Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   117128
Name   oriT_pHP-42 in_silico
Organism   Marinobacter adhaerens HP15
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NC_017508 (14316..14415 [-], 100 nt)
oriT length   100 nt
IRs (inverted repeats)      24..31, 35..42  (TAATCGGC..GCCGATTA)
Location of nic site      61..62
Conserved sequence flanking the
  nic site    		  TCCTGCCCGC
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 100 nt

>oriT_pHP-42
GAATAAGGGAAAGTGAAGATAGTTAATCGGCTCCGCCGATTAGCTAACTTCACCTATCCTGCCCGCCTTACGGCGTTGTTTACACCAAGGAAAGTGTACA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   10908 GenBank   WP_041646712
Name   traI_HP15_RS20735_pHP-42 insolico UniProt ID   _
Length   762 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 762 a.a.        Molecular weight: 84199.33 Da        Isoelectric Point: 10.5526

>WP_041646712.1 MULTISPECIES: TraI/MobA(P) family conjugative relaxase [Pseudomonadales]
MIAKHVPMRSLKKSDFAGLVKYITDEQSKTERLGLVNATNCEADTMQAVIGEVLATQQGNTRAKGDKTYH
LIVSFPAGEKPEDDVLKAVEERICAGLGYADHQRVSAVHHDTDNVHIHIAINKIHPTRNTMHEPYQDYRT
LGGLCDALEDEYGLQKDNHQGRKSVSQGRASDMERHAGIESLVSWIKRECLEEIKTAKTWEELHQVMSDN
GLEIRQRANGFVIESEDGTQVKASTVARDLSKPKLEARLGAFEETAAQAERKAKRRYDKRPTHFKVNTTE
LYARYQEEQKNLTAARKVEWNNARGRKDRRIEAAKRSNRLRRSAIKLMGGSRISKKLLYAQAHKALKDEI
QSINKDYKREKQELYDQYKRRAWADWLKQQALNGDKKALEALRAREQSKGLQGDTIKGEGGSKPGHAPVT
DNITKKGTIIFRTGKSAVRDDGDKLQVSKAANGDTVTEALRVAMERYGSRITVTGSPQFKAQVIVAAATS
NLPITFADAGLERRRQQLLQQENSNDRRNEQARRGNERGRADRRSNGRAERGPADDNGRGRGTADSRATT
AGRAGDGQRGRGQSASTGSTTAGGRNDAGNGSRPILNKPHVGRIGGEPPSFAKNRLRTLSSLGVVRFARG
GEVLLPGNAPSELEHQGAKPDNQLRWGVSGSGGITPDQTSAADKYIAEREAKRLKGFDIPNHSRYTNQDG
AVTYGGTRNVQGQSLALLNRGDEVLVLPIDKATAQRMKRVRIGEAVTVTPQGSLKRSKGRSR

  Protein domains


Predicted by InterproScan.

Large polyvalent protein-associated domain 7 (LPD7)

(419-508)

Relaxase/Mobilisation nuclease domain (Relaxase)

(12-250)


  Protein structure



No available structure.




Auxiliary protein

ID   6414 GenBank   WP_014579484
Name   WP_014579484_pHP-42 insolico UniProt ID   A0A5J6LJG6
Length   123 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 123 a.a.        Molecular weight: 13767.87 Da        Isoelectric Point: 9.4637

>WP_014579484.1 MULTISPECIES: conjugal transfer transcriptional regulator TraJ [Gammaproteobacteria]
MSEEKKPGKKRSHHLRVPVFDDEKEAIEAQAARAGMSVARYLREVGQGYQIKGVVDYEQVRELARINGDL
GRLGGLLKLWLTDDVRTAQFGQSTILAVLSKIEATQEEMGKVMTKVVMPRSEP

  Protein domains



No domain identified.



  Protein structure


Source ID Structure
AlphaFold DB A0A5J6LJG6


T4CP

ID   12738 GenBank   WP_014579486
Name   t4cp2_HP15_RS20740_pHP-42 insolico UniProt ID   _
Length   635 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 635 a.a.        Molecular weight: 69921.78 Da        Isoelectric Point: 7.3667

>WP_014579486.1 MULTISPECIES: type IV secretory system conjugative DNA transfer family protein [Pseudomonadota]
MKPKINNAVGPQVRDRKPKKQRLLPALGAVSVLGGLQAATQFFAYTFNYQDNLGGHINHVYAPWSILSWA
SDWYSIYPDEFMRSGSIGMVVTTVGLLGVAIAKVVTSNSSKASEYLHGSARWAEKKDIQAAGLLPRERTA
LEVVTGKDAPTSTGVYVGGWEDKDGNFFYLRHNGPEHVLTYAPTRSGKGVGLVVPTLLSWPQSSVITDLK
GELWALTAGWRQKHAKNKVLRFEPASSNGGVCWNPLDEIRIGTEYEVGDVQNLATLIVDPDGKGMDSHWQ
KTSYALLVGVILHALYKSKNEGTPATLPVVDAMLADPERDTGELWMEMATYGHVDGQNHPAVGSAARDMM
DRPEEEGGSVLSTAKSYLALYRDPVVARNVSKSEFRIKDLMNHDDPVSLYIVTQPNDKARLRPLVRVLTN
MIIRLLADEMSFEKGRPVAHYKHRLLAMLDEFPSLGKLEILQESLAFVAGYGIKCYLICQDLNQLKSRET
GYGPDETITSNCHVQNAYPPNRIETAEHLSRLTGQTTVVKEQITTSGRRTSAMLGQVSRTIQEVQRPLLT
PDECLRMPGPTKNAAGDIEKAGDMVIYVAGYPAVYGKQPLYFKDPVFQARASVDAPKISDKLRIVAEPEG
EGVTI

  Protein domains


Predicted by InterproScan.

