Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   102551
Name   oriT_pSM52_Rh13 in_silico
Organism   Rhizobium leguminosarum strain SM52
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_SILH01000005 (103706..103755 [-], 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_pSM52_Rh13
GGATCCAAGGGCGCAATTATACGTCGCTGACGCGACGCCCTGCTGAAGGG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1902 GenBank   WP_011654745
Name   traA_ELH04_RS35635_pSM52_Rh13 insolico UniProt ID   Q1M997
Length   1197 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1197 a.a.        Molecular weight: 131887.62 Da        Isoelectric Point: 9.1379

>WP_011654745.1 MULTISPECIES: Ti-type conjugative transfer relaxase TraA [Rhizobium]
MAVPHFSVSIVARGSGRSAVLSAAYRHCAKMEFEREARTIDYSRKQGLLHEEFVIPETAPDWLRSMIADR
SVSGASEAFWNKVEAFEKRADAQLAKDVTIALPVELSNDQNIALVRDFVERHITAKGMVADWVYHDALGN
PHIHLMTTLRPLTEDGFGAKKVAVLAPAGKPVRNDAGKIVYELWAGSTDDFNAFRDGWFACQNRHLALAG
LDIRIDGRSFEKQGIELTPTIHLGVGTKAIERKGDNKTGWGEEKVALERLELQEERRAENARRIQRNPEI
VLDLITREKSVFDERDIAKILYRYIDDAALFQNLMARILQSPQTLRLDRERMDLVTGVRAPSKYTTRELI
RLEAQMANQAIWLSQRSSHGVRHAVLSGVFSRHDRLSDEQKTAIEHVAGPERIAAVIGRAGAGKTTMMKA
ARQAWEAAGYRVVGGALAGKAAEGLEKEAGIASRTLSAWELRWDQERDRLDEKSVFVLDEAGMVSSRQMA
RFVEAVTVSGAKLVLVGDPEQLQPIEAGAAFRAISGRIGYAELETIYRQREQWMRDASLDLARGNVSAAL
DAYAQRDMVRTGWTRDEAITALIADWDHEYDPAKSTLILAHRRIDVRLLNEMARSKLVERGLIEAGHAFK
TEDGTRQLAAGDQIVFLKNEGSLGVKNGMLARVVDAQPGRIVAEIGNGEDRRRVVVEQRFYANVDHGYAT
TVHKSQGATVDRVKVLASSTLDRHLSYVAMTRHRETAELYVGLEEFAQRRGGVLIAHGEAPYEHKPGNRD
SYYVTLGFADGQERTVWGVDLARAMDASGARIGDRIGLKHVGSQRVTLPDGTEVDRNSWKVVPVEELAMA
RLHERLSRPGSKETTLDYQDASHYRAALRFAEARSLHLMNVARTIAHDQLQWTIRQSSKLAELGARLVAV
AAKLGLGGAKSTVSTTSAIKEAKPMVSGTTTFPRSIGQAAEDKLSADPGLKASWQEVSARFHHVFADPQA
AFKTVNVDAMLANGTVAATTIVQIAEQPESFGALKGKTGLFAGSAEKRAHDTALVNAPALARDLQGFIAK
RAEAASRYEDEERAVRTKLSLDIPALSASAKQVLERVRDAIDRNDIPAGLEFALADKMVKAELEGFAKAV
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)

Viral (Superfamily 1) RNA helicase (Viral_helicase1)

(696-739)

MobA/MobL family (MobA_MobL)

(17-243)


  Protein structure


Source ID Structure
AlphaFold DB Q1M997


T4CP

ID   1513 GenBank   WP_011654760
Name   t4cp2_ELH04_RS35550_pSM52_Rh13 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: 90895.34 Da        Isoelectric Point: 5.8208

>WP_011654760.1 MULTISPECIES: conjugal transfer protein TrbE [Rhizobium]
MVALRTFRSTGPSFADLVPYAGLVDNGILLLKDGSLMAGWYFAGPDSESATDFERNELSRQINSILSRLG
TGWMIQVEAVRVPTTEYPSAERSHFPDAVTLLIDHERRRHFGQERGHFESRHALILTYRPPERRRSGLTR
YIYSDNESRSAKYADTALDAFRRSIREIEQYLGNVLSVQRMQTREVSERDGARVARYDELFQFIRFAITG
ENHPVRLPEIPMYLDWLATAELEHGLTPRVEGRFLGVIAIDGLPAESWPGILNSLNLMPLTYRWSSRFIF
LDAEEAKQRLERARKKWQQKVRPFFDQLFQTQSRSVDQDAMAMVAETEDAIAEASSQLVAYGYYTPVIVL
FDESRSALQEKAEAVRRLIQAEGFGARIETLNATDAFLGSLPGNWYCNIREPLINTRNLADLVPLNSVWS
GQPFAPCPFYPPDAPPLMQVASGSTPFRLNLHVDDVGHTLIFGPTGSGKSTLLALIAAQFCRYEKAQVFA
FDKGNSMLTLTLGVGGDHYEIGGESGEGASLAFCPLSELSTDADRAWASEWIETLVSLQGVTIAPDHRNA
ISRQIGLMASAPGRSLSDFVSGVQMREIKDALHHYTVDGPMGLLLDAEEDGLTLGRFQCFEIEQLMNMGE
RNLVPVLTYLFRRIEKRLDGSPSLIVLDEAWLMLGHPVFRDKIREWLKVLRKANCAVILATQSISDAERS
GIIDVLKESCPTKICLPNGAARETGTREFYERIGFNARQIEIVANAIPKREYYVTSPDGRRLFDMSLGPV
TLSFVGASGKADLARIRALSSTHGLEWPGQWLIERGINRNE

  Protein domains


Predicted by InterproScan.

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

(186-400)

Helicase HerA, central domain (DUF87)

(457-492)

  Protein structure



No available structure.



ID   1514 GenBank   WP_011654742
Name   traG_ELH04_RS35650_pSM52_Rh13 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: 70597.42 Da        Isoelectric Point: 9.7031

>WP_011654742.1 MULTISPECIES: Ti-type conjugative transfer system protein TraG [Rhizobium]
MTPKRILVAGIPAVAMVAIALTFPGIERWLSAFGTTDQAKLMLGRIGLALPYALAGACGVMFLFGTKGSI
NVKTSGWSVAAGGLGVIAVAALREGSRLLTFASQVPARRTLLSYADPSTIIGAGTALLVTFFALRVARMG
NAAFTRSEPRRIRGKRALHGEADWMTMQEAEKLFPETGGIVIGERYRVDRDDPAATSFRPGEPTSWGRGG
SPPLLCFDGSFGSSHGIVFAGSGGFKTTSVTIPTALKWGGSLVVLDPSNEVAPMVMEHRRKAGRRVIVLD
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: 83081..98309

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
ELH04_RS35520 (ELH04_35520) 79041..80258 - 1218 WP_011654635 plasmid replication protein RepC -
ELH04_RS35525 (ELH04_35525) 80433..81392 - 960 WP_011654634 plasmid partitioning protein RepB -
ELH04_RS35530 (ELH04_35530) 81516..82712 - 1197 WP_011654633 plasmid partitioning protein RepA -
ELH04_RS35535 (ELH04_35535) 83081..84046 + 966 WP_011654763 P-type conjugative transfer ATPase TrbB virB11
ELH04_RS35540 (ELH04_35540) 84036..84428 + 393 WP_011654762 TrbC/VirB2 family protein virB2
ELH04_RS35545 (ELH04_35545) 84421..84720 + 300 WP_011654761 conjugal transfer protein TrbD virB3
ELH04_RS35550 (ELH04_35550) 84731..87166 + 2436 WP_011654760 conjugal transfer protein TrbE virb4
ELH04_RS35555 (ELH04_35555) 87159..87968 + 810 WP_011654759 P-type conjugative transfer protein TrbJ virB5
ELH04_RS35560 (ELH04_35560) 87965..88165 + 201 WP_028744197 entry exclusion protein TrbK -
ELH04_RS35565 (ELH04_35565) 88159..89340 + 1182 WP_011654758 P-type conjugative transfer protein TrbL virB6
ELH04_RS35570 (ELH04_35570) 89362..90024 + 663 WP_011654757 conjugal transfer protein TrbF virB8
ELH04_RS35575 (ELH04_35575) 90040..90870 + 831 WP_011654756 P-type conjugative transfer protein TrbG virB9
ELH04_RS35580 (ELH04_35580) 90874..91320 + 447 WP_011654755 conjugal transfer protein TrbH -
ELH04_RS35585 (ELH04_35585) 91336..92634 + 1299 WP_011654754 IncP-type conjugal transfer protein TrbI virB10
ELH04_RS35590 (ELH04_35590) 92836..93135 + 300 WP_011654753 transcriptional repressor TraM -
ELH04_RS35595 (ELH04_35595) 93136..93840 - 705 WP_011654752 autoinducer binding domain-containing protein -
ELH04_RS35600 (ELH04_35600) 94128..95747 + 1620 WP_130749038 hypothetical protein -
ELH04_RS35605 (ELH04_35605) 95737..96732 + 996 WP_011654750 alpha/beta hydrolase -
ELH04_RS35610 (ELH04_35610) 96875..97054 + 180 WP_018010295 hypothetical protein -
ELH04_RS35615 (ELH04_35615) 97051..97668 + 618 WP_011654749 hypothetical protein -
ELH04_RS35620 (ELH04_35620) 97692..98309 - 618 WP_011654748 TraH family protein virB1
ELH04_RS35625 (ELH04_35625) 98325..99491 - 1167 WP_011654747 conjugal transfer protein TraB -
ELH04_RS35630 (ELH04_35630) 99481..100047 - 567 WP_011654746 conjugative transfer signal peptidase TraF -

Host bacterium

ID   2995 GenBank   NZ_SILH01000005
Plasmid name   pSM52_Rh13 Incompatibility group   -
Plasmid size   147600 bp Coordinate of oriT [Strand]   103706..103755 [-]
Host baterium   Rhizobium leguminosarum strain SM52

Cargo genes

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