Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   102237
Name   oriT_ALD9|unnamed in_silico
Organism   Shewanella sp. ALD9
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_PJCD01000039 (123604..123754 [-], 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_ALD9|unnamed
TGGTCGATGTGAACCCTTTTGACCGGGTTATGAATGAATTGAAAAATCGTGGCCGCAAAAATGCTCATATCCTGAGCATCCTTCAATTCGATTGGCCTGCATCAGAGGTCATCATCGAGAAGCTGAGCTGCTACATCACAGACGGTATTAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1725 GenBank   WP_022635535
Name   mobH_CXF88_RS16240_ALD9|unnamed 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: 109302.52 Da        Isoelectric Point: 4.7694

>WP_022635535.1 MULTISPECIES: MobH family relaxase [Gammaproteobacteria]
MLKALNKLFGGRSGVIEATPSARVLPLKDVEDEEIPRYPPFAKGLPVAPLDKILATQAELIEKVRNSLGF
TVDDFNRLVLPVIQRYAAFVHLLPASESHHHRGAGGLFRHGLEVAFWATQASESVIFSIEGTPRERRDNE
PRWRLASCFSGLLHDVGKPLSDVSITDKDGSITWNPYSESLHDWAHRHGIERYFIRWRDKRHKRHEQFSL
LAWHRIIPAETQEFLSKSGPSIIEAMLEAISGTTVNQPVTRLMLRADQESVSRDLRQSRLDVDEFSYGVP
VERYVFDAIRRLVKTGKWKVNEPGAKVWHLNQGVFIAWKQLGDLYDLISQDKIPGIPRDPDTLADILIER
GFAVPNTVQEKGERAYYRYWEVLPEMLQEATGSLKILMLRLESNDLVFTNEPPSAVAAEVVGDVEDAEIE
FVDPDESDDDQDEGGVSLNDDMLAAEQEAEKALAGLGFGDAMEMLKSTSTEPEDTPAQGAAETKDSPKAP
SATTPSKGKQVKAKPKKDTEEQTEKPEAKEELSPQDIAKNAPPLANDNPLQALKDVGGGLGDIDFPFDAF
NASTDACIADEESLKNSNEAELEQPKPDFVPEEQNSLQDDDFPMFSGSDEPPSWAIEPLPMLAVESEEAS
ATTEMSQANIPNQQEKDSKTLLSEMLAGYGEASALLEQAIMPVLEGKKTLGEVLCLMKGQAVILYPEGAR
SLGAPSEVLSKLSHANAIVPDPIMPGRKVRDFSGVKAIVLAQQLSDAVVAAIKEVEASMGGYQDVFELVS
PPDSDVRKSKSAPKQQSQPMQKKNQQQKSDAGSGQAAPAKDTKGKAAQKPQKEKKGDTSSVVAGHESKPI
EEKQNVARLPKREAQPEAVVVTKVEREKELGHIEVREREEQEVREFEPPKAKTNPKDIKDEDFLPPGVTP
EKAILILKEMIQKRSGRWLVTPVLEEDGCLVTSDKAFDMIAGENIGINKHILCGMLSRAQKRPLLKKRQG
KLYLEVNET

  Protein domains


Predicted by InterproScan.

Putative helicase (TraI_2)

(51-357)


  Protein structure



No available structure.




T4CP

ID   1309 GenBank   WP_022635545
Name   traC_CXF88_RS16160_ALD9|unnamed 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: 92275.44 Da        Isoelectric Point: 6.0244

>WP_022635545.1 MULTISPECIES: type IV secretion system protein TraC [Gammaproteobacteria]
MIVTIKKKLQETLIPEHLRAAGIIPVLAYDEDDHVFLMDDHSVGFGFMCEPLCGADEKVQERMNGFLNQE
FPSKATLQFVLFRSPDINQEMYRMMGLRDGFRHELLTSVIKERINFLQHHTTDRISAKTNKGTYDNGLIQ
DLKLFVTCKVPINNNNPSESELQNLAQLRTKVESSLQTVGLRPRTMTAVNYIRIMSTILNWGPDASWRHD
AVDWEMDKPICEQVFDYGTDVEVSKNGLRLGDYHAKVMSAKKLPDVFYFGDALTYAGDLSGGNSSIKENY
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.



ID   1310 GenBank   WP_022635536
Name   traD_CXF88_RS16235_ALD9|unnamed 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.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 100513..125670

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
CXF88_RS16100 (CXF88_16100) 95641..96546 - 906 WP_071681736 hypothetical protein -
CXF88_RS16105 (CXF88_16105) 96557..97525 - 969 WP_022635552 AAA family ATPase -
CXF88_RS16110 (CXF88_16110) 97745..97930 - 186 WP_154398366 hypothetical protein -
CXF88_RS16115 (CXF88_16115) 98235..98555 - 321 WP_013141561 hypothetical protein -
CXF88_RS16120 (CXF88_16120) 98849..99490 + 642 WP_071681740 hypothetical protein -
CXF88_RS16125 (CXF88_16125) 99612..100475 + 864 WP_022635550 hypothetical protein -
CXF88_RS16130 (CXF88_16130) 100513..103317 - 2805 WP_071681742 conjugal transfer mating pair stabilization protein TraN traN
CXF88_RS16135 (CXF88_16135) 103433..104416 - 984 WP_231398180 TraU family protein traU
CXF88_RS16140 (CXF88_16140) 104437..105108 - 672 WP_071681744 EAL domain-containing protein -
CXF88_RS16145 (CXF88_16145) 105105..106370 - 1266 WP_071681746 TrbC family F-type conjugative pilus assembly protein traW
CXF88_RS16150 (CXF88_16150) 106333..106863 - 531 WP_022635546 S26 family signal peptidase -
CXF88_RS16155 (CXF88_16155) 106860..107177 - 318 WP_013141553 hypothetical protein -
CXF88_RS16160 (CXF88_16160) 107192..109636 - 2445 WP_022635545 type IV secretion system protein TraC virb4
CXF88_RS16165 (CXF88_16165) 109633..110340 - 708 WP_022635544 DsbC family protein trbB
CXF88_RS16170 (CXF88_16170) 110489..115975 - 5487 WP_071681748 Ig-like domain-containing protein -
CXF88_RS16175 (CXF88_16175) 116178..116561 - 384 WP_089140452 TraA family conjugative transfer protein -
CXF88_RS16180 (CXF88_16180) 116574..117152 - 579 WP_010845916 type IV conjugative transfer system lipoprotein TraV traV
CXF88_RS16185 (CXF88_16185) 117149..118468 - 1320 WP_071681777 TraB/VirB10 family protein traB
CXF88_RS16190 (CXF88_16190) 118468..119385 - 918 WP_022635540 type-F conjugative transfer system secretin TraK traK
CXF88_RS16195 (CXF88_16195) 119369..119995 - 627 WP_022635539 TraE/TraK family type IV conjugative transfer system protein traE
CXF88_RS16200 (CXF88_16200) 119992..120273 - 282 WP_000805625 type IV conjugative transfer system protein TraL traL
CXF88_RS16205 (CXF88_16205) 120421..120783 - 363 WP_231897578 hypothetical protein -
CXF88_RS16210 (CXF88_16210) 121120..121782 - 663 WP_101087657 hypothetical protein -
CXF88_RS16215 (CXF88_16215) 121782..122159 - 378 WP_013141541 hypothetical protein -
CXF88_RS16220 (CXF88_16220) 122169..122615 - 447 WP_071681752 hypothetical protein -
CXF88_RS16225 (CXF88_16225) 122624..123253 - 630 WP_022635537 DUF4400 domain-containing protein tfc7
CXF88_RS16230 (CXF88_16230) 123210..123755 - 546 WP_023044870 hypothetical protein -
CXF88_RS16235 (CXF88_16235) 123805..125670 - 1866 WP_022635536 conjugative transfer system coupling protein TraD virb4
CXF88_RS16240 (CXF88_16240) 125667..128636 - 2970 WP_022635535 MobH family relaxase -
CXF88_RS16245 (CXF88_16245) 128804..129421 + 618 WP_071681756 hypothetical protein -

Host bacterium

ID   2681 GenBank   NZ_PJCD01000039
Plasmid name   ALD9|unnamed Incompatibility group   IncA/C2
Plasmid size   141872 bp Coordinate of oriT [Strand]   123604..123754 [-]
Host baterium   Shewanella sp. ALD9

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   merP, merT, merR
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -