Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   122450
Name   oriT1_MI12|p1HDM12 in_silico
Organism   Candidatus Hamiltonella defensa strain MI12 isolate MI12
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP023989 (42434..42537 [-], 104 nt)
oriT length   104 nt
IRs (inverted repeats)      55..60, 73..78  (TGGAAT..ATTCCA)
 45..50, 55..60  (ATTCCA..TGGAAT)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 104 nt

>oriT1_MI12|p1HDM12
ATTTTAAAAATTCCAAATATGGGTTAGCCTGGTGGTAAAAGTAGATTCCAGTATTGGAATGAGCATCTTTAAATTCCAGATAGATAGTTATTTGGATAGGAATT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   14154 GenBank   WP_171967928
Name   mobH_CJJ19_RS10895_MI12|p1HDM12 insolico UniProt ID   _
Length   833 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 833 a.a.        Molecular weight: 93186.87 Da        Isoelectric Point: 5.5726

>WP_171967928.1 MobH family relaxase [Candidatus Hamiltonella defensa]
MMRALKKLFGGRSGVIETAPSDRVMPLKDVEDEEIPRYPPFAKGLPVAPLDKILATQAELIEKVRNSLGF
TVDEFNRLVLPVIYRYAAFVHLLPASESHHHRGAGGLFRHGLEVAFWAAQASESVIFSIEGTPRERRDNE
PRWRLASCFSGLLHDVGKPLSDVSITDKDGSITWNPYSESLHDWANRHKIDRYFIRWRDKRHKRHEQFSL
LTIDRIIPAESREFLSTSGPSIMEAMLEAISGTRVNQPVTRLMLRADQESVSRDLRQSRLDVDEFSYGVP
VERYVFDAIRRLVKTGKWKVNQPGAKVWHLNQGIFIAWKHLGDLYDLISHDKIPGIPRDPDTLADILIER
GFAIPNTVQEKGERAYYRYWKVLPEMLQETAGSVKILMLRLESNDLVFTTEPPAAVTAEVVGDVEDAEIE
FVDPEEDDDEQEEGEAALNNDMLAAEQEAGKALAGIGFGNAENDNPLFTDAPEQKRPESDLPQTDKLEQK
GKDAKTVLNEILAGYGEASILLEQAIIPVLEGKTTLGEVLCLMKGQAVILYPEGARSLGAPSEVLSKLSH
ANAIVPDPIMPGRKVRDFSGVKAIVLAEQLSSAVVAAIKDAETSMGGYQDAFELVSPPGADARKSQSAQK
KQSQKKPQQQQQKTDVGSGETAPAQNATGKSSQQPPKEKKVDVDTVVEDKKRKPVEEKQNLARLPKREAQ
PTAVEPKFEREKELGHVEWREREDQEVREFEPPKAKTNPKDIKEEDFLPSGVTPQKAIQMLKDMIQKRSG
RWLVTPVLEEDGCLVTSDKAFEMIAGENTGISKHILCGLLSRAQRRPLLKKRQGKLYLEVDET

  Protein domains


Predicted by InterproScan.

Putative helicase (TraI_2)

(51-357)


  Protein structure



No available structure.




T4CP

ID   16456 GenBank   WP_100097193
Name   traD_CJJ19_RS10900_MI12|p1HDM12 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: 69452.97 Da        Isoelectric Point: 7.3339

>WP_100097193.1 MULTISPECIES: conjugative transfer system coupling protein TraD [Candidatus Hamiltonella]
MTMSYDPLAYEMPWRPNYEKNAVAGWLAASGAALAVEQVSTMPPEPFYWMTGICGVMAMARLPKAIKLHL
LQKHLRGRDLEFISIAELQKYIKDRPEDMWLGSGFLWENRHAQRVFEILKRDWTSIVGRESTLKKVVRKI
RGKRKALPIGQPWIHGVEPKEEQLMQPLKHTEGHTLIVGTTGSGKTRLFDILISQAILRGEAVIIIDPKG
DKEMRDNARRACEAMGQPERFVSFHPAFPAESVRIDPLRNFTRVTEIASRLAALIPSEAGADPFKSFGWQ
ALNNITQGLVITHDRPNLTKLRRFLEGGAAGLVIRAVQTYSERVMSDWETEAAAYLEKVKNGSREKIAFA
LMKFYYEVIQPEHANSDLEGLLSMFQHDQTHFSKMVANLLPIMNMLTSGELGPLLSPDSSDLSDERQITD
SAKIINNAQVAYLGLDSLTDNMVGSAMGSIFLSDLTAVAGDRYNYGVNNRPVNIFVDEAAEVINDPFIQL
LNKGRGAKLRLFIATQTFADFAARLGSKDKALQVLGNINNTFALRIVDGETQEYIADNLPKTRLKYVMRT
QGQNSDGKEPIMHEGNQGERLMEEEADLFPAQLLGMLPNLEYIAKISGGTIVKGRLPILIQ

  Protein domains


Predicted by InterproScan.

