Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   118500
Name   oriT_MSB1_1H|3 in_silico
Organism   Citrobacter freundii strain MSB1_1H isolate MSB1_1H
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_LR890183 (46484..46634 [+], 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_MSB1_1H|3
TGGTCGATGTGAACCCGTTTGACCGGGTTATGAATGAGTTGAAAAGTCGTGGCCGCAAGAACGCTCATATCCTGAGCATCCTTCAATTCGACTGGCCCGCATCGGAGGTCATCATCGAGAAGCTGAGCTGTTACATCACAGATGGGATTAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   11745 GenBank   WP_000909947
Name   mobH_JMV71_RS24630_MSB1_1H|3 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: 109404.96 Da        Isoelectric Point: 4.8922

>WP_000909947.1 MULTISPECIES: MobH family relaxase [Gammaproteobacteria]
MLKALHKLFGGRSGAIETAPSARVLPLKDVEDEEIPRYPPFAKGLPVAPLDKILATQAELIEKVRNSLGF
TVDDFNRLVLPVIQRYAAFVHLLPASESHHHRGAGGLFRHGLEVAFWATQASESVIFSIEGTPRERRDNE
PRWRLASCFSGLLHDVGKPLSDVSITDKDGSITWNPYSESLHDWAYRHGIDRYFIRWRDKRHKRHEQFSL
LAWHRIIPAETQEFLSKSGPSIIEAMLEAISGTSVNQPVTKLMLRADQESVSRDLRQSRLDVNEFSYGVP
VERYVFDAIRRLVKTGKWKVNEPGAKVWHLNQGVFIAWKQLGDLYDLISQDKIPGIPRDPDTLADILIER
GFAVPNTVQEKGERAYYRYWEVLPEMLQEAAGPVKILMLRLESNDLVFTTEPPAAVTGEVVGDVEDAEIE
FVDPEEADEDQAEGDAGLNNDMLAAELEAEKALAGLGFGDAMAMLKSTSDIAEEKPEQEDTESTELPKPD
ASKKGKQQSKPGKARAEKQPQKPEVKEDLSPQDIAKNAPPLANDDPLQALKDVGGGLGDIDFPFDVFNAS
AETACTDATNLEIPDITEPEKQEEQPKPDFVPQEQNSLQNGDFPIFSDSDEPPSWAIEPLPMLTDTPEQT
IPAPDMQHAGKPKELEKDAKTLLSEMLAGYGEASTLLEQAIMPVLEGKTTLGEVLCLMKGQAVILYPEGA
RSLGAPSEVLSKLSHANAIVPDPIMPGRKVRDFSGVKAIVLVDQLSDAVVAAIKDAEASMGGYQEAFELV
SPPGSGVSKNKSAPKQQSRKKTQQQKPEVDAGAGSEQKTKDKSLQQQPKEKQGNVASLVEEQKRKPVQDQ
EKQNVARLPKREAQPVAPKPKVEHERELGHVEVRERDEPEVREFEPPKAKTNPKDINEEDFLPSGVTPEK
ALLMLKDMIQKRSGRWLVTPVLEEDGCLVTSVKAFDMIAGENVGISKHILYGLLSRAQRRPLLKKRQGKL
YLEVDKA

  Protein domains


Predicted by InterproScan.

Putative helicase (TraI_2)

(51-357)


  Protein structure



No available structure.




T4CP

ID   13756 GenBank   WP_000178858
Name   traD_JMV71_RS24635_MSB1_1H|3 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   13757 GenBank   WP_012766329
Name   traC_JMV71_RS24715_MSB1_1H|3 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: 44568..69672

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
JMV71_RS24620 40608..40841 - 234 WP_001191893 hypothetical protein -
JMV71_RS24625 40823..41440 - 618 WP_012766323 hypothetical protein -
JMV71_RS24630 41608..44571 + 2964 WP_000909947 MobH family relaxase -
JMV71_RS24635 44568..46433 + 1866 WP_000178858 conjugative transfer system coupling protein TraD virb4
JMV71_RS24640 46483..47028 + 546 WP_023356350 hypothetical protein -
JMV71_RS24645 46985..47614 + 630 WP_057521214 DUF4400 domain-containing protein tfc7
JMV71_RS24650 47625..48071 + 447 WP_057521213 hypothetical protein -
JMV71_RS24655 48081..48458 + 378 WP_000869260 hypothetical protein -
JMV71_RS24660 48458..49120 + 663 WP_057521212 hypothetical protein -
JMV71_RS24665 49299..49442 + 144 WP_023356351 hypothetical protein -
JMV71_RS24670 49455..49802 + 348 WP_001102160 hypothetical protein -
JMV71_RS24675 49945..50226 + 282 WP_000805626 type IV conjugative transfer system protein TraL traL
JMV71_RS24680 50223..50849 + 627 WP_057521211 TraE/TraK family type IV conjugative transfer system protein traE
JMV71_RS24685 50833..51750 + 918 WP_012766326 type-F conjugative transfer system secretin TraK traK
JMV71_RS24690 51747..53063 + 1317 WP_057521210 TraB/VirB10 family protein traB
JMV71_RS24695 53060..53638 + 579 WP_039272410 type IV conjugative transfer system lipoprotein TraV traV
JMV71_RS24700 53642..54034 + 393 WP_012766327 TraA family conjugative transfer protein -
JMV71_RS24705 54235..59721 + 5487 WP_057521209 Ig-like domain-containing protein -
JMV71_RS24710 59870..60577 + 708 WP_057521208 DsbC family protein -
JMV71_RS24715 60574..63021 + 2448 WP_012766329 type IV secretion system protein TraC virb4
JMV71_RS24720 63036..63353 + 318 WP_000364398 hypothetical protein -
JMV71_RS24725 63350..63880 + 531 WP_000672456 S26 family signal peptidase -
JMV71_RS24730 63843..65111 + 1269 WP_057521207 TrbC family F-type conjugative pilus assembly protein traW
JMV71_RS24735 65108..65785 + 678 WP_012766331 EAL domain-containing protein -
JMV71_RS24740 65779..66783 + 1005 WP_000911304 TraU family protein traU
JMV71_RS24745 66934..69672 + 2739 WP_057521206 conjugal transfer mating pair stabilization protein TraN traN
JMV71_RS24750 69711..70571 - 861 WP_000679674 hypothetical protein -
JMV71_RS24755 70683..71333 - 651 WP_000796641 hypothetical protein -
JMV71_RS24760 71624..71944 + 321 WP_000547567 hypothetical protein -
JMV71_RS24765 72189..72440 + 252 WP_226453752 hypothetical protein -
JMV71_RS24770 72661..73629 + 969 WP_001553257 AAA family ATPase -
JMV71_RS24775 73641..74546 + 906 WP_000739141 hypothetical protein -

Host bacterium

ID   18933 GenBank   NZ_LR890183
Plasmid name   MSB1_1H|3 Incompatibility group   IncA/C
Plasmid size   126853 bp Coordinate of oriT [Strand]   46484..46634 [+]
Host baterium   Citrobacter freundii strain MSB1_1H isolate MSB1_1H

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -