Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   102997
Name   oriT_pKM01 in_silico
Organism   Staphylococcus pseudintermedius strain HR547/11
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_KT373969 (48526..48561 [+], 36 nt)
oriT length   36 nt
IRs (inverted repeats)      4..10, 14..20  (GCGAACG..CGTTCGC)
Location of nic site      29..30
Conserved sequence flanking the
  nic site    		  GTGCGCCCTT
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 36 nt

>oriT_pKM01
CACGCGAACGGAACGTTCGCATAAGTGCGCCCTTAC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2248 GenBank   WP_001252101
Name   MobA_MobL_HTG38_RS00260_pKM01 insolico UniProt ID   A0A141HMI9
Length   665 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 665 a.a.        Molecular weight: 78908.86 Da        Isoelectric Point: 5.3910

>WP_001252101.1 MULTISPECIES: MobA/MobL family protein [Bacilli]
MAMYHFQNKFVSKANGQSATAKSAYNSASRIKDFKENEFKDYSNKQCDYSEILLPNNADDKFKDREYLWN
KVHDVENRKNSQVAREIIIGLPNEFDPNSNIELAKEFAESLSNEGMIVDLNIHKINEENPHAHLLCTLRG
LDKNNEFEPKRKGNDYIRDWNTKEKHNEWRKRWENVQNKHLEKNGFSVRVSADSYKNQNIDLEPTKKEGW
KARKFEDETGKKSSISKHNESIKKRNQQKIDKMFNEVDDMKSHKLNAFSYMNKSDSTTLKNMAKDLKIYV
TPINMYKENERLYDLKQKTSLITDDEDRLNKIEDIEDRQKKLESINEVFEKQAGIFFDKNYPDQSLNYSD
DEKIFITRTILNDRDVLPANNELEDIVKEKRIKEAQISLNTVLGNRDISLESIEKESNFFADKLSNILEK
NNLSFDDVLENKHEGMEDSLKIDYYTNKLEVFRNAENILEDYYDVQIKELFTDDEDYKAFNEVTDIKEKQ
QLIDFKTYHGTENTIEMLETGNFIPKYSDEDRKYITEQVKLLQEKEFKPNKNQHDKFVFGAIQKKLLSEY
DFDYSDNNDLKHLYQESNEVGDEISKDNIEEFYEGNDILVDKETYNNYNRKQQAYGLINAGLDSMIFNFN
EIFRERMPKYINHQYKGKNHSKQRHELKNKRGMHL

  Protein domains


Predicted by InterproScan.

MobA/MobL family (MobA_MobL)

(17-216)


  Protein structure


Source ID Structure
AlphaFold DB A0A141HMI9


T4CP

ID   1936 GenBank   WP_000209435
Name   t4cp2_HTG38_RS00060_pKM01 insolico UniProt ID   _
Length   546 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 546 a.a.        Molecular weight: 62671.66 Da        Isoelectric Point: 7.6569

>WP_000209435.1 MULTISPECIES: VirD4-like conjugal transfer protein, CD1115 family [Staphylococcus]
MTTLLGELESKATSINKKNLVIQDFDTKCPNRNIFVVGGPGSYKSAGYVIPNVIVKNQQSIVVTDPSGEV
YEKTSNIKRMQGFDVRVVNFKNFLASDRQNFFDYIDKDSDCSIVAELIIKSAGDSKINKDVWYKASVGLL
NSLLLYAKYEFEPEKRTIGNIIKFIQNNKPNQDEEGSVELDKRFNELSKDHPARESYEFGFAVSEGRTRA
SIILTFVADLRNYIDNEIRSYTSDSDFDLRDVGLRKTIIYVMLPVLGNTVQSLSSLFFSQMFQQLYRLGD
ENGARLPVPVDFLLDEWPNIGAIPDYEETLATCRKYGISITTIVQSISQAVDKYNKDKANAIIGNHAVIL
CLGNVNNDTAKYIKEELGNATVEFETSSEGSSSGKDSRSKSSNKNVSYTGRALLNEDEISNMQQDKAILI
TKNRNPKIIKKLAYFKMFPNLTETYIAPQNEYKRKKNQSMIDKHNRLREEWDKKQEKIKQQKLEEYKEEQ
RQKELEKEQQPQEEQQNEKVKESKDKNDQEDKKDEQQKINDSKKAFYEKLKQKQAK

  Protein domains


Predicted by InterproScan.

Type IV secretory system Conjugative DNA transfer (T4SS-DNA_transf)

(3-462)

  Protein structure



No available structure.



ID   1937 GenBank   WP_172686247
Name   t4cp2_HTG38_RS00145_pKM01 insolico UniProt ID   _
Length   612 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 612 a.a.        Molecular weight: 70511.60 Da        Isoelectric Point: 6.9244

>WP_172686247.1 VirD4-like conjugal transfer protein, CD1115 family [Staphylococcus pseudintermedius]
MKKICLKFLIVLLVAEILMLILSYLYACVIVTDEIQNLSITVTDNIKQFFNFSNNIGKIRKEFLFNLNTQ
LVAIAVAIFLYFKWFFNWKKESAGAKKSKQKTYGSSQIAEDKEIAPLKKDNGNYLIGKHKRKYVYQPKRS
KMNRHVLINAPTASGKTTAYSIPNIKKIADRGESFVSTDTKGDTYNATAKYLKEQGYKIRVINLIDKTRS
DAINPFDYIFSISDAQNFVDSFLKSTGTSSSDESYWDRAESLYMSTLVLYVIKHFEKEFKNIPNWINLYL
EIGDDVEKRNALFDAIKDDKDIAKRSYELYRVNTSSKVESSILLGISSRMQYFLDEDTESLLAKSDFEYA
DIVNEKTALFIITQERDVISSIVSSVIMTQTIDKLIEYADNLPELSYAKPIHLMMDEFANIAKLKAFAKT
LTTIRAKNIILTAIVQELNQIKVKYGEDYNTILSSFDTKILMGTTDTDTIDYFVKLGGEYTADIYSDSEK
DDEHSKSTRIGQINVLNSSLIRELDVNNEIIAFIRGHNPMFLKRTYYFEEKEFKEVLEKSYWHDIAARKN
VVNYKSLKLETNDTIMNTEHISNQDLAGLEYKDEFPIESKEENKSFKGFGKW

  Protein domains


Predicted by InterproScan.

Type IV secretory system Conjugative DNA transfer (T4SS-DNA_transf)

