Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   112018
Name   oriT_pADAP in_silico
Organism   Serratia entomophila
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NC_002523 (133975..134057 [+], 83 nt)
oriT length   83 nt
IRs (inverted repeats)     _
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 83 nt

>oriT_pADAP
ACGGGACCAGATGTGTTTTGTAGCACCGCCTGCACGCAGTCGGTTCAACAAAACGCTGGGTCAGGGCAGAGCCCCGACACCCC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   7748 GenBank   WP_010895859
Name   Relaxase_HKJ47_RS00590_pADAP insolico UniProt ID   A7M7H3
Length   651 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 651 a.a.        Molecular weight: 73395.58 Da        Isoelectric Point: 7.4747

>WP_010895859.1 MULTISPECIES: TraI/MobA(P) family conjugative relaxase [Serratia]
MIIRIPEKRRDGKSSFLQLVAYTVVRDEDKPDSPLEPEHPGWRRPRSKDAIFNHLVDYISRNGDADLQQI
MHADPNGHTQVMFDGVMCETNCFNIATASVEMNAVALQNTRCKDPVLHYFLSWPETDNPSTEHIFDSVRH
SLSALGMSEHQYVAAIHTDTNNIHCHVAANRIHPETYKAADDSFTRIRLQQAARELELKYNWTPTNGFFA
VNEQGEIVRSKREKNLTPSGAKTLEYYADVESLHTYAVTECGFKIDEAMADPNLAWKDIHCILVNAGLAL
KPKGKGLAIYSIDNPELPPVKASSVHPDLTLNCLEKDLGQFQLLENAGTYTKEHTTTAADAIVHEFRYEP
TLHARDLTARLERRLARADARADLKARYQAYKNAWKRPKLDAGAVKRRYQNESKRFAWQKARARVAIGDP
LLRKLTYHIIEVERMKAMAALRLTVKDERAAFKADPANRRLSYREWVEQQALSHDQAAIAQLRAFAYRMK
RTQRTAPLSTNSIVCAVADDTPAFALEGYATRVTRDGTVQYVRDGRVQLQDKGERIDVGDHRVNEGEHIA
GGMALAENKSGEHLKFEGEAAFVQQACSMVPWFNEGGDAPLPLSDPQQRTMAGYESTYQSASTGEGQRKP
SAVEQPEVEQNKPRSGHRPQQ

  Protein domains


Predicted by InterproScan.

Large polyvalent protein-associated domain 7 (LPD7)

(518-589)

Relaxase/Mobilisation nuclease domain (Relaxase)

(55-320)


  Protein structure


Source ID Structure
AlphaFold DB A7M7H3


T4CP

ID   8861 GenBank   WP_010895767
Name   t4cp2_HKJ47_RS00135_pADAP insolico UniProt ID   _
Length   577 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 577 a.a.        Molecular weight: 64155.03 Da        Isoelectric Point: 5.2094

>WP_010895767.1 MULTISPECIES: ATP-binding protein [Serratia]
MPIFNFRDEDALGKVASVDTTNVIVDVENVEQLKRLQVNHLAVLQSSRPGQHLIGLITQVTRKRGIEDIA
NDGISEQTSELNLCKIALIGTMLDRDGERENVFRRTLESVPEIDANCFSLEGQNLTNFMRTLSSVSADGN
ALTLGKYTLDEHAIAYLNGNKFFQRHAFIGGSTGSGKSWTTAKIIEQMAGLSTANAIVFDLHGEYSPLVG
KGIQHFKVAGPADVEAQRTIDNGVLYLPYWLLSYEALVAMFVDRSDQNAPNQAMIMSREINQAKRKYLED
GDHKEILKHFTVDSPVPFDLDVLMGRLNEINVEMVPGASQGKEKQGDFFGKLARMISRLENKISDRRLGF
IFSGGGDVLNFSWLEKFTTAVLGSSEENGNAGIKIINFSEVPSDVLPLIVSLVARVTFSVQQWTPSELRH
PIALLCDEAHLYMPQRNMAESADDISLDIFERIAKEGRKYGVSLIVISQRPSEVNKTMLSQCSNFVSMRL
TNAEDQGVIKRLLPDSLGGFSDILPTLDTGEALVVGDASLLPSRIRIDEPINKPNSGTVNFWDEWQKPVK
DKRLLIAVENWRKQNIQ

  Protein domains


Predicted by InterproScan.

Helicase HerA, central domain (DUF87)

(144-405)

  Protein structure



No available structure.



