Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   113930
Name   oriT_pCf587 in_silico
Organism   Citrobacter freundii strain 33587
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_MG053108 (47408..47558 [+], 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_pCf587
TGGTCGATGTGAACCCGTTTGACCGGGTTATGAATGAGTTGAAAAGTCGTGGCCGCAAGAACGCTCATATCCTGAGCATCCTTCAATTCGACTGGCCCGCATCGGAGGTCATCATCGAGAAGCTGAGCTGTTACATCACAGATGGGATTAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   8944 GenBank   WP_172692072
Name   mobH_HTQ01_RS00345_pCf587 insolico UniProt ID   _
Length   987 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 987 a.a.        Molecular weight: 109388.97 Da        Isoelectric Point: 4.8922

>WP_172692072.1 MULTISPECIES: MobH family relaxase [Enterobacteriaceae]
MLKALHKLFGGRSGAIETAPSARVLPLKDVEDEEIPRYPPFAKGLPVAPLDKILATQAELIEKVRNSLGF
TVDDFNRLVLPVIQRYAAFVHLLPASESHHHRGAGGLFRHGLEVAFWATQASESVIFSIEGTPRERRDNE
PRWRLASCFSGLLHDVGKPLSDVSITDKDGSITWNPYSESLHDWAYRHGIDRYFIRWRDKRHKRHEQFSL
LAWHRIIPAETQEFLSKSGPSIIEAMLEAISGTSVNQPVTKLMLRADQESVSRDLRQSRLDVNEFSYGVP
VERYVFDAIRRLVKTGKWKVNEPGAKVWHLNQGVFIAWKQLGDLYDLISQDKIPGIPRDPDTLADILIER
GFAVPNTVQEKGERAYYRYWEVLPEMLQEAAGPVKILMLRLESNDLVFTTEPPAAVTGEVVGDVEDAEIE
FVDPEEADEDQAEGDAGLNNDMLAAELEAEKALAGLGFGDAMAMLKSTSDIAEEKPEQEDTESTELPKPD
ASKKGKQQSKPGKARAEKQPQKPEVKEDLSPQDIAKNAPPLANDDPLQALKDVGGGLGDIDFPFDVFNAS
AETACTDATNLEIPDITEPEKQEEQPKPDFVPQEQNSLQNGDFPIFSDSDEPPSWAIEPLPMLTDTPEQT
IPAPDMQHAGKPKELEKDAKTLLSEMLAGYGEASTLLEQAIMPVLEGKTTLGEVLCLMKGQAVILYPEGA
RSLGAPSEVLSKLSHANAIVPDPIMPGRKVRDFSGVKAIVLVDQLSDAVVAAIKDAEASMGGYQEAFELV
SPPGSGVSKNKSAPKQQSRKKTQQQKPEVDAGAGAEQKTKDKSLQQQPKEKQGNVASLVEEQKRKPVQDQ
EKQNVARLPKREAQPVAPKPKVEHERELGHVEVRERDEPEVREFEPPKAKTNPKDINEEDFLPSGVTPEK
ALLMLKDMIQKRSGRWLVTPVLEEDGCLVTSVKAFDMIAGENVGISKHILYGLLSRAQRRPLLKKRQGKL
YLEVDKA

  Protein domains


Predicted by InterproScan.

Putative helicase (TraI_2)

(51-357)


  Protein structure



No available structure.




