Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   108327
Name   oriT_pCC283b_5 in_silico
Organism   Rhizobium leguminosarum strain CC283b
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP121640 (107343..107392 [+], 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_pCC283b_5
GGATCCAAGGGCGCAATTATACGTCGCTGACGCGACGCCCTGCTGAAGGG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   5568 GenBank   WP_027690605
Name   traA_QA638_RS39070_pCC283b_5 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: 131914.80 Da        Isoelectric Point: 9.2524

>WP_027690605.1 Ti-type conjugative transfer relaxase TraA [Rhizobium leguminosarum]
MAVPHFSVSIVARGSGRSAVLSAAYRHCAKMEFEREARTIDYSRKQGLLHEEFVIPETAPDWLRSMIADR
SVSGASEAFWNKVEAFEKRADAQLAKDVTIALPVELSNDQNIALVRDFVERHITAKGMVADWVYHDALGN
PHIHLMTTLRPLTEDGFGAKKVAVLAPDGKPVRNDAGKIVYELWAGSTDDFNAFRDGWFACQNRHLALAG
LDIRIDGRSFEKQGIELTPTIHLGVGTKAIERKAASGNGLAEEKVALERLELQEERRAENARRIQRNPEI
VVDLITREKSVFDERDIAKVLYRYIDDAALFQNLMARLLQSPQTLRLDRERMDLVTGVRAPAKYTTRELI
RLEAQMANQAIWLSQRSSHRVNRTVLSGIVSRHDRLSDEQKTAIEHVAGPERIAAVIGRAGAGKTTMMKA
AREAWEAAGYRVVGGALAGKAADGLEKEAGIASRTLSAWELRWDQERDRLDEKSVFVLDEAGMVSSRQMA
RFVEAVTLSGAKLVLVGDPEQLQPIEAGAAFRAIAERIGYAELETIYRQREQWMRDASLDLARGNVSAAL
DAYAQRDLVRTGWTRDEAITALIAEWDHEYDPAKSTLILAHRRVDVRLLNEMARSKLVERGLIEAGHAFK
TEDGTRQFAAGDQIVFLKNEGSLGVKNGMLALVVDAQPGRIVAEIGNGEDRRRVVVEQRFYANVDHGYAT
TVHKSQGATVDRVKVLASSTLDRHLSYVAMTRHRETAELYVGLEEFAQRRGGVLIAHGEAPYEHKPGNRD
SYYVTLGFANGQERTVWGVDLARAMDASDSRIGDRIGLKHVGSQRVTLPNGTEVDRNSWKVVPIQELAMA
RLHERLSRAGSKETTLDYQDASHYRAALRFAEARGLHLMNVARTIAHDQLQWTVRQSSKLAELGARLVAV
AAKLGLGGAKSTVSTISVIKEAKPMVFGTTTFPRSIGQAVEDKLSADPGLKASWQEVSARFHHVFADPQA
AFKAVNVDAMLANGTVAATTIVRIAEQPESFGALKGKTGLFAGSAEKQARDTALVNAPALARDLQGFIAK
RAAAARRYEDEERAVRAQLSLDIPALSASGKQVLERVRDAIDRNDIPAGLEFALADKMVKAELEGFAKAV
SERFGERTFLPLAAKTADGKAFEVASAGMQPAQKNELRSAWDTIRTVQQLAAHERTAVALKQAEAIRQTQ
TKGLSLK

  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)

(386-572)

MobA/MobL family (MobA_MobL)

(17-243)


  Protein structure



No available structure.




T4CP

ID   5937 GenBank   WP_027690606
Name   traG_QA638_RS39055_pCC283b_5 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: 70599.44 Da        Isoelectric Point: 9.7031

>WP_027690606.1 Ti-type conjugative transfer system protein TraG [Rhizobium leguminosarum]
MTPKRILVAGIPAVAMLAIALTFPGIERWLSAFGTTDQAKLMLGRIGLALPYALAGACGVMFLFGTKGSI
NVKTSGWSVAAGGLGVIAVAALREGSRLLTFASQVPARRTLLSYADPSTIIGAGTALLVTFFALRVARMG
NAAFTRSEPRRIRGKRALHGEADWMTMQEAEKLFPETGGIVIGERYRVDRDDPAATSFRPGEPTSWGRGG
SAPLLCFDGSFGSSHGIVFAGSGGFKTTSVTIPTALKWGGSLVVLDPSNEVAPMVMEHRRKAGRRVIVLD
PKNAQSGFNALDWIGRHGGTKEEDIAAVASWIMSDSGRATGVRDDFFRASGLQLLTAMIADVCLSGHTDE
KHQTLRQVRANLSEPEPKLRARLQEIYDNSASDFVKENVAAFVNMTPETFSGVYANAIKETHWLSYANYG
ALVSGSSFSTEALADGETDVFINIDLKALETHAGLARVIIGSFLNAIYHRDGAIKGRALFLLDEVARLGY
MRVLETARDAGRKYGITLTMIYQSIGQLRETYGGRDASSKWFESASWISFAAINDPETADYISRRCGTTT
VEIDQISRSFQSRGSSRTRSKQLASRQLIQPHEVLRMRADEQIVFTAGNAPLRCGRAIWFRRSDMKSCVG
ENRFQQRGDRPEVSASAEPN

  Protein domains


Predicted by InterproScan.

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

(163-635)

  Protein structure



No available structure.



ID   5938 GenBank   WP_027690590
Name   t4cp2_QA638_RS39155_pCC283b_5 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: 90951.41 Da        Isoelectric Point: 5.8208

>WP_027690590.1 conjugal transfer protein TrbE [Rhizobium leguminosarum]
MVALRTFRSTGPSFADLVPYAGLVDNGILLLKDGSLMAGWYFAGPDSESATDFERNELSRQINSILSRLG
TGWMIQVEAVRVPTTEYPSAERSHFPDAVTLLIDHERRRHFGQERGHFESRHALILTYRPPERRRSGLTR
YIYSDNESRSAKYADTALDAFRRSIREIEQYLGNVLSVQRMQTREVSERDGARVARYDELFQFIRFAITG
ENHPVRLPEIPMYLDWLATAELEHGLTPRVEGRFLGVIAIDGLPAESWPGILNSLNLMPLTYRWSSRFIF
LDAEEAKQRLERTRKKWQQKVRPFFDQLFQTQSRSVDQDAMAMVAETEDAIAEASSQLVAYGYYTPVIVL
FDESRSALQEKAEAVRRLIQAEGFGARIETLNATDAFLGSLPGNWYCNIREPLINTRNLADLVPLNSVWS
GQPFAPCPFYPPDAPPLMQVASGSTPFRLNLHVDDVGHTLIFGPTGSGKSTLLALIAAQFCRYEKAQVFA
FDKGNSMLTLTLGVGGDHYEIGGESGEGPSLAFCPLSELSTDADRAWASEWIETLVSLQGVTIAPDHRNA
ISRQIGLMASAPGRSLSDFVSGVQMREIKDALHHYTVDGPMGLLLDAEEDGLTLGRFQCFEIEQLMNMGE
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: 112789..128018

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
QA638_RS39075 (QA638_39075) 111054..111617 + 564 WP_050595854 conjugative transfer signal peptidase TraF -
QA638_RS39080 (QA638_39080) 111607..112773 + 1167 WP_027690603 conjugal transfer protein TraB -
QA638_RS39085 (QA638_39085) 112789..113406 + 618 WP_027690602 TraH family protein virB1
QA638_RS39090 (QA638_39090) 113430..114047 - 618 WP_027690601 hypothetical protein -
QA638_RS39095 (QA638_39095) 114044..114223 - 180 WP_018010295 hypothetical protein -
QA638_RS39100 (QA638_39100) 114373..115368 - 996 WP_027690600 alpha/beta hydrolase -
QA638_RS39105 (QA638_39105) 115358..116974 - 1617 WP_027690599 hypothetical protein -
QA638_RS39110 (QA638_39110) 117257..117961 + 705 WP_027690598 autoinducer binding domain-containing protein -
QA638_RS39115 (QA638_39115) 117962..118261 - 300 WP_027690597 transcriptional repressor TraM -
QA638_RS39120 (QA638_39120) 118462..119763 - 1302 WP_027690596 IncP-type conjugal transfer protein TrbI virB10
QA638_RS39125 (QA638_39125) 119779..120225 - 447 WP_027690595 conjugal transfer protein TrbH -
QA638_RS39130 (QA638_39130) 120229..121059 - 831 WP_027690594 P-type conjugative transfer protein TrbG virB9
QA638_RS39135 (QA638_39135) 121075..121737 - 663 WP_027690593 conjugal transfer protein TrbF virB8
QA638_RS39140 (QA638_39140) 121759..122940 - 1182 WP_027690592 P-type conjugative transfer protein TrbL virB6
QA638_RS39145 (QA638_39145) 122934..123134 - 201 WP_027690591 entry exclusion protein TrbK -
QA638_RS39150 (QA638_39150) 123131..123940 - 810 WP_011654759 P-type conjugative transfer protein TrbJ virB5
QA638_RS39155 (QA638_39155) 123933..126368 - 2436 WP_027690590 conjugal transfer protein TrbE virb4
QA638_RS39160 (QA638_39160) 126379..126678 - 300 WP_011654761 conjugal transfer protein TrbD virB3
QA638_RS39165 (QA638_39165) 126671..127063 - 393 WP_011654762 TrbC/VirB2 family protein virB2
QA638_RS39170 (QA638_39170) 127053..128018 - 966 WP_027690589 P-type conjugative transfer ATPase TrbB virB11

Host bacterium

ID   8762 GenBank   NZ_CP121640
Plasmid name   pCC283b_5 Incompatibility group   -
Plasmid size   128397 bp Coordinate of oriT [Strand]   107343..107392 [+]
Host baterium   Rhizobium leguminosarum strain CC283b

Cargo genes

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