Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100581
Name   oriT_pNDM-Iz4b in_silico
Organism   Acinetobacter lwoffii
Sequence Completeness      incomplete
NCBI accession of oriT (coordinates [strand])   NC_025000 (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-Iz4b
AGGGATTCATAAGGGAATTATTCCCTTATGTGGGGCTT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   653 GenBank   YP_009062724
Name   TraA_pNDM-Iz4b 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_009062724.1 conjugal transfer relaxase 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: 22716..36011

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HPF09_RS00090 (D701_p3021) 18594..19241 - 648 WP_004993315 recombinase family protein -
HPF09_RS00095 (D701_p3022) 19393..19617 + 225 WP_015056389 hypothetical protein -
HPF09_RS00100 (D701_p3023) 19801..21513 + 1713 WP_015060705 zeta toxin family protein -
HPF09_RS00105 (D701_p3024) 21510..21992 - 483 WP_015060706 thermonuclease family protein -
HPF09_RS00110 (D701_p3025) 22192..22653 - 462 WP_015060707 hypothetical protein -
HPF09_RS00115 (D701_p3026) 22716..23357 - 642 WP_004999358 type IV secretion system protein virB5
HPF09_RS00120 (D701_p3027) 23354..26065 - 2712 WP_015060708 VirB4 virb4
HPF09_RS00125 (D701_p3028) 26077..26370 - 294 WP_017480461 TrbC/VirB2 family protein virB2
HPF09_RS00130 (D701_p3029) 26381..27091 - 711 WP_017480462 lytic transglycosylase domain-containing protein -
HPF09_RS00135 (D701_p3030) 27136..27336 - 201 WP_004999346 hypothetical protein -
HPF09_RS00140 (D701_p3031) 27355..28872 - 1518 WP_015060710 type IV secretion system DNA-binding domain-containing protein virb4
HPF09_RS00145 (D701_p3032) 28869..30122 - 1254 WP_015060711 lytic transglycosylase domain-containing protein -
HPF09_RS00150 (D701_p3033) 30198..30650 - 453 WP_004999340 hypothetical protein -
HPF09_RS00155 (D701_p3034) 30654..30983 - 330 WP_004999338 hypothetical protein -
HPF09_RS00160 (D701_p3035) 30952..31989 - 1038 WP_031942508 P-type DNA transfer ATPase VirB11 virB11
HPF09_RS00165 (D701_p3036) 32005..33384 - 1380 WP_005000433 TrbI/VirB10 family protein virB10
HPF09_RS00170 (D701_p3037) 33386..34123 - 738 WP_005000435 TrbG/VirB9 family P-type conjugative transfer protein virB9
HPF09_RS00175 (D701_p3038) 34138..34926 - 789 WP_005000436 VirB8/TrbF family protein virB8
HPF09_RS00180 (D701_p3039) 34926..36011 - 1086 WP_005000437 type IV secretion system protein virB6
HPF09_RS00185 (D701_p3040) 36019..36438 - 420 WP_005000439 hypothetical protein -
HPF09_RS00190 (D701_p3041) 36425..36796 - 372 WP_005000442 hypothetical protein -
HPF09_RS00195 (D701_p3043) 38418..38657 + 240 WP_005000443 hypothetical protein -
HPF09_RS00200 (D701_p3044) 38674..39363 + 690 WP_005000446 ParA family partition ATPase -
HPF09_RS00205 (D701_p3045) 39360..39764 + 405 WP_005000449 hypothetical protein -

Host bacterium

ID   1041 GenBank   NC_025000
Plasmid name   pNDM-Iz4b Incompatibility group   _
Plasmid size   46570 bp Coordinate of oriT [Strand]   259..296 [+]
Host baterium   Acinetobacter lwoffii

Cargo genes

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