Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   106887
Name   oriT_pLPU83a in_silico
Organism   Rhizobium favelukesii strain LPU83
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_HG916853 (130706..130755 [+], 50 nt)
oriT length   50 nt
IRs (inverted repeats)      22..27, 32..37  (CGTCGC..GCGACG)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 50 nt

>oriT_pLPU83a
GGATCCAAGGGCGCAATTATACGTCGCTGACGCGACGCCCTGCTGAAGGG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   4554 GenBank   WP_024316914
Name   traA_LPU83_RS59815_pLPU83a insolico UniProt ID   V5RE37
Length   1197 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1197 a.a.        Molecular weight: 131785.69 Da        Isoelectric Point: 9.3457

>WP_024316914.1 Ti-type conjugative transfer relaxase TraA [Rhizobium favelukesii]
MAVPHFSVSIVARGSGRSAVLSAAYRHCAKMEFEREARTIDYSRKQGLLHEEFVIPETAPDWLRSMIADR
SVSGASEAFWNKVEAFEQRADAQLAKDVTIALPVELSNDQNIALVRDFVERHITAKGMVADWVYHDALGN
PHIHLMTTLRPLTEDGFGAKKVAVLAPDGKPVRNDAGKIVYELWAGSAADFNAFRDGWFACQNRHLALAG
LDIRIDGRSFEKQGIELTPTIHLGVGTKAIERKAASGNGLAEEKVALERLELQEERRAENARRIQRNPEI
VVDLITREKSVFDERDIAKVLYRYIDDAALFQNLMARLLQSPQTLRLDRERMDLVTGVRAPAKYTTRELI
RLEAQMANQAIWLSQRSSHRVNRTVLSGIVSRHDRLSDEQKTASEHVAGPERIAAVIGRAGAGKTTMMKA
AREAWEAAGYRVVGGALAGKAADGLEKEAGIASRTLSAWELRWDQERDRLDEKSVFVLDEAGMVSSRQMA
RFVEAVTLSGAKLVLVGDPEQLQPIEAGAAFRAIAERIGYAELETIYRQREQWMRDASLDLARGNVSAAL
DAYAQRDLVRTGWTRDEAITALIAEWDHEYDPAKSTLILAHRRVDVRLLNEMARSKLVERGLIEAGHAFK
TEDGTRQFAAGDQIVFLKNEGSLGVKNGMLALVVDAQPGRIVAEIGNGEDRRRVVVEQRFYANVDHGYAT
TVHKSQGATVDRVKVLASSTLDRHLSYVAMTRHRETAELYVGLEEFAQRRGGVLIAHGEAPYEHKPGNRD
SYYVTLGFANGQERTVWGVDLARAMDASGARIGDRIGLKHVGSQRVTLPDGTEVDRNSWKVVPIEELAMA
RLHERLSRAGSKETTLDYQDASHYRAALRFAEARGLHLMNVARTIAHDQLQWTIRQSSKLAELGARLVAV
AAKLGLGGAKSTVSTTSVIKEAKPMVFGTTTFPRSIGQAVEDKLSADPGLKASWQEVSARFHHVFADPQA
AFKAVNVDAMLANGTVAVTTIVRIAEQPESFGALKGKTGLFAGSAEKQARDTALVNAPALARDLQGFIAK
RAAAARRYEDEERAVRAQLSLDIPALSASAKQVLERVRDAIDRNDIPAGLEFALADKMVKAELEGFAKAV
SKRFGERTFLPLAAKTADGKAFEVASAGMQPAQKNELRSAWDTIRTVQQLAAHERTAVALKQAEAIRQTQ
TKGLSLK

  Protein domains


Predicted by InterproScan.

Viral (Superfamily 1) RNA helicase (Viral_helicase1)

(696-739)

AAA domain (AAA_30)

(386-572)

MobA/MobL family (MobA_MobL)

(17-243)

BID domain of Bartonella effector protein (Bep) (Bep_C_terminal)

(953-1047)


  Protein structure


Source ID Structure
AlphaFold DB V5RE37


T4CP

ID   4637 GenBank   WP_024316912
Name   traG_LPU83_RS59800_pLPU83a insolico UniProt ID   _
Length   650 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 650 a.a.        Molecular weight: 70571.38 Da        Isoelectric Point: 9.7031

>WP_024316912.1 Ti-type conjugative transfer system protein TraG [Rhizobium favelukesii]
MTPKRILVAGIPAVAMLAIALTFPGIERWLSAFGTTDQAKLMLGRIGLALPYALAGACGVMFLFGTKGSI
NVKTSGWSVAAGGLGVIAVAALREGSRLLTFASQVPARRTLLSYADPSTIVGAGTALLVTFFALRVARMG
NAAFTRSEPRRIRGKRALHGEADWMTMQEAEKLFPETGGIVIGERYRVDRDDPAATSFRPGEPTSWGRGG
SAPLLCFDGSFGSSHGIVFAGSGGFKTTSVTIPTALKWGGSLVVLDPSNEVAPMVMEHRRKAGRRVIVLD
PKNAQSGFNALDWIGRHGGTKEEDIAAVASWIMSDSGRATGVRDDFFRASGLQLLTAMIADVCLSGHTDE
KHQTLRQVRANLSEPEPKLRARLQEIYDNSASDFVKENVAAFVNMTPETFSGVYANAIKETHWLSYANYG
ALVSGSSFSTEALADGETDVFINIDLKALETHAGLARVIIGSFLNAIYHRDGAIKGRALFLLDEVARLGY
MRVLETARDAGRKYGITLTMIYQSIGQLRETYGGRDASSKWFESASWISFAAINDPETADYISRRCGTTT
VEIDQVSRSFQSRGSSRTRSKQLASRQLIQPHEVLRMRADEQIVFTAGNAPLRCGRAIWFRRSDMKSCVG
ENRFQQRGDRPEVSASAEPN

  Protein domains


Predicted by InterproScan.

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

(163-635)

  Protein structure



No available structure.



ID   4638 GenBank   WP_024316929
Name   t4cp2_LPU83_RS59900_pLPU83a insolico UniProt ID   _
Length   811 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 811 a.a.        Molecular weight: 90869.25 Da        Isoelectric Point: 5.5107

>WP_024316929.1 conjugal transfer protein TrbE [Rhizobium favelukesii]
MVALRTFRSTGPSFADLVPYAGLVDNGILLLKDGSLMAGWYFAGPDSESATDFERNELSRQINSILSRLG
TGWMIQVEAVRVPTTEYPSAERSHFPDTVTLLIDDERRRHFGQERGHFESRHALILTYRPPERRRSGLTR
YIYSDTESRSAKYADTALDAFQRSIREIEQYLGNVLSVQRMQTREVSERDGSRVARYDELFQFIRFAITG
ENHPVRLPEIPMYLDWLATAELEHGLTPRVEGRFLGVIAIDGLPAESWPGILNSLNLMPLTYRWSSRFIF
LDAEEAKQRLERTRKKWQQKVRPFFDQLFQTQSRSVDQDAMAMVAETEDAIAEASSQLVAYGYYTPVIIL
FDESRTALQEKAEAVRRLIQAEGFGARIETLNATDAFLGSLPGNWYCNIREPLINTRNLADLVPLNSVWS
GQPAAPCPFYPPAAPPLMQVASGSTPFRLNLHVDDVGHTLIFGPTGSGKSTLLALIAAQFCRYEKAQVFA
FDKGNSMLPLTLGVGGDHYEIGGESGEGASLAFCPLSELETDADRAWASEWIETLVSLQGVTIAPDHRNA
ISRQIGLMASAPGRSLSDFVSGVQMREIKDALHHYTVDGPMGQLLDAEEDGLTLGRFQCFEIEQLMNMGE
RNLVPVLTYLFRRIEKRLDGSPSLIVLDEAWLMLGHPVFRDKIREWLKVLRKANCAVILATQSISDAERS
GILDVLKESCPTKICLPNGAARETGTREFYERIGFNARQIEIVANAIPKREYYVTSPDGRRLFDMSLGPV
TLSFVGASGKADLARIRALSSTHGLEWPGQWLIERGINRNE

  Protein domains


Predicted by InterproScan.

Helicase HerA, central domain (DUF87)

(457-492)

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

(186-400)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 136152..151386

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
LPU83_RS59820 (LPU83_pLPU83a_0142) 134417..134980 + 564 WP_051166711 conjugative transfer signal peptidase TraF -
LPU83_RS59825 (LPU83_pLPU83a_0143) 134970..136136 + 1167 WP_024316916 conjugal transfer protein TraB -
LPU83_RS59830 (LPU83_pLPU83a_0144) 136152..136769 + 618 WP_024316917 TraH family protein virB1
LPU83_RS59835 (LPU83_pLPU83a_0145) 136793..137410 - 618 WP_024316918 hypothetical protein -
LPU83_RS59840 137407..137586 - 180 WP_018010295 hypothetical protein -
LPU83_RS59845 (LPU83_pLPU83a_0146) 137736..138731 - 996 WP_024316919 alpha/beta hydrolase -
LPU83_RS59850 (LPU83_pLPU83a_0148) 138721..140345 - 1625 Protein_150 hypothetical protein -
LPU83_RS59855 (LPU83_pLPU83a_0149) 140613..141332 + 720 WP_032495735 autoinducer binding domain-containing protein -
LPU83_RS59860 (LPU83_pLPU83a_0150) 141333..141632 - 300 WP_024316922 transcriptional repressor TraM -
LPU83_RS59865 (LPU83_pLPU83a_0151) 141833..143131 - 1299 WP_024316923 IncP-type conjugal transfer protein TrbI virB10
LPU83_RS59870 (LPU83_pLPU83a_0152) 143147..143593 - 447 WP_024316924 conjugal transfer protein TrbH -
LPU83_RS59875 (LPU83_pLPU83a_0153) 143597..144427 - 831 WP_024316925 P-type conjugative transfer protein TrbG virB9
LPU83_RS59880 (LPU83_pLPU83a_0154) 144443..145105 - 663 WP_024316926 conjugal transfer protein TrbF virB8
LPU83_RS59885 (LPU83_pLPU83a_0155) 145127..146308 - 1182 WP_024316927 P-type conjugative transfer protein TrbL virB6
LPU83_RS59890 (LPU83_pLPU83a_0156) 146302..146502 - 201 WP_024316928 entry exclusion protein TrbK -
LPU83_RS59895 (LPU83_pLPU83a_0157) 146499..147308 - 810 WP_011654759 P-type conjugative transfer protein TrbJ virB5
LPU83_RS59900 (LPU83_pLPU83a_0158) 147301..149736 - 2436 WP_024316929 conjugal transfer protein TrbE virb4
LPU83_RS59905 (LPU83_pLPU83a_0159) 149747..150046 - 300 WP_024316930 conjugal transfer protein TrbD virB3
LPU83_RS59910 (LPU83_pLPU83a_0160) 150039..150431 - 393 WP_024316931 TrbC/VirB2 family protein virB2
LPU83_RS59915 (LPU83_pLPU83a_0161) 150421..151386 - 966 WP_024316932 P-type conjugative transfer ATPase TrbB virB11

Host bacterium

ID   7324 GenBank   NZ_HG916853
Plasmid name   pLPU83a Incompatibility group   -
Plasmid size   151687 bp Coordinate of oriT [Strand]   130706..130755 [+]
Host baterium   Rhizobium favelukesii strain LPU83

Cargo genes

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