T4CP

ID   10388 GenBank   WP_172692073
Name   traD_HTQ01_RS00350_pCf587 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: 69276.81 Da        Isoelectric Point: 7.1093

>WP_172692073.1 MULTISPECIES: conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MTMSYDPLAYEMPWRPNYEKNAVAGWMAASCAALAVEQVSTMPSEPFYWMTGICGVMAMARLPKAIKLHL
LQKHLKGRDLEFISIAELQKYIKDTPEDMWLGSGFLWENRHAQRVFEILKRDWTSIVGKESTVKKVVRKI
QGKKKELPIGQPWIHGVEPKEEKLMQPLKHTEGHSLIVGTTGSGKTRMFDILISQAILRGEAVIIIDPKG
DKEMRDNARRACEAMGQPERFVSFHPAFPEESVRIDPLRNFTRVTEIASRLAALIPSEAGADPFKSFGWQ
ALNNIAQGLVLTHDRPNLTKLRRFLEGGAAGLVIKAVQAYSERVKPDWEAEAVAYLEKAKNGSREKIAFA
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)

(170-294)

  Protein structure



No available structure.



ID   10389 GenBank   WP_012766329
Name   traC_HTQ01_RS00430_pCf587 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: 92529.82 Da        Isoelectric Point: 5.8328

>WP_012766329.1 MULTISPECIES: type IV secretion system protein TraC [Gammaproteobacteria]
MIITIKKKLEETLIPEHLRAAGIIPVLAYDEDDHVFLMDDQSVGFGFMCEPLCGADEKVQERMNGFLNQE
FPSKTSLQFVLFRSPDINQEMYRMMGLRDGFRHELLTSVIKERINFLQHHTTDRILAKTSKGIYDNGLIQ
DLKLFVTCKVPIKNNNPTESELQYLAQIRTKVESSLQTVGLRPRTMTAVNYIRIMSTILNWGPDASWRHD
SVDWEMDKPICEQIFDYGTDVEVSKNGIRLGDYHAKVMSAKKLPDVFYFGDALTYAGDLSGGNSSIKENY
MVVTNVFFPEAESTKNTLERKRQFTVNQAYGPMLKFVPVLADKKESFDTLYESMKEGAKPVKITYSVVLF
APTKERVEAAAMAARNIWRESRFELMEDKFVALPMFLNCLPFCTDREAVRDLFRYKTMTTEQAAVVLPVF
GEWKGTGTYHAALISRNGQLMSLSLHDSNTNKNLVIAAESGSGKSFLTNELIFSYLSEGAQVWVIDAGKS
YQKLSEMLNGDFVHFEEGTHVCLNPFELIQNYDDEEDAIVSLVCAMASAKGLLDEWQISALKQVLSRLWE
EKGKEMKVDDIAERCLEEENDQRLKDIGQQLYAFTSKGSYGKYFSQKNNVSFQNQFTVLELDELQGRKHL
RQVVLLQLIYQIQQEVFLGERNRKKVVIVDEAWDLLKEGEVSTFMEHAYRKFRKYGGSVVIATQSINDLY
ENAVGRAIAENSASMYLLGQTEETVESVKRSGRLTLSDGGFHTLKTVHTIQGVYSEIFIKSKSGMGVGRL
IVGDFQKLLYSTDPVDVNAIDQFVKQGMSIPEAIKAVMRSRKQAA

  Protein domains


Predicted by InterproScan.

TraC protein (TraC_F_IV)

(21-255)

TraG P-loop domain (P-loop_TraG)

(449-809)

Family of unknown function (DUF5934) (DUF5934)

