Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100488
Name   oriT_pNDM-BJ02 in_silico
Organism   Acinetobacter lwoffii
Sequence Completeness      incomplete
NCBI accession of oriT (coordinates [strand])   NC_019281 (259..296 [+], 38 nt)
oriT length   38 nt
IRs (inverted repeats)      8..17, 21..30  (CATAAGGGAA..TTCCCTTATG)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   predicted by the oriTfinder

  oriT sequence  


Download         Length: 38 nt

>oriT_pNDM-BJ02
AGGGATTCATAAGGGAATTATTCCCTTATGTGGGGCTT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   559 GenBank   YP_006961792
Name   TraA_pNDM-BJ02 insolico UniProt ID   H6VYP3
Length   996 a.a. PDB ID   
Note   putative relaxase

  Relaxase protein sequence


Download         Length: 996 a.a.        Molecular weight: 113758.44 Da        Isoelectric Point: 9.0108

>YP_006961792.1 TraA (plasmid) [Acinetobacter lwoffii]
MTIAVGMHASAFLSEKQKKQKQKRHKMAIYHLSVKTGRQYGSTGTRGANHYAYINRDGKYKRDDLENIKS
GNLPSWATDAKHFWKSADKNERINGRVYTELEISLPRELNKEQREELVEKFVEKTLGENFTYSYAIHSPL
ASDGQQNPHVHLMFSERKLDGIERDEVKHFKRYNPVNPEKGGAGKDRYFSSKMFVVDTRLEWANHVNDFC
ENLGIDARIDHRSFKEQGIELSSQNFRADYVSSHKYHINENIKQVRHQNGEIIIERPSEAIKALTSNQSV
FSVRELERFLMAHTDGEEQYLKAYESVITCPDMATLYGKDKVVFSSKELVGIEESISTFIYNANEESRIQ
KPFNLVEKLPLNAVRVAETRTFNSEQEKAFYTLTSTDRITLLNGSAGTGKSYVLSAVSEAYKESDYQVYG
IALQAITAKAIANDCDIPSSTIASFLSKYDSGNLEINNKTVLILDEAGMVGSRDMQRLLMLVEKHDAQIK
LVGDSYQLSAVSAGHVFANIQENLDKKNIASLEDIQRQKHAKESDKMIQASKYLSKHEVGKAIDIYKSIN
MVNEYESHDLALAKTVKSWSEDSSESKLMLAHSNSDVNELNRMARALLIKQGKLNPESVSVKNYQGDLDI
SIGEKIVFKQNNSQMKVSNGELAKVIGFEKDKFNNPKAMMVQMESDSRIVRVDLKEYDQFKHGYANTIHS
SQGMTVDSAYIVASENMNANLTYVALTRHKQNIQINYSALTFATNEKETVKTPDGKVSYDHNYKPVEREV
TAFENFKKVLGRSETKEFSTDFTLVESKDNLMKSYLNDHRLHLENKRELFGINSKLYSLTSENKTFTKEE
IVSEVRASLKSKALLGDEIVKFNGNMNIAKGELVKLTNDLEIKTGLFKKVTFEKGTELKVIDAYKVKDKP
VMKARIKNEEYEIPFNKLNLEYSDKYFNEFKDQSKARFDSRHKTEVYTEFREQLLKQKANAPKDNLNAPN
QRIKNPNTPNRNTPKY

  Protein domains


Predicted by InterproScan.

AAA domain (AAA_30)

(372-564)

MobA/MobL family (MobA_MobL)

(69-234)

Viral (Superfamily 1) RNA helicase (Viral_helicase1)

(687-735)


  Protein structure


Source ID Structure
AlphaFold DB H6VYP3


T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 21607..34902

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HPE92_RS00085 (D701_p1017) 17485..18132 - 648 WP_004993315 recombinase family protein -
HPE92_RS00090 18284..18508 + 225 WP_015056389 hypothetical protein -
HPE92_RS00095 (D701_p1018) 18692..20404 + 1713 WP_015060705 zeta toxin family protein -
HPE92_RS00100 (D701_p1011) 20401..20883 - 483 WP_015060706 thermonuclease family protein -
HPE92_RS00105 (D701_p1019) 21083..21544 - 462 WP_015060707 hypothetical protein -
HPE92_RS00110 (D701_p1020) 21607..22248 - 642 WP_004999358 type IV secretion system protein virB5
HPE92_RS00115 (D701_p1021) 22245..24956 - 2712 WP_015060708 VirB4 virb4
HPE92_RS00120 24968..25261 - 294 WP_017480461 TrbC/VirB2 family protein virB2
HPE92_RS00125 (D701_p1022) 25272..25982 - 711 WP_017480462 lytic transglycosylase domain-containing protein -
HPE92_RS00130 26027..26227 - 201 WP_004999346 hypothetical protein -
HPE92_RS00135 (D701_p1023) 26246..27763 - 1518 WP_015060710 type IV secretion system DNA-binding domain-containing protein virb4
HPE92_RS00140 (D701_p1024) 27760..29013 - 1254 WP_015060711 lytic transglycosylase domain-containing protein -
HPE92_RS00145 (D701_p1025) 29089..29541 - 453 WP_004999340 hypothetical protein -
HPE92_RS00150 (D701_p1027) 29545..29874 - 330 WP_004999338 hypothetical protein -
HPE92_RS00155 (D701_p1028) 29843..30880 - 1038 WP_015060713 P-type DNA transfer ATPase VirB11 virB11
HPE92_RS00160 (D701_p1029) 30896..32275 - 1380 WP_005000433 TrbI/VirB10 family protein virB10
HPE92_RS00165 (D701_p1030) 32277..33014 - 738 WP_005000435 TrbG/VirB9 family P-type conjugative transfer protein virB9
HPE92_RS00170 (D701_p1031) 33029..33817 - 789 WP_005000436 VirB8/TrbF family protein virB8
HPE92_RS00175 (D701_p1033) 33817..34902 - 1086 WP_005000437 type IV secretion system protein virB6
HPE92_RS00180 (D701_p1034) 34910..35329 - 420 WP_005000439 hypothetical protein -
HPE92_RS00185 (D701_p1035) 35316..35687 - 372 WP_005000442 hypothetical protein -
HPE92_RS00190 37309..37548 + 240 WP_005000443 hypothetical protein -
HPE92_RS00195 (D701_p1026) 37565..38254 + 690 WP_005000446 ParA family partition ATPase -
HPE92_RS00200 (D701_p1036) 38251..38655 + 405 WP_005000449 hypothetical protein -

Host bacterium

ID   949 GenBank   NC_019281
Plasmid name   pNDM-BJ02 Incompatibility group   _
Plasmid size   46165 bp Coordinate of oriT [Strand]   259..296 [+]
Host baterium   Acinetobacter lwoffii

Cargo genes

Drug resistance gene   aminoglycoside resistance; bleomycin resistance
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -