVMRSRKQAA

  Protein domains


Predicted by InterproScan.

TraG P-loop domain (P-loop_TraG)

(449-809)

Family of unknown function (DUF5934) (DUF5934)

(284-434)

TraC protein (TraC_F_IV)

(21-255)

  Protein structure



No available structure.



ID   2344 GenBank   WP_000178858
Name   traD_H1R18_RS00135_pIB2020_IncA 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: 69248.76 Da        Isoelectric Point: 7.1093

>WP_000178858.1 MULTISPECIES: conjugative transfer system coupling protein TraD [Gammaproteobacteria]
MTMSYDPLAYEMPWRPNYEKNAVAGWMAASCAALAVEQVSTMPSEPFYWMTGICGVMAMARLPKAIKLHL
LQKHLKGRDLEFISIAELQKYIKDTPEDMWLGSGFLWENRHAQRVFEILKRDWTSIVGKESTVKKVVRKI
QGKKKELPIGQPWIHGVEPKEEKLMQPLKHTEGHSLIVGTTGSGKTRMFDILISQAILRGEAVIIIDPKG
DKEMRDNARRACEAMGQPERFVSFHPAFPEESVRIDPLRNFTRVTEIASRLAALIPSEAGADPFKSFGWQ
ALNNIAQGLVLTHDRPNLTKLRRFLEGGAAGLVIKAVQAYSERVKPDWEAEAAAYLEKAKNGSREKIAFA
LMKFYYDIIQPEHPNSDLEGLLSMFQHDQTHFSKMVANLLPIMNMLTSGELGPLLSPDSSDLSDERQITD
SAKIINNAQVAYLGLDSLTDNMVGSAMGSIFLSDLTAVAGDRYNYGVNNRPVNIFVDEAAEVINDPFIQL
LNKGRGAKLRLFVATQTFADFAARLGSKDKALQVLGNINNTFALRIVDGETQEYIADNLPKTRLKYVMRT
QGQNTDGKEPIMHGGNQGERLMEEEADLFPAQLLGMLPNLEYIAKISGGTIVKGRLPILTQ

  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)

(170-297)

  Protein structure



No available structure.



ID   2345 GenBank   WP_051479468
Name   traC_H1R18_RS00925_pIB2020_IncA insolico UniProt ID   _
Length   815 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 815 a.a.        Molecular weight: 92523.78 Da        Isoelectric Point: 5.9204

>WP_051479468.1 MULTISPECIES: type IV secretion system protein TraC [Gammaproteobacteria]
MIITIKKKLEETLIPEHLRAAGIIPVLAYDEDDHVFLMDDQSVGFGFMCEPLCGADEKVQERMNGFLNQE
FPSKTSLQFVLFRSPDINQEMYRMMGLRDGFRHELLTSVIKERINFLQHHTTDRIFAKTSKGIYDNGLIQ
DLKLFVTCKVPIKNNNPTESELQHLAQIRTKVESSLQTVGLRPRTMTAVNYIRIMSTILNWGPDASWRHD
SVDWEMDKPICEQIFDYGTDVEVSKNGIRLGDYHAKVMSAKKLPDVFYFGDALTYAGDLSGGNSSIKENY
MVVTNVFFPEAESTKNTLERKRQFTVNQAYGPMLKFVPVLADKKESFDTLYESMKEGAKPVKITYSVVLF
APTKERVEAAAMAARNIWRESRFELMEDKFVALPMFLNCLPFCTDRDAVRDLFRYKTMTTEQAAVVLPVF
GEWKGTGTYHAALISRNGQLMSLSLHDSNTNKNLVIAAESGSGKSFLTNELIFSYLSEGAQVWVIDAGKS
YQKLSEMLNGDFVHFEEGTHVCLNPFELIQNYDDEEDAIVSLVCAMASAKGLLDEWQISALKQVLSRLWE
EKGKEMKVDDIAERCLEEENDQRLKDIGQQLYAFTSKGSYGKYFSQKNNVSFQNQFTVLELDELQGRKHL
RQVVLLQLIYQIQQEVFLGERNRKKVVIVDEAWDLLKEGEVSTFMEHAYRKFRKYGGSVVIATQSINDLY
ENAVGRAIAENSASMYLLGQTEETVESVKRSGRLTLSDGGFHTLKTVHTIQGVYSEIFIKSKSGMGVGRL
IVGDFQKLLYSTDPVDVNAIDQFVKQGMSIPEAIKAVMRSRKQAA

  Protein domains


Predicted by InterproScan.

TraG P-loop domain (P-loop_TraG)

(449-809)

Family of unknown function (DUF5934) (DUF5934)

(284-434)

TraC protein (TraC_F_IV)

(21-255)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 5586..28631

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
H1R18_RS00005 (H1R18_00005) 1166..2273 - 1108 Protein_0 IS3 family transposase -
H1R18_RS00010 (H1R18_00010) 2337..3764 - 1428 Protein_1 conjugal transfer mating pair stabilization protein TraN -
H1R18_RS00015 (H1R18_00015) 3915..4917 - 1003 Protein_2 TraU family protein -
H1R18_RS00020 (H1R18_00020) 4911..5354 - 444 WP_244637333 EAL domain-containing protein -
H1R18_RS26570 5371..5589 - 219 WP_244637334 hypothetical protein -
H1R18_RS00025 (H1R18_00025) 5586..6854 - 1269 WP_039272404 TrbC family F-type conjugative pilus assembly protein traW
H1R18_RS00030 (H1R18_00030) 6817..7347 - 531 WP_000672456 S26 family signal peptidase -
H1R18_RS00035 (H1R18_00035) 7344..7661 - 318 WP_000364398 hypothetical protein -
H1R18_RS00040 (H1R18_00040) 7676..10123 - 2448 WP_051479468 type IV secretion system protein TraC virb4
H1R18_RS00045 (H1R18_00045) 10120..10827 - 708 WP_001259344 DsbC family protein -
H1R18_RS00050 (H1R18_00050) 10976..13582 - 2607 Protein_10 hypothetical protein -
H1R18_RS00055 (H1R18_00055) 13670..14077 + 408 WP_048242260 transposase -
H1R18_RS00060 (H1R18_00060) 14074..14424 + 351 WP_021567584 IS66 family insertion sequence element accessory protein TnpB -
H1R18_RS00065 (H1R18_00065) 14455..16047 + 1593 WP_044596437 IS66 family transposase -
H1R18_RS00070 (H1R18_00070) 16067..18964 - 2898 WP_244637335 Ig-like domain-containing protein -
H1R18_RS00075 (H1R18_00075) 19165..19557 - 393 WP_012766327 TraA family conjugative transfer protein -
H1R18_RS00080 (H1R18_00080) 19561..20139 - 579 WP_039272410 type IV conjugative transfer system lipoprotein TraV traV
H1R18_RS00085 (H1R18_00085) 20136..21452 - 1317 WP_039272412 TraB/VirB10 family protein traB
H1R18_RS00090 (H1R18_00090) 21449..22366 - 918 WP_012766326 type-F conjugative transfer system secretin TraK traK
H1R18_RS00095 (H1R18_00095) 22350..22976 - 627 WP_039272415 TraE/TraK family type IV conjugative transfer system protein traE
H1R18_RS00100 (H1R18_00100) 22973..23254 - 282 WP_000805626 type IV conjugative transfer system protein TraL traL
H1R18_RS00105 (H1R18_00105) 23397..23744 - 348 WP_039272417 hypothetical protein -
H1R18_RS00110 (H1R18_00110) 24079..24741 - 663 WP_039272419 hypothetical protein -
H1R18_RS00115 (H1R18_00115) 24741..25118 - 378 WP_000869260 hypothetical protein -
H1R18_RS00120 (H1R18_00120) 25128..25574 - 447 WP_039272421 hypothetical protein -
H1R18_RS00125 (H1R18_00125) 25585..26214 - 630 WP_000743448 DUF4400 domain-containing protein tfc7
H1R18_RS00130 (H1R18_00130) 26171..26716 - 546 WP_023356350 hypothetical protein -
H1R18_RS00135 (H1R18_00135) 26766..28631 - 1866 WP_000178858 conjugative transfer system coupling protein TraD virb4
H1R18_RS00140 (H1R18_00140) 28628..31591 - 2964 WP_058662807 MobH family relaxase -
H1R18_RS00145 (H1R18_00145) 31759..32376 + 618 WP_012766323 hypothetical protein -
H1R18_RS00150 (H1R18_00150) 32358..32591 + 234 WP_039272424 hypothetical protein -

Host bacterium

ID   3870 GenBank   NZ_CP059480
Plasmid name   pIB2020_IncA Incompatibility group   IncA/C
Plasmid size   165722 bp Coordinate of oriT [Strand]   26565..26715 [-]
Host baterium   Enterobacter kobei strain IB2020

Cargo genes

Drug resistance gene   sul1, qacE, catB2, ant(3'')-Ia, aph(3')-XV, blaVIM-1, ARR-3, catB3, blaOXA-1, aac(6')-Ib-cr, qnrS2
Virulence gene   -
Metal resistance gene   merR, merT, merP, merA
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -