Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100134
Name   oriT_KOPRI126573 in_silico
Organism   Pseudomonas sp. MC1
Sequence Completeness      intact
NCBI accession of oriT (coordinates [strand])   NC_016644 (_)
oriT length   430 nt
IRs (inverted repeats)      IR1: 276..280, 287..291nt  (AAAAA..TTTTT)
  299..304, 305..310  (ATACAT..ATGTAT)
  335..340, 343..348  (AAAATC..GCTTTT)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   

  oriT sequence  


Download         Length: 430 nt

>oriT_KOPRI126573
TTTGCACCCTATCTGCACCCCTATTGCACTCTATGTGCATCTTACTCGCCCCCTACCTGTAGTCAAGTTGCACTCTTCCTGCTCTCTTCTAGCACCCTTTCTGCATACCATCTGTGCTACCCCCCTACGGCCTTCGGCCTGGCTAGTGGATACGCCCTTAACAAGAGCTTCAACTTTTCCCCTTAACAGGGTCAAAGTCTCAATTCAAAGTCTCAATACACAATACGCACCCCCCTAGCGGGAGGTGACAGCCGCGCTGTGCGCGGCCTGCAGAGAAAAAGTGGTGTTTTTATGCGCTATACATATGTATTACAAAAGTACAGTCTAGATCAGCAAAATCAAGCTTTTTGTGTATTACATTTGCTATACACTGTTTCGGCAGTTATCGTTAGCCTGAATATGTCCCATTTTGGGCTCAGAGAGGAACACC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file

  Reference


[1] Dziewit L et al. (2014) Plasmids of psychrophilic and psychrotolerant bacteria and their role in adaptation to cold environments. Front Microbiol. 0.622222222. [PMID:25426110]


Relaxase

ID   129 GenBank   YP_005083667
Name   TraC_KOPRI126573 insolico UniProt ID   G9G7H8
Length   978 a.a. PDB ID   
Note   TrwC relaxase; pfam08751

  Relaxase protein sequence


Download         Length: 978 a.a.        Molecular weight: 108592.12 Da        Isoelectric Point: 9.9224

>YP_005083667.1 putative plasmid transfer protein TraC (plasmid) [Pseudomonas sp. MC1]
MFNVTSIKGSNQYAAAGYYTAADDYYAKESPGEWQGIGAELLGLAGPIDQKELAKLFDGKLPNGEVMPKT
FDKETGNRRMGLDLTFSAPKSVSMQALIAGDKDVVAAHDRAVTKAMEHVEKLAQARRKEHGKSMLERTGN
LIIGKFRHELSRAKDPQLHTHAVVMNATRREDGKWRAIHNDDIFKIQPQIDAMYKGELAKELRELGYEIR
VLDKDGNFELAHISRDQIEAFSSRAKVIEEALAKDGKTRSNATALEKQIIAMATRPRKDERDRHLVKEYW
VTKARDLGIEFGGRSQLDNQEYGRRSESIHAEHNLPEGITAGQAVVQYAINHLTEREQVVGESDLRTAAL
RRAVGLASPSEVDDEIKRLVKQGTLIESPPTYRMATGKDGAALSPAGWRALLKEQKGWSEKEAQQYVKMA
INRGSLVEAEKRYTTQRALKREKAILAIERSGRGQVAPLLSKEQVAKALESSTLSAGQYQAVEVIVSTSN
RFVGIQGDAGTGKTYSVDRAVKLIESVNNAMTERSTTTDAVFRVVALAPYGNQVTALKNEGLDAHTLASF
FHTKDKKLDERTIVVLDEAGVVGARQMEQLMRIIEQSGARLVQLGDTKQTEAIEAGKPFAQLQQNGMQTA
RIKEIQRQKNQELKIAVQHAADGNPGKSLEHVNHVEELREPGQRHQAIVRDYMSLTPQERKEVLIVAGTN
KDRKQINAMTRESLGLVGNGKELPTLNRVDTTQAERRYAPSYKKGMIVQPEKDYIRAGLSRGELYTVDQA
LPGNVLVVKDKNGNRVEFNPRKLTKLSVYNLEKPEFSVGDLVRITRNDQKLDLTNGDRMRVVGNANGVIE
LASLKEKDGTPERVVALPTNRPLHLEHAYSATVHSAQGLTNDRVMISINTKSLTTSQNLWYVAISRARHE
ARIYTDSIAGLPAAIANRYDKTTALSLQQARERQRNESIKPRTVLDGKELERKQRSALDGAGLGKSGV

  Protein domains


Predicted by InterproScan.

TrwC relaxase (TrwC)

(15-286)

Viral (Superfamily 1) RNA helicase (Viral_helicase1)

(869-915)

AAA domain (AAA_30)

(473-666)


  Protein structure


Source ID Structure
AlphaFold DB G9G7H8

  Reference


[1] Dziewit L et al. (2014) Plasmids of psychrophilic and psychrotolerant bacteria and their role in adaptation to cold environments. Front Microbiol. 0.622222222. [PMID:25426110]


T4CP

ID   129 GenBank   YP_005083666
Name   TraB_KOPRI126573 insolico UniProt ID   G9G7H7
Length   519 a.a. PDB ID   _
Note   Type IV secretion-system coupling protein DNA-binding domain; pfam10412

  T4CP protein sequence


Download         Length: 519 a.a.        Molecular weight: 58521.92 Da        Isoelectric Point: 8.5125

>YP_005083666.1 putative plasmid transfer protein TraB (plasmid) [Pseudomonas sp. MC1]
MHKREVDSAVMTAGFGLPIAGWAAGVYFAQMPLTPFPAAFKETLHNGWHNPIVLGATIATSAVAASLVYY
LYEYCDDGFRGEQYQEFLRGSEIKNWHTVKAKVRRRNEKTNRERKKWGLAKSEPIMIGKLPMPLHLEDRN
TMICASIGAGKSVTMEGMIASALKRGDRLAVVDPNGTFYSKFSFKGDSILNPFDERSVGWTIFNEIRGIH
DFNRMAKSIIPPQVDPSDEQWCAYARDVLSDTMRKLKETNNPDQDTLVNLLVREDGDTIRAFLANTDSEG
YFRDNAEKAIASIQFMMNKYIRPLRYMSKGEFSIYKWVNDPNAGNLFITWREDMRDTMKPLVATWIDTIC
ATILSSEPMTGKRLWLFLDELQSLGKLESFVPAATKGRKHGLRMVGSLQDWSQLNASYGRDDAETLLSCF
RNYVILAAANAKNAGMASEILGSHDVKRWRKSYTAGKLTRTEEVTRDEPVVQASEISNLPDLVAYVKFGE
DFPITKVKTPYIDYKERAQAIMLTGQAAA

  Protein domains


Predicted by InterproScan.

Type IV secretion-system coupling protein DNA-binding domain (TrwB_AAD_bind)

(125-499)

  Protein structure


Source ID Structure
AlphaFold DB G9G7H7


T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 70644..80942

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HS902_RS00400 (pYIC1_65) 66191..67678 - 1488 WP_011475407 SulP family inorganic anion transporter -
HS902_RS00405 (pYIC1_66) 68197..68493 - 297 WP_011475408 hypothetical protein -
HS902_RS00410 (pYIC1_67) 68507..69145 - 639 WP_011475409 hypothetical protein -
HS902_RS00415 (pYIC1_68) 69193..69675 - 483 WP_011475410 hypothetical protein -
HS902_RS00420 (pYIC1_69) 69690..70295 - 606 WP_011475411 phospholipase D family protein -
HS902_RS00425 (pYIC1_70) 70285..70635 - 351 WP_238841818 TrbM/KikA/MpfK family conjugal transfer protein -
HS902_RS00430 (pYIC1_71) 70644..71549 - 906 WP_011475413 lytic transglycosylase domain-containing protein virB1
HS902_RS00435 (pYIC1_72) 71533..72561 - 1029 WP_011475414 P-type DNA transfer ATPase VirB11 virB11
HS902_RS00440 (pYIC1_73) 72571..73854 - 1284 WP_011475415 TrbI/VirB10 family protein virB10
HS902_RS00445 (pYIC1_74) 73857..74648 - 792 WP_011475416 TrbG/VirB9 family P-type conjugative transfer protein virB9
HS902_RS00450 (pYIC1_75) 74673..75338 - 666 WP_011475417 type IV secretion system protein virB8
HS902_RS00455 (pYIC1_76) 75342..76205 - 864 WP_011475418 type IV secretion system protein virB6
HS902_RS00460 (pYIC1_77) 76193..76597 - 405 WP_011475419 hypothetical protein -
HS902_RS00465 (pYIC1_78) 76590..76802 - 213 WP_011475420 hypothetical protein -
HS902_RS00470 (pYIC1_79) 76830..77513 - 684 WP_011475421 type IV secretion system protein virB5
HS902_RS00475 (pYIC1_80) 77513..80155 - 2643 WP_151140442 type VI secretion protein virb4
HS902_RS00480 (pYIC1_81) 80184..80477 - 294 WP_011475423 VirB3 family type IV secretion system protein virB3
HS902_RS00485 (pYIC1_82) 80481..80942 - 462 WP_011475424 TrbC/VirB2 family protein virB2
HS902_RS00490 (pYIC1_83) 80959..81234 - 276 WP_238841819 hypothetical protein -

Host bacterium

ID   129 GenBank   NC_016644
Plasmid name   KOPRI126573 Incompatibility group   -
Plasmid size   81814 bp Coordinate of oriT [Strand]   
Host baterium   Pseudomonas sp. MC1

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   -
Degradation gene   nahAa, nahAb, nahAc, nahAd, nahB, nahF, nahC, nahE, nahD, nahG, nahH, nahI, nahN, nahL, nahO, nahM, nahK, nahJ
Symbiosis gene   -
Anti-CRISPR   -