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

(121-617)

  Protein structure



No available structure.



ID   12739 GenBank   WP_041646736
Name   t4cp2_HP15_RS20860_pHP-42 insolico UniProt ID   _
Length   845 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 845 a.a.        Molecular weight: 94103.81 Da        Isoelectric Point: 6.3050

>WP_041646736.1 VirB4 family type IV secretion/conjugal transfer ATPase [Marinobacter adhaerens]
MIQAISFAIAVCGAALLLILFARIRAVDAELKLKKHRSKDAGLADLLNYAAVVDDGVIVCKNGAFMASWL
YKGDDNASSTDEQREMVSFRINQALAGLGNGWMVHVDAVRRPAPNYSERNTSAFPDPVSAAIDEERRQLF
EGLGAMYEGYFVLTLTWFPPLLAQRKFVELMFDDDAEVVGKKARTKGLINQFKREISGIENRLTTAVKLT
RLRGQKIVNEDGSKVTHDDFLSWLQFCVTGVSHPVQLPNNPMYMDAYIGGQEMWGGVVPKVGRKFIQVVS
IEGFPLESHPGILSALAELPVEYRWSSRFIFMDQHESIKHLDKFRKKWKQKVRGFFDQVFNTNSGNVDQD
ALTMVQDAESAIAEVNSGLVAVGYYTSVVVLMDESRDRLEQSARQVEKSINRLGFAARTETINTLDAYLG
SLPGHGVENVRRPLINTMNLADLLPTSTIWTGNADAPCPMYPPLSPALMHCVTSGSTPFRLNLHVRDLGH
TFMFGPTGAGKSTHLALIAAQLRRYAGMSIFAFDKGMSMYPLTKAVGGLHFSVGADDDHLSFCPLQYLET
KSDRAWAMEWIDTILALNGVQSTPAQRNEIAHAIVSMHESGARTLSEFSLTIQDESIREAIRQYTVDGSM
GHLLDADEDGLSLTDFTTFEIEELMNLGEKFALPVLLYLFRRIERSLKGQPAVIILDEAWLMLGHPAFRE
KIREWLKVLRKANCLVLMATQSLSDAANSGILDVIVESTATKIFLPNVYARDEDTSALYRRMGLNARQID
ILATAVPKRQYYYVSENGRRLYDLALGPLALSFVGASDKESVAAIKQLEAKYGEQWVHEWLAGRGLKLDN
YLEAA

  Protein domains


Predicted by InterproScan.

TraG P-loop domain (P-loop_TraG)

(617-747)

CagE, TrbE, VirB family, component of type IV transporter system (CagE_TrbE_VirB)

(221-431)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 31529..42329

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HP15_RS22955 (HP15_p42g32) 26964..27095 + 132 WP_014579495 hypothetical protein -
HP15_RS20785 (HP15_p42g33) 27104..27727 + 624 WP_049784535 recombinase family protein -
HP15_RS20790 (HP15_p42g34) 27748..28053 - 306 WP_020933256 helix-turn-helix domain-containing protein -
HP15_RS20795 (HP15_p42g35) 28138..28644 - 507 WP_014579498 hypothetical protein -
HP15_RS20800 28649..28903 - 255 WP_020933254 hypothetical protein -
HP15_RS20805 (HP15_p42g37) 28928..29197 - 270 WP_014579500 hypothetical protein -
HP15_RS22065 (HP15_p42g38) 29216..29641 - 426 WP_014579501 OmpA family protein -
HP15_RS20810 (HP15_p42g39) 29655..30383 - 729 WP_014579502 TraX family protein -
HP15_RS20815 (HP15_p42g40) 30380..31012 - 633 WP_041646732 muramidase -
HP15_RS20820 (HP15_p42g41) 31027..31509 - 483 WP_014579504 hypothetical protein -
HP15_RS20825 (HP15_p42g42) 31529..33385 - 1857 WP_014579505 P-type conjugative transfer protein TrbL virB6
HP15_RS20830 (HP15_p42g43) 33397..33624 - 228 WP_014579506 entry exclusion lipoprotein TrbK -
HP15_RS20835 (HP15_p42g44) 33634..34395 - 762 WP_014579507 P-type conjugative transfer protein TrbJ virB5
HP15_RS20840 (HP15_p42g45) 34414..35841 - 1428 WP_014579508 TrbI/VirB10 family protein virB10
HP15_RS20845 (HP15_p42g46) 35845..36360 - 516 WP_014579509 conjugal transfer protein TrbH -
HP15_RS20850 (HP15_p42g47) 36363..37268 - 906 WP_014579510 P-type conjugative transfer protein TrbG virB9
HP15_RS20855 (HP15_p42g48) 37286..38068 - 783 WP_014579511 conjugal transfer protein TrbF virB8
HP15_RS20860 (HP15_p42g49) 38068..40605 - 2538 WP_041646736 VirB4 family type IV secretion/conjugal transfer ATPase virb4
HP15_RS20865 40605..40916 - 312 WP_008929954 conjugal transfer protein TrbD virB3
HP15_RS20870 (HP15_p42g51) 40919..41344 - 426 WP_014579514 conjugal transfer system pilin TrbC virB2
HP15_RS20875 (HP15_p42g52) 41370..42329 - 960 WP_014579515 P-type conjugative transfer ATPase TrbB virB11

Host bacterium

ID   17561 GenBank   NC_017508
Plasmid name   pHP-42 Incompatibility group   -
Plasmid size   42349 bp Coordinate of oriT [Strand]   14316..14415 [-]
Host baterium   Marinobacter adhaerens HP15

Cargo genes

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