Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100520
Name   oriT_pNDM-AB in_silico
Organism   Acinetobacter baumannii
Sequence Completeness      incomplete
NCBI accession of oriT (coordinates [strand])   NC_020818 (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-AB
AGGGATTCATAAGGGAATTATTCCCTTATGTGGGGCTT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   591 GenBank   YP_007652788
Name   TrA_pNDM-AB insolico UniProt ID   M4UT67
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_007652788.1 TrA (plasmid) [Acinetobacter baumannii]
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 M4UT67


T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 19010..32305

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HPF14_RS00070 (pNDM-AB_015) 14888..15535 - 648 WP_004993315 recombinase family protein -
HPF14_RS00075 15687..15911 + 225 WP_015056389 hypothetical protein -
HPF14_RS00080 (pNDM-AB_016) 16095..17807 + 1713 WP_015060705 zeta toxin family protein -
HPF14_RS00085 (pNDM-AB_017) 17804..18286 - 483 WP_015060706 thermonuclease family protein -
HPF14_RS00090 (pNDM-AB_018) 18486..18947 - 462 WP_015060707 hypothetical protein -
HPF14_RS00095 (pNDM-AB_019) 19010..19651 - 642 WP_004999358 type IV secretion system protein virB5
HPF14_RS00100 (pNDM-AB_020) 19648..22359 - 2712 WP_015060708 VirB4 virb4
HPF14_RS00105 22371..22664 - 294 WP_017480461 TrbC/VirB2 family protein virB2
HPF14_RS00110 (pNDM-AB_021) 22675..23385 - 711 WP_017480462 lytic transglycosylase domain-containing protein -
HPF14_RS00115 23430..23630 - 201 WP_004999346 hypothetical protein -
HPF14_RS00120 (pNDM-AB_022) 23649..25166 - 1518 WP_015060710 type IV secretion system DNA-binding domain-containing protein virb4
HPF14_RS00125 (pNDM-AB_023) 25163..26416 - 1254 WP_015060711 lytic transglycosylase domain-containing protein -
HPF14_RS00130 (pNDM-AB_024) 26492..26944 - 453 WP_004999340 hypothetical protein -
HPF14_RS00135 26948..27277 - 330 WP_004999338 hypothetical protein -
HPF14_RS00140 (pNDM-AB_025) 27246..28283 - 1038 WP_015060713 P-type DNA transfer ATPase VirB11 virB11
HPF14_RS00145 (pNDM-AB_026) 28299..29678 - 1380 WP_015472974 TrbI/VirB10 family protein virB10
HPF14_RS00150 (pNDM-AB_027) 29680..30417 - 738 WP_005000435 TrbG/VirB9 family P-type conjugative transfer protein virB9
HPF14_RS00155 (pNDM-AB_028) 30432..31220 - 789 WP_005000436 VirB8/TrbF family protein virB8
HPF14_RS00160 (pNDM-AB_029) 31220..32305 - 1086 WP_005000437 type IV secretion system protein virB6
HPF14_RS00165 (pNDM-AB_030) 32313..32732 - 420 WP_005000439 hypothetical protein -
HPF14_RS00170 (pNDM-AB_031) 32719..33090 - 372 WP_005000442 hypothetical protein -
HPF14_RS00175 34712..34951 + 240 WP_005000443 hypothetical protein -
HPF14_RS00180 (pNDM-AB_032) 34968..35657 + 690 WP_005000446 ParA family partition ATPase -
HPF14_RS00185 (pNDM-AB_033) 35654..36058 + 405 WP_005000449 hypothetical protein -

Host bacterium

ID   981 GenBank   NC_020818
Plasmid name   pNDM-AB Incompatibility group   _
Plasmid size   47098 bp Coordinate of oriT [Strand]   259..296 [+]
Host baterium   Acinetobacter baumannii

Cargo genes

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