(111-550)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 1729..30261

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HTG38_RS00005 (SP547_pKM00305) 1..189 - 189 WP_001063224 hypothetical protein -
HTG38_RS00010 (SP547_pKM00005) 361..1335 + 975 WP_000368849 conjugative transfer protein TrsA -
HTG38_RS00015 (SP547_pKM00010) 1352..1669 + 318 WP_172686244 CagC family type IV secretion system protein -
HTG38_RS00020 (SP547_pKM00015) 1729..2136 + 408 WP_000110157 hypothetical protein trsC
HTG38_RS00025 (SP547_pKM00020) 2123..2806 + 684 WP_000979860 TrsD/TraD family conjugative transfer protein trsD
HTG38_RS00030 (SP547_pKM00025) 2821..4839 + 2019 WP_001795400 DUF87 domain-containing protein virb4
HTG38_RS00035 (SP547_pKM00030) 4851..6131 + 1281 WP_000702361 membrane protein trsF
HTG38_RS00040 (SP547_pKM00035) 6149..7225 + 1077 WP_000269385 CHAP domain-containing protein trsG
HTG38_RS00045 (SP547_pKM00040) 7235..7720 + 486 WP_000735569 TrsH/TraH family protein -
HTG38_RS00050 (SP547_pKM00045) 7736..9838 + 2103 WP_001094109 DNA topoisomerase III -
HTG38_RS00055 (SP547_pKM00050) 9854..10318 + 465 WP_000715273 hypothetical protein trsJ
HTG38_RS00060 (SP547_pKM00055) 10315..11955 + 1641 WP_000209435 VirD4-like conjugal transfer protein, CD1115 family -
HTG38_RS00065 (SP547_pKM00060) 12033..12950 + 918 WP_000383804 conjugal transfer protein TrbL family protein trsL
HTG38_RS00070 (SP547_pKM00065) 12967..13359 + 393 WP_000608970 single-stranded DNA-binding protein -
HTG38_RS00075 (SP547_pKM00070) 13416..14147 + 732 WP_000869300 hypothetical protein -
HTG38_RS00080 (SP547_pKM00075) 14184..14807 + 624 WP_000831307 hypothetical protein -
HTG38_RS00085 14823..15059 + 237 WP_237449473 hypothetical protein -
HTG38_RS00090 (SP547_pKM00085) 15117..15791 - 675 WP_001105987 IS6-like element IS257 family transposase -
HTG38_RS00095 15807..16739 + 933 WP_237449478 CHAP domain-containing protein trsG
HTG38_RS00100 (SP547_pKM00095) 16755..17249 + 495 WP_099994923 hypothetical protein -
HTG38_RS00105 (SP547_pKM00105) 17518..17856 + 339 WP_099994922 single-stranded DNA-binding protein -
HTG38_RS00110 (SP547_pKM00110) 18263..18523 + 261 WP_237449474 hypothetical protein -
HTG38_RS00115 (SP547_pKM00115) 18580..18930 + 351 WP_233519680 hypothetical protein -
HTG38_RS00120 (SP547_pKM00120) 18924..19223 + 300 WP_237449475 hypothetical protein -
HTG38_RS00125 (SP547_pKM00130) 19864..20013 + 150 WP_172686245 hypothetical protein -
HTG38_RS00130 (SP547_pKM00135) 20337..20795 + 459 WP_140223247 HTH domain-containing protein -
HTG38_RS00135 (SP547_pKM00145) 22266..22685 + 420 WP_140223246 hypothetical protein -
HTG38_RS00140 (SP547_pKM00150) 22699..23418 + 720 WP_237449476 hypothetical protein -
HTG38_RS00145 (SP547_pKM00155) 23479..25317 + 1839 WP_172686247 VirD4-like conjugal transfer protein, CD1115 family -
HTG38_RS00150 (SP547_pKM00160) 25389..25847 + 459 WP_140223243 hypothetical protein -
HTG38_RS00155 (SP547_pKM00165) 25902..26237 + 336 WP_237449477 hypothetical protein virB2
HTG38_RS00160 (SP547_pKM00170) 26340..27266 + 927 WP_140223242 conjugal transfer protein TrbL family protein -
HTG38_RS00165 (SP547_pKM00175) 27270..27863 + 594 WP_172686248 hypothetical protein -
HTG38_RS00170 (SP547_pKM00180) 27745..30261 + 2517 WP_237449468 hypothetical protein virb4
HTG38_RS00175 (SP547_pKM00185) 30378..30938 + 561 WP_237449469 hypothetical protein -
HTG38_RS00180 (SP547_pKM00195) 31163..31837 - 675 WP_001105987 IS6-like element IS257 family transposase -
HTG38_RS00185 31875..33527 - 1653 WP_237449470 ArdC family protein -
HTG38_RS00190 (SP547_pKM00205) 33531..33719 - 189 WP_000921494 hypothetical protein -

Host bacterium

ID   3440 GenBank   NZ_KT373969
Plasmid name   pKM01 Incompatibility group   -
Plasmid size   52602 bp Coordinate of oriT [Strand]   48526..48561 [+]
Host baterium   Staphylococcus pseudintermedius strain HR547/11

Cargo genes

Drug resistance gene   aph(3')-III, mupA
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   AcrIIA21