ID   8862 GenBank   WP_234591458
Name   trbC_HKJ47_RS00605_pADAP insolico UniProt ID   _
Length   725 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 725 a.a.        Molecular weight: 81497.36 Da        Isoelectric Point: 8.5425

>WP_234591458.1 MULTISPECIES: F-type conjugative transfer protein TrbC [Serratia]
MSRPVEVDPRRVRRPLGYTFINDALLSPMGVQLSLLAGLIAGFVMPATLLLTVPGLLLLVMLFADRPFRM
PLRMPTDIGGMDLTTEREMPKYRKGLGGFFRYVVRTRKYMPAAGVMCLGYARGKGLARELWLTLDDALRH
MLLLATTGSGKTEALLSVFLNSICWGRGICYSDGKGQNTLAFAMWSLARRFGREDDFYVLNFMTGGTDKL
LQLLLNDKKRQPSNTINLFGTANTTFIIQLMESMLPPAGSGDQGWQDKAKSMLSALVYAIYYKCKREKRR
ISQKVIQEYLPLRKLADLYQEAKRDGWHREAYNPLENYFNTLAGFRIELISKPSEWEQGVYDQHGYLIQQ
FNRMLTMFNDLYGHIFSTDAGDIDIEDVLHNDRILCTTIPALELSKGEASNIGKLYISAIRMTMARDLGC
ELEGMMNDVLIVKKYSGKFPYPIAMDELGAYFGPGMDNLASQMRSLGYMLIVSAQDIQRFIAEHKGEYMT
VNANLLTKWFMTLQDEKDTFELARITGGKGYYAELGSVEQAGGFITPNYEDAANNYIREKDRLDLGDLKD
MSPGEGMISFKSALVPSNAIYIPDDQKMTSALPMRINRFIDVETPTEAELFALNPSLKRKLPPTAQEVDG
ILQRLDLAVDTTASVGIMDPVLKRVAAVALDLDNRADVSYSPAQRGVLLFEAAREALHKNKRKWRQLPTP
PKPIRVSKEVAQSLANAGTNEITFR

  Protein domains



No domain identified.


  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 691..14099

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HKJ47_RS00010 691..1365 - 675 WP_010895742 DotI/IcmL/TraM family protein traM
HKJ47_RS00015 1456..1947 - 492 WP_010895743 hypothetical protein traL
HKJ47_RS00020 1957..5193 - 3237 WP_010895744 LPD7 domain-containing protein -
HKJ47_RS00025 5336..5602 - 267 WP_010895745 IcmT/TraK family protein traK
HKJ47_RS00030 5602..6759 - 1158 WP_010895746 plasmid transfer ATPase TraJ virB11
HKJ47_RS00035 6949..7737 - 789 WP_010895747 type IV secretory system conjugative DNA transfer family protein traI
HKJ47_RS00040 7734..8192 - 459 WP_010895748 DotD/TraH family lipoprotein -
HKJ47_RS00045 8230..9663 - 1434 WP_010895749 shufflon system plasmid conjugative transfer pilus tip adhesin PilV -
HKJ47_RS00050 9660..10322 - 663 WP_169558203 prepilin peptidase -
HKJ47_RS00055 10328..10813 - 486 WP_010895751 lytic transglycosylase domain-containing protein virB1
HKJ47_RS00060 10868..11461 - 594 WP_010895752 type 4 pilus major pilin -
HKJ47_RS00065 11497..12609 - 1113 WP_241389818 type II secretion system F family protein -
HKJ47_RS00070 12609..14099 - 1491 WP_010895754 GspE/PulE family protein virB11
HKJ47_RS00075 14105..14689 - 585 WP_010895755 type IV pilus biogenesis protein PilP -
HKJ47_RS00080 14676..15986 - 1311 WP_010895756 type 4b pilus protein PilO2 -
HKJ47_RS00085 15990..17624 - 1635 WP_010895757 PilN family type IVB pilus formation outer membrane protein -
HKJ47_RS00090 17649..18074 - 426 WP_010895758 type IV pilus biogenesis protein PilM -
HKJ47_RS00095 18074..19087 - 1014 WP_010895759 toxin co-regulated pilus biosynthesis Q family protein -

Region 2: 139650..153518

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HKJ47_RS00595 136425..136748 - 324 WP_010895860 hypothetical protein -
HKJ47_RS00600 136758..137294 - 537 WP_234591459 phospholipase D family protein -
HKJ47_RS00605 137435..139612 - 2178 WP_234591458 F-type conjugative transfer protein TrbC -
HKJ47_RS00610 139650..140648 - 999 WP_010895863 hypothetical protein trbB
HKJ47_RS00615 140661..141971 - 1311 WP_010895864 hypothetical protein trbA
HKJ47_RS00620 142109..142690 - 582 WP_010895865 hypothetical protein -
HKJ47_RS00625 142687..144981 - 2295 WP_234591456 DotA/TraY family protein traY
HKJ47_RS00630 144896..145459 - 564 WP_010895867 conjugal transfer protein TraX -
HKJ47_RS00635 145452..146678 - 1227 WP_010895868 conjugal transfer protein TraW traW
HKJ47_RS00640 146819..149893 - 3075 WP_010895869 TraU traU
HKJ47_RS00645 149896..150501 - 606 WP_010895870 TraT traT
HKJ47_RS00650 150587..150988 - 402 WP_010895871 DUF6750 family protein traR
HKJ47_RS00655 151004..151534 - 531 WP_010895872 conjugal transfer protein TraQ traQ
HKJ47_RS00660 151543..152286 - 744 WP_010895873 hypothetical protein traP
HKJ47_RS00665 152286..153518 - 1233 WP_010895874 conjugal transfer protein TraO traO

Host bacterium

ID   12453 GenBank   NC_002523
Plasmid name   pADAP Incompatibility group   -
Plasmid size   153842 bp Coordinate of oriT [Strand]   133975..134057 [+]
Host baterium   Serratia entomophila

Cargo genes

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