Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   107642
Name   oriT_pRL23b4 in_silico
Organism   Rhizobium leguminosarum bv. trifolii strain 23B
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP050090 (33944..33993 [-], 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_pRL23b4
GGATCCAAGGGCGCAATTATACGTCGCTGACGCGACGCCCTGCTGAAGGG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   5136 GenBank   WP_166481265
Name   traA_HA463_RS37625_pRL23b4 insolico UniProt ID   _
Length   1197 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1197 a.a.        Molecular weight: 131875.34 Da        Isoelectric Point: 8.3961

>WP_166481265.1 Ti-type conjugative transfer relaxase TraA [Rhizobium leguminosarum]
MAVPHFSVSIVARGSGRSAVLSAAYRHCAKMEFEREARTIDYSRKQGLLHEEFVIPETAPDWLRSMIADR
SVSGASEAFWNKVEAFEKRADAQLAKDVTIALPVELSNDQNIALVRDFVERHITAKGMVADWVYHDALGN
PHIHLMTTLRPLTEDGFGAKKVAVLAPDGKPVRNDAGKIVYELWAGSTDDFNAFRDGWFACQNRHLALAG
LDIRIDGRSFEKQGIELTPTIHLGVGTKAIERKAASGNGLAEEKVALERLELQEERRAENARRIQRNPEI
VVDLITREKSVFDGRDIAKVLYRYIDDAALFQNLMARLLQSPQTLRLDRERMDLVTGVRAPAKYTTRELI
RLEAQMANQAIWLSQRSSHRVNRTVLSGIVSRHDRLSDEQKTAIEHVAGPERIAAVIGRAGAGKTTMMKA
AREAWEAAGYRVVGGALAGKAADGLEKEAGIASRTLSAWELRWDQERDRLDEKTVFVLDEAGMVSSRQMA
RFVEAVTASGSKLVLVGDPEQLQPIEAGAAFRAISERIGYAELETIYRQREQWMRDASLDLARGNVSAAL
DAHAQRDLVRTSWTRDEAVTALIADWDHEYDPAKSTLILAHRRVDVRLLNEMARSKLVERGVIEAGHAFK
TEDGTRHFAAGDQIVFLKNEGSLGVKNGMLALVVDAQPGRIVADIGDGEDHRQVVVEQRFYANVDHGYAT
TVHKSQGATVDRVKVLASSTLDRHLSYVAMTRHRETAELYVGLEEFAQRRGGVLIAHGEAPYEHKSDNRN
SYYVTLSFADGQERTVWGVDLARAMDASDAKIGDRIGLKHVGSQRVTLPNGTEVDRNSWKVVPIEELAMA
RLHERLSRAGSKETTLDYQDASHYRAALRFAEARGLHLMNVARTIAHDQLQWTVRQSSKLAELGARLAAV
AARLGLGRAKSTASTTSVIKEVKPMVSGTTTFPRSIGQAVEDRLSTDPSLKDSWGEVSARFHHVFADPQA
AFKAVNVDAMLANGTVAATTIARIAEQPESFGALKGKTGLFAGSAEKQARDTALVNAPALARDLQGFIAK
RAEAASRYEDEERAVRTKLSLDIPALSASAKQVLERVRDAIDRNDIPAGLEFALADKMVKAELEGFAKAV
SERFGERTFLPLAAKTADGKAFEAASAGMQPAQKNELRSAWDTIRTVQQLAAHERTAVALKQAETMRQTQ
AKGLSLK

  Protein domains


Predicted by InterproScan.

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

(953-1047)

Viral (Superfamily 1) RNA helicase (Viral_helicase1)

(696-739)

AAA domain (AAA_30)

(386-571)

MobA/MobL family (MobA_MobL)

(17-243)


  Protein structure



No available structure.




T4CP

ID   5370 GenBank   WP_128409068
Name   traG_HA463_RS37640_pRL23b4 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: 70644.48 Da        Isoelectric Point: 9.7942

>WP_128409068.1 Ti-type conjugative transfer system protein TraG [Rhizobium leguminosarum]
MTPKRILVAGIPAVAMLAIALTFPGIERWLSAFGTTDQAKLMLGRIGLALPYALAGACGVMFLFGTKGSI
NVKTSGWSVAAGGLGVIAVAALREGSRLLTFASQVPARRTLLSYADPSTIIGAGTALLVTFFALRVARMG
NAAFTRSEPRRIRGKRALHGEADWMTMQEAEKLFPETGGIVIGERYRVDRDDPAATSFRPGEPTSWGRGG
SAPLLCFDGSFGSSHGIVFAGSGGFKTTSVTIPTALKWGGSLVVLDPSNEVAPMVMEHRRKAGRRVIVLD
PKNAQSGFNALDWIGRHGGTKEEDIAAVASWIMSDSGRATGVRDDFFRASGLQLLTAMIADVCLSGHTDE
KHQTLRQVRANLSEPEPKLRARLQEIYDNSASDFVKENVAAFVNMTPETFSGVYANAIKETHWLSYANYG
ALVSGSSFSTEALADGETDVFINIDLKALETHAGLARVIIGSFLNAIYHRDGAIKGRALFLLDEVARLGY
MRVLETARDAGRKYGITLTMIYQSIGQLRETYGGRDASSKWFESASWISFAAINDPETADYISRRCGTTT
VEIDQVSRSFQSRGSSRTRSKQLASRQLIQPHEVLRMRADEQIVFTAGNAPLRCGRAIWFRRSDMKSCVG
ENRFQQRGDRREVSASAEPN

  Protein domains


Predicted by InterproScan.

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

(163-635)

  Protein structure



No available structure.



ID   5371 GenBank   WP_166481280
Name   t4cp2_HA463_RS38590_pRL23b4 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: 90941.41 Da        Isoelectric Point: 5.9352

>WP_166481280.1 conjugal transfer protein TrbE [Rhizobium leguminosarum]
MVALRTFRSTGPSFADLVPYAGLVDNGILLLKDGSLMAGWYFAGPDSESATDFERNELSRQINSILSRLG
TGWMIQVEAVRVPTTEYPSAERSHFPDAVTLLIDHERRRHFGQERGHFESRHALILTYRPPERRRSGLTR
YIYSDKESRSAKYADTALDAFRRSIREIEQYLGNVLSVQRMQTREVSERDGARVARYDELFQFIRFAITG
ENHPVRLPEIPMYLDWLATAELEHGLTPRVEGRFLGVIAIDGLPAESWPGILNSLNLMPLTYRWSSRFIF
LDAEEAKQRLERTRKKWQQKVRPFFDQLFQTQSRSVDQDAMAMVAETEDAIAEASSQLVAYGYYTPVIVL
FDESRSALQEKAEAVRRLIQAEGFGARIETLNATDAFLGSLPGNWYCNIREPLINTRNLADLVPLNSVWS
GQPFGPCPFYPPDAPPLMQVASGSTPFRLNLHVDDVGHTLIFGPTGSGKSTLLALIAAQFCRYEKAQVFA
FDKGNSMLTLTLGVGGDHYEIGGESGEGASLAFCPLSELSTDADRAWASEWIETLVSLQGVTIAPDHRNA
ISRQIGLMASAPGRSLSDFVSGVQMREIKDALHHYTVDGPMGLLLDAEEDGLTLGRFQCYEIEQLMNMGE
RNLVPVLTYLFRRIEKRLDGSPSLIVLDEAWLMLGHPVFRDKIREWLKVLRKANCAVILATQSISDAERS
GIIDVLKESCPTKICLPNGAARETGTREFYERIGFNARQIEIVANAIPKREYYVTSPDGRRLFDMSLGPV
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: 204485..214041

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HA463_RS39420 199543..199737 - 195 Protein_214 segregation and condensation protein B -
HA463_RS38525 (HA463_38520) 199793..200494 - 702 WP_166481279 IS6 family transposase -
HA463_RS39425 201086..202450 + 1365 WP_245458346 ATP-binding protein -
HA463_RS38535 (HA463_38530) 202754..202849 + 96 Protein_217 integrase -
HA463_RS39430 (HA463_38535) 203008..203309 + 302 Protein_218 DDE-type integrase/transposase/recombinase -
HA463_RS38545 (HA463_38540) 203352..203567 + 216 WP_164903359 hypothetical protein -
HA463_RS38550 (HA463_38545) 203636..204343 + 708 Protein_220 IS630 family transposase -
HA463_RS38555 (HA463_38550) 204485..205786 - 1302 WP_028744200 IncP-type conjugal transfer protein TrbI virB10
HA463_RS38560 (HA463_38555) 205802..206248 - 447 WP_028744199 conjugal transfer protein TrbH -
HA463_RS38565 (HA463_38560) 206252..207082 - 831 WP_011654756 P-type conjugative transfer protein TrbG virB9
HA463_RS38570 (HA463_38565) 207098..207760 - 663 WP_027690593 conjugal transfer protein TrbF virB8
HA463_RS38575 (HA463_38570) 207782..208963 - 1182 WP_128409161 P-type conjugative transfer protein TrbL virB6
HA463_RS38580 (HA463_38575) 208957..209157 - 201 WP_028744197 entry exclusion protein TrbK -
HA463_RS38585 (HA463_38580) 209154..209963 - 810 WP_011654759 P-type conjugative transfer protein TrbJ virB5
HA463_RS38590 (HA463_38585) 209956..212391 - 2436 WP_166481280 conjugal transfer protein TrbE virb4
HA463_RS38595 (HA463_38590) 212402..212701 - 300 WP_011654761 conjugal transfer protein TrbD virB3
HA463_RS38600 (HA463_38595) 212694..213086 - 393 WP_032993671 TrbC/VirB2 family protein virB2
HA463_RS38605 (HA463_38600) 213076..214041 - 966 WP_128409163 P-type conjugative transfer ATPase TrbB virB11

Host bacterium

ID   8077 GenBank   NZ_CP050090
Plasmid name   pRL23b4 Incompatibility group   -
Plasmid size   214420 bp Coordinate of oriT [Strand]   33944..33993 [-]
Host baterium   Rhizobium leguminosarum bv. trifolii strain 23B

Cargo genes

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