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

(170-327)

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

(471-598)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 32435..65108

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
CJJ19_RS10795 28111..28287 - 177 WP_158530227 hypothetical protein -
CJJ19_RS10800 (CJJ19_10860) 28307..28525 + 219 WP_171967925 hypothetical protein -
CJJ19_RS10805 (CJJ19_10865) 28543..28716 + 174 WP_157791491 hypothetical protein -
CJJ19_RS10810 (CJJ19_10870) 28942..29727 + 786 WP_171967926 ParA family protein -
CJJ19_RS10815 (CJJ19_10875) 29731..30911 + 1181 Protein_32 KorB domain-containing protein -
CJJ19_RS10820 (CJJ19_10880) 30960..31232 + 273 WP_100097208 helix-turn-helix domain-containing protein -
CJJ19_RS10825 (CJJ19_10885) 31278..31819 - 542 Protein_34 FlhC family transcriptional regulator -
CJJ19_RS10830 (CJJ19_10890) 31816..32424 - 609 WP_100097206 flagellar transcriptional regulator FlhD -
CJJ19_RS10835 (CJJ19_10895) 32435..32968 - 534 WP_100097205 transglycosylase SLT domain-containing protein virB1
CJJ19_RS10840 (CJJ19_10900) 33007..33174 - 168 Protein_37 nucleotide excision repair protein -
CJJ19_RS10845 (CJJ19_10905) 33858..34233 + 376 Protein_38 permease -
CJJ19_RS10850 (CJJ19_10910) 34271..37843 - 3573 WP_171967927 conjugal transfer protein TraG N-terminal domain-containing protein traG
CJJ19_RS10855 (CJJ19_10915) 37856..39289 - 1434 WP_100097200 conjugal transfer protein TraH traH
CJJ19_RS10860 (CJJ19_10920) 39291..40335 - 1045 Protein_41 conjugal transfer protein TraF -
CJJ19_RS10865 (CJJ19_10925) 40437..41303 - 867 WP_100097198 DsbA family protein -
CJJ19_RS10870 (CJJ19_10930) 41365..41553 - 189 Protein_43 zinc ribbon domain-containing protein -
CJJ19_RS12405 41634..41761 - 128 Protein_44 hypothetical protein -
CJJ19_RS12410 41778..41864 - 87 Protein_45 hypothetical protein -
CJJ19_RS10875 (CJJ19_10935) 41869..42408 - 540 WP_171967939 conjugative transfer protein MobI(A/C) -
CJJ19_RS10880 (CJJ19_10940) 42945..43223 + 279 Protein_47 hypothetical protein -
CJJ19_RS10885 (CJJ19_10945) 43225..43644 + 420 WP_100097196 H-NS histone family protein -
CJJ19_RS10890 (CJJ19_10950) 44021..44635 - 615 WP_100097195 hypothetical protein -
CJJ19_RS10895 (CJJ19_10955) 44803..47304 + 2502 WP_171967928 MobH family relaxase -
CJJ19_RS10900 (CJJ19_10960) 47301..49166 + 1866 WP_100097193 conjugative transfer system coupling protein TraD virb4
CJJ19_RS10905 (CJJ19_10965) 49216..49761 + 546 WP_234817548 hypothetical protein -
CJJ19_RS10910 (CJJ19_10970) 49718..50347 + 630 WP_100097191 DUF4400 domain-containing protein tfc7
CJJ19_RS10915 (CJJ19_10975) 50514..50765 + 252 WP_100097190 hypothetical protein -
CJJ19_RS10920 (CJJ19_10980) 50810..51091 + 282 WP_100097189 type IV conjugative transfer system protein TraL traL
CJJ19_RS12735 (CJJ19_10985) 51088..51712 + 625 Protein_56 TraE/TraK family type IV conjugative transfer system protein -
CJJ19_RS10930 (CJJ19_10990) 51696..52613 + 918 WP_171967929 type-F conjugative transfer system secretin TraK traK
CJJ19_RS10935 (CJJ19_10995) 52613..53926 + 1314 WP_216657378 TraB/VirB10 family protein traB
CJJ19_RS10940 (CJJ19_11000) 53923..54489 + 567 WP_100103813 type IV conjugative transfer system lipoprotein TraV traV
CJJ19_RS10945 (CJJ19_11005) 54502..54885 + 384 WP_100097184 TraA family conjugative transfer protein -
CJJ19_RS10950 (CJJ19_11010) 55369..56076 + 708 WP_100097183 DsbC family protein -
CJJ19_RS10955 (CJJ19_11015) 56073..58516 + 2444 Protein_62 type IV secretion system protein TraC -
CJJ19_RS10960 (CJJ19_11020) 58530..58847 + 318 WP_100097181 hypothetical protein -
CJJ19_RS10965 (CJJ19_11025) 58844..59374 + 531 WP_100103810 S26 family signal peptidase -
CJJ19_RS10970 (CJJ19_11030) 59337..60602 + 1266 WP_100097179 TrbC family F-type conjugative pilus assembly protein traW
CJJ19_RS12740 (CJJ19_11035) 60612..60812 + 201 Protein_66 EAL domain-containing protein -
CJJ19_RS10975 (CJJ19_11040) 60839..61822 + 984 WP_234811159 TraU family protein traU
CJJ19_RS10980 (CJJ19_11045) 61959..64729 + 2771 Protein_68 conjugal transfer mating pair stabilization protein TraN -
CJJ19_RS10985 64815..65108 + 294 WP_158531017 DUF6750 family protein traR
CJJ19_RS10990 (CJJ19_11055) 65427..65873 + 447 WP_171967931 hypothetical protein -
CJJ19_RS10995 (CJJ19_11060) 65870..66313 + 444 WP_235661289 transposase -
CJJ19_RS11000 (CJJ19_11065) 66348..67517 + 1170 WP_100097175 YopJ family acetyltransferase -
CJJ19_RS11005 67790..67951 - 162 WP_158531013 hypothetical protein -
CJJ19_RS11010 69016..69246 - 231 WP_171967933 Tn3 family transposase -

Host bacterium

ID   22876 GenBank   NZ_CP023989
Plasmid name   MI12|p1HDM12 Incompatibility group   -
Plasmid size   84572 bp Coordinate of oriT [Strand]   42434..42537 [-]; 49217..49361 [+]
Host baterium   Candidatus Hamiltonella defensa strain MI12 isolate MI12

Cargo genes

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