(284-434)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 45492..70596

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HTQ01_RS00335 (pCf587_0072) 41532..41765 - 234 WP_001191893 hypothetical protein -
HTQ01_RS00340 (pCf587_0073) 41747..42364 - 618 WP_012766323 hypothetical protein -
HTQ01_RS00345 (pCf587_0074) 42532..45495 + 2964 WP_172692072 MobH family relaxase -
HTQ01_RS00350 (pCf587_0075) 45492..47357 + 1866 WP_172692073 conjugative transfer system coupling protein TraD virb4
HTQ01_RS00355 (pCf587_0076) 47368..47952 + 585 WP_000332867 hypothetical protein -
HTQ01_RS00360 (pCf587_0077) 47909..48538 + 630 WP_057521214 DUF4400 domain-containing protein tfc7
HTQ01_RS00365 48549..48995 + 447 WP_099360028 hypothetical protein -
HTQ01_RS00370 (pCf587_0079) 49005..49382 + 378 WP_000869260 hypothetical protein -
HTQ01_RS00375 (pCf587_0080) 49382..50044 + 663 WP_057521212 hypothetical protein -
HTQ01_RS00380 (pCf587_0081) 50223..50366 + 144 WP_023356351 hypothetical protein -
HTQ01_RS00385 (pCf587_0082) 50379..50726 + 348 WP_001102160 hypothetical protein -
HTQ01_RS00390 (pCf587_0083) 50869..51150 + 282 WP_000805626 type IV conjugative transfer system protein TraL traL
HTQ01_RS00395 (pCf587_0084) 51147..51773 + 627 WP_057521211 TraE/TraK family type IV conjugative transfer system protein traE
HTQ01_RS00400 (pCf587_0085) 51757..52674 + 918 WP_012766326 type-F conjugative transfer system secretin TraK traK
HTQ01_RS00405 (pCf587_0086) 52671..53987 + 1317 WP_057521210 TraB/VirB10 family protein traB
HTQ01_RS00410 (pCf587_0087) 53984..54562 + 579 WP_039272410 type IV conjugative transfer system lipoprotein TraV traV
HTQ01_RS00415 (pCf587_0088) 54566..54958 + 393 WP_012766327 TraA family conjugative transfer protein -
HTQ01_RS00420 (pCf587_0089) 55159..60645 + 5487 WP_057521209 Ig-like domain-containing protein -
HTQ01_RS00425 (pCf587_0090) 60794..61501 + 708 WP_001259344 DsbC family protein -
HTQ01_RS00430 (pCf587_0091) 61498..63945 + 2448 WP_012766329 type IV secretion system protein TraC virb4
HTQ01_RS00435 (pCf587_0092) 63960..64277 + 318 WP_000364398 hypothetical protein -
HTQ01_RS00440 (pCf587_0093) 64274..64804 + 531 WP_000672456 S26 family signal peptidase -
HTQ01_RS00445 (pCf587_0094) 64767..66035 + 1269 WP_001553264 TrbC family F-type conjugative pilus assembly protein traW
HTQ01_RS00450 (pCf587_0095) 66032..66709 + 678 WP_012766331 EAL domain-containing protein -
HTQ01_RS00455 (pCf587_0096) 66703..67707 + 1005 WP_000911304 TraU family protein traU
HTQ01_RS00460 (pCf587_0097) 67846..70596 + 2751 WP_234805065 conjugal transfer mating pair stabilization protein TraN traN
HTQ01_RS00465 (pCf587_0098) 70634..71494 - 861 WP_012766333 hypothetical protein -
HTQ01_RS00470 (pCf587_0099) 71606..72256 - 651 WP_000796641 hypothetical protein -
HTQ01_RS00475 (pCf587_0100) 72547..72867 + 321 WP_012766334 hypothetical protein -
HTQ01_RS00480 (pCf587_0101) 73178..73363 + 186 WP_001186892 hypothetical protein -
HTQ01_RS00485 (pCf587_0102) 73584..74552 + 969 WP_001553257 AAA family ATPase -
HTQ01_RS00490 (pCf587_0103) 74693..75469 + 777 WP_234805066 hypothetical protein -

Host bacterium

ID   14365 GenBank   NZ_MG053108
Plasmid name   pCf587 Incompatibility group   IncA/C
Plasmid size   191541 bp Coordinate of oriT [Strand]   47408..47558 [+]
Host baterium   Citrobacter freundii strain 33587

Cargo genes

Drug resistance gene   blaTEM-1B, aph(3')-VIa, catA1, ant(3'')-Ia, qacE, sul1, blaPER-2, ere(A)
Virulence gene   -
Metal resistance gene   merE, merD, merA, merC, merP, merT, merR
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -