Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   101178
Name   oriT_pSM141A_Rh17 in_silico
Organism   Rhizobium ruizarguesonis strain SM141A
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_SIOX01000008 (29964..30013 [-], 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_pSM141A_Rh17
GGATCCAAGGGCGCAATTATACGTCGCTGACGCGACGCCCTGCTGAAGGG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1175 GenBank   WP_115039354
Name   traA_ELH98_RS29865_pSM141A_Rh17 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: 131867.79 Da        Isoelectric Point: 9.4235

>WP_115039354.1 Ti-type conjugative transfer relaxase TraA [Rhizobium ruizarguesonis]
MAVPHFSVSIVARGSGRSAVLSAAYRHCAKMEFEREARTIDYSRKQGLLHEEFVIPETAPDWLRSMIADR
SVSGASEAFWNKVEAFEKRADAQLAKDVTIALPVELSNDQNIALVRDFVERHITAKGMVADWVYHDALGN
PHIHLMTTLRPLTEDGFGAKKVAVLAPDGKPVRNDAGKIVYELWAGSTDDFNAFRDGWFACQNRHLALAG
LDIRIDGRSFEKQGIELTPTIHLGVGTKAIERKAASGNGLAEEKVALERLELQEERRAENARRIQRNPEI
VVDLITREKSVFDERDIAKVLYRYIDDAALFQNLMARLLQSPQTLRLDRERMDLVTGVRAPAKYTTRELI
RLEAQMANQAIWLSQRSSHRVNRTVLSGIVSRHDRLSDEQKTAIEHVAGPERIAAVIGRAGAGKTTMMKA
AREAWEAAGYRVVGGALAGKAADGLEKEAGIASRTLSAWELRWDQERDRLDEKSVIVLDEAGMVSSRQMA
RFVEAVTLSGAKLVLVGDPEQLQPIEAGAAFRAIAERIGYAELETIYRQREQWMRDASLDLARGNVSAAL
DAYAQRDLVRTGWTRDEAITALIAEWDHKYDPAKSTLILAHRRVDVRLLNEMARSKLVERGLIEAGHAFK
TEDGTRQFAAGDQIVFLKNEGSLGVKNGMLALVVDAQPGRIVAEIGNGEDRRRVVVEQRFYANVDHGYAT
TVHKSQGATVDRVKVLASSTLDRHLSYVAMTRHRETAELYVGLEEFAQRRGGVLIAHGEAPYEHKPGNRD
SYYVTLGFANGQERTVWGVDLARAMDASDSRIGDRIGLKHVGSQRVTLPNGTEVDRNSWKVVPIQELAMA
RLHERLSRAGSKETTLDYQDASHYRAALRFAEARGLHLMNVARTIAHDQLQWTVRQSSKLAELGARLVAV
AAKLGLGGAKSTVSTTSVIKEAKPMVFGTTTFPRSIGQAVEDKLSADPGLKASWQEVSARFHHVFADPQA
AFKAVNVDAMLANGTVAATTIVRIAEQPESFGALKGKTGLFAGSAEKQARDTALVNAPALARDLQGFIAK
RAAAARRYEDEERAVRAQLSLDIPALSASGKQVLERVRDAIDRNDIPAGLEFALADKMVKAELEGFAKAV
SERFGERTFLPLAAKTADGKAFEVASAGMQPAQKNELRSAWDTIRTVQQLAAHERTAVALKQAEAIRQTQ
TKGLSLK

  Protein domains


Predicted by InterproScan.

AAA domain (AAA_30)

(386-572)

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

(953-1047)

MobA/MobL family (MobA_MobL)

(17-243)

Viral (Superfamily 1) RNA helicase (Viral_helicase1)

(696-739)


  Protein structure



No available structure.




T4CP

ID   769 GenBank   WP_115039372
Name   t4cp2_ELH98_RS29780_pSM141A_Rh17 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: 90978.39 Da        Isoelectric Point: 5.8031

>WP_115039372.1 conjugal transfer protein TrbE [Rhizobium ruizarguesonis]
MVALRTFRSTGPSFADLVPYAGLVDNGILLLKDGSLMAGWYFAGPDSESATDFERNELSRQINSILSRLG
TGWMIQVEAVRVPTTEYPSAERSHFPDAVTLLIDHERRRHFGQERGHFESRHALILTYRPPERRRSGLTR
YIYSDNESRSAKYADTALDAFRRSIREIEQYLGNVLSVQRMQTREVSERDGARVARYDELFQFIRFAITG
ENHPVRLPEIPMYLDWLATAELEHGLTPRVEGRFLGVIAIDGLPAESWPGILNSLNLMPLTYRWSSRFIF
LDAEEAKQRLERTRKKWQQKVRPFFDQLFQTQSRSVDQDAMAMVAETEDAIAEASSQLVAYGYYTPVIVL
FDESRSALQEKAEAVRRLIQAEGFGARIETLNATDAFLGSLPGNWYCNIREPLINTRNLADLVPLNSVWS
GQPFAPCPFYPPDAPPLMQVASGSTPFRLNLHVDDVGHTLIFGPTGSGKSTLLALIAAQFCRYEKAQVFA
FDKGNSMLTLTLGVGGDHYEIGGESGEGASLAFCPLSELSTDADRAWASEWIETLVSLQGVTIAPDHRNA
ISRQIGLMASAPGRSLSDFVSGVQMREIKDALHHYTVDGPMGLLLDAEEDGLTLGRFQCFEIEQLMNMGE
RNLVPVLTYLFRRIEKRLDGSPSLIVLDEAWLMLGHPVFRDKIREWLKVLRKANCGVILATQSISDAERS
GIIDVLKESCPTKICLPNGAARETGTREFYERIGFNARQIEIVANAIPKREYYVTSPDGRRLFDMSLGPV
TLSFVGASGKADLARIRALSSTHGLEWPDHWLIERGINRNE

  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.



ID   770 GenBank   WP_130749266
Name   traG_ELH98_RS29880_pSM141A_Rh17 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: 70585.41 Da        Isoelectric Point: 9.7031

>WP_130749266.1 MULTISPECIES: Ti-type conjugative transfer system protein TraG [Rhizobium]
MTPKRILVAGIPAVAMLAIALTFPGIERWLSAFGTTDQAKLMLGRIGLALPYALAGACGVMFLFGTKGSI
NVKTSGWSVAAGGLGVIAVAALREGSRLLTFASQVPARRTLLSYADPSTIIGAGTALLVTFFALRVARMG
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.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 9338..24567

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
ELH98_RS29750 (ELH98_29745) 5292..6536 - 1245 WP_115039376 plasmid replication protein RepC -
ELH98_RS29755 (ELH98_29750) 6694..7686 - 993 WP_064251333 plasmid partitioning protein RepB -
ELH98_RS29760 (ELH98_29755) 7768..8958 - 1191 WP_018009855 plasmid partitioning protein RepA -
ELH98_RS29765 (ELH98_29760) 9338..10303 + 966 WP_028744194 P-type conjugative transfer ATPase TrbB virB11
ELH98_RS29770 (ELH98_29765) 10293..10685 + 393 WP_115039374 TrbC/VirB2 family protein virB2
ELH98_RS29775 (ELH98_29770) 10678..10977 + 300 WP_011654761 conjugal transfer protein TrbD virB3
ELH98_RS29780 (ELH98_29775) 10988..13423 + 2436 WP_115039372 conjugal transfer protein TrbE virb4
ELH98_RS29785 (ELH98_29780) 13416..14225 + 810 WP_011654759 P-type conjugative transfer protein TrbJ virB5
ELH98_RS29790 (ELH98_29785) 14222..14422 + 201 WP_028744197 entry exclusion protein TrbK -
ELH98_RS29795 (ELH98_29790) 14416..15597 + 1182 WP_028744198 P-type conjugative transfer protein TrbL virB6
ELH98_RS29800 (ELH98_29795) 15619..16281 + 663 WP_115039370 conjugal transfer protein TrbF virB8
ELH98_RS29805 (ELH98_29800) 16333..17127 + 795 Protein_15 P-type conjugative transfer protein TrbG -
ELH98_RS29810 (ELH98_29805) 17131..17577 + 447 WP_115039367 conjugal transfer protein TrbH -
ELH98_RS29815 (ELH98_29810) 17593..18894 + 1302 WP_115039365 IncP-type conjugal transfer protein TrbI virB10
ELH98_RS29820 (ELH98_29815) 19095..19394 + 300 WP_027690597 transcriptional repressor TraM -
ELH98_RS29825 (ELH98_29820) 19395..20099 - 705 WP_115039418 autoinducer binding domain-containing protein -
ELH98_RS29830 (ELH98_29825) 20382..21998 + 1617 WP_115039363 hypothetical protein -
ELH98_RS29835 (ELH98_29830) 21988..22983 + 996 WP_115039362 dienelactone hydrolase-related enzyme -
ELH98_RS29840 (ELH98_29835) 23133..23312 + 180 WP_018010295 hypothetical protein -
ELH98_RS29845 (ELH98_29840) 23369..23926 + 558 WP_245486992 hypothetical protein -
ELH98_RS29850 (ELH98_29845) 23950..24567 - 618 WP_115039357 TraH family protein virB1
ELH98_RS29855 (ELH98_29850) 24583..25749 - 1167 WP_115039355 conjugal transfer protein TraB -
ELH98_RS29860 (ELH98_29855) 25739..26302 - 564 WP_050595854 conjugative transfer signal peptidase TraF -

Host bacterium

ID   1622 GenBank   NZ_SIOX01000008
Plasmid name   pSM141A_Rh17 Incompatibility group   -
Plasmid size   252224 bp Coordinate of oriT [Strand]   29964..30013 [-]
Host baterium   Rhizobium ruizarguesonis strain SM141A

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   fixB, fixA
Anti-CRISPR   -