Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   121140
Name   oriT_pRRI128_4 in_silico
Organism   Sinorhizobium meliloti strain RRI128
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP088117 (75492..75528 [-], 37 nt)
oriT length   37 nt
IRs (inverted repeats)     _
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 37 nt

>oriT_pRRI128_4
GGATCCAAGGGCGCAATTATACGTCGCTGGCGCTACG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   13347 GenBank   WP_231198767
Name   traA_SmelRRI128_RS33605_pRRI128_4 insolico UniProt ID   _
Length   1208 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1208 a.a.        Molecular weight: 133745.21 Da        Isoelectric Point: 7.0409

>WP_231198767.1 Ti-type conjugative transfer relaxase TraA [Sinorhizobium meliloti]
MAVPHFSVSIVARGSGRSAVLSAAYRHCAKMDFEREARTIDYTRKQGLLHEEFVVPEDAPEWLRAMISDE
SVSGASEAFWNSVESCEKRSDAQLAKDVTIALPIELSAEQNIALIRDFVERHIIARGMVADWVYHDAPGN
PHIHMMTTLRPLTDDGFGSKKVAILGPDGRRQRNDAGKIVYELWAGGADDFNAFRDGWFACQNRHLALAG
LDVRVDGRSFEKQGIALEPTIHVGVGATAIERKADGAGETASTAKLERIELQEERRDENARRIQRDPGLV
LDLITREKSVFDERDIAKVLHRYIDDPGLFRDLMARVLHHPDALRLDSERILFSTGARSPAKYTTHDLIR
IEAEMANRAVWLARQRSHQIARRVLAQTFERHDLLSGEQKSAIEHIAGDARIAAVVGRAGAGKTTMMKAA
REAWEAAGYRVVGAALAGKAAEGLEKEAGIASRTLSAWELRWDQDRDNLDDKIVMVLDEAGMVSSRQMAR
FVEAATMSGAKLVLIGDPDQLQPIEAGAAFRAISERIGYAELETIYRQREQWMRDASLDLARGNVSAALA
AYESQDMVRTGWTRDDAITDLIADWDRDYDPAKSSLILAHRRRDVRVLNEMARGKLVERGLIEAGHAFKT
EDGPRQFAAGDQIVFLRNEGSLGVNNGMLARVVEAQPGRLVADIESGDDRRVVVVEQSFYANVDYGYATT
VHKSQGATVDRVKVLASSTLDRHLSYVAMTRHRETAELYVGLEEFAQRRAGVLIAHGEAPYEHKPGNRDS
YYVTLGFADGQERTVWGVDLARAMDVADVRIGDRIGLERVASERVRLPDGTEAERNSWKVVPVADLAMAR
MRERLSRDASKETTLDYQNASSYRAALHFADMRGLHLMNVGRTLLRDRLHWTIRQKQKLTDLVSRLAAVG
ARLGLRPSVGGERQVRGASEIQNQPNSVVQEDRKPMVAGITTFAKSIEKSVEDKVSADPASMSQWQEVSA
RFHLVYADPQGAFNKVNVEAMVGSSETAKTTLATISKQPESFGPLKGKTGLFAGKGESRARETALVNVPA
LARDLDGYLQKRAEAERRYDAEERAVRLKVSIDIPALSGAAKQTLERVRDAIDRNDLPSGLEYALADRQV
KAELEGFAKAVSERFGERTFLPLAAKEADGKVFEKLSAGMAPAQKADLQSAWNTIRTVQQLSAHERTVTA
LKQVETMCQAKTTGLSLK

  Protein domains


Predicted by InterproScan.

MobA/MobL family (MobA_MobL)

(17-243)

Viral (Superfamily 1) RNA helicase (Viral_helicase1)

(698-738)

AAA domain (AAA_30)

(385-571)

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

(964-1060)


  Protein structure



No available structure.




T4CP

ID   15635 GenBank   WP_231198696
Name   t4cp2_SmelRRI128_RS33700_pRRI128_4 insolico UniProt ID   _
Length   764 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 764 a.a.        Molecular weight: 84236.76 Da        Isoelectric Point: 6.1404

>WP_231198696.1 DUF87 domain-containing protein [Sinorhizobium meliloti]
MLVSGLPYLSAVDDVTLMLRDGDLMGSFVVEGINAETVDSVHTVELCNAFSRFIAQQRSDVAYYVHRISV
EARPTMPPVDGHPFNAEIDRRWQGYLQTVGLRDRVTVVTLVIRPPRKTAKFLSLFGGRDVHSRHEVEARA
LRLDQMINTCMVGVGEARPSRLTVSDGRWLGLLRTLIDGSGGSLIPGTKFLPVADLLASSQITFQGPVFE
CEGTDPGRRRFGTIVSVKDYPAETYPGILDRLNLPYNTVVTQSFTPIDPISAQGKIARVRKQMRAAEDAA
ISLMAQLEEAQDDVASGRVIFGDHHCSVAVFCDSLKELDGAMAYVTRAMQDAGSAIVRENFSSRVVYFAQ
HPGNFAYRTRPAMISSQNFAQLCAMHGQSKGSPPDKCPWGDAVTMFPTARGETFRFNFHLPGKPGQRTVG
HTLVLGQTGSGKTLGTAFLISQAQRLGARTILFDKDNGFEMAVRAMGGRYSAVRMGDETGFNPMRAEADS
RGAAWLTDWLAALAENDGGKLNPVQIQALSDAVQANTTADPRLQNLEQFRSQLRATDDDGDLYNRLGRWD
ETGQFGWLFGGKGLNPLAFDNRLTAFDLTEIFDNDVVRTAWLSYVFRRVEQLVEDEHPTLLVLDEAWKLL
DDPYFEARLKDWMLTMRKKNVAVVLLTQRVSHIKNSAAGDAILESAVTRIVYTSSFNTAAELAPLHLTPM
ESAFLQMSNVDNHLVLLKSGSDSVVLDFDLVAIGKGIDVLGGGRGEKAIAGWRDRPDFQMEMLQ

  Protein domains


Predicted by InterproScan.

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

(172-360)

TraG P-loop domain (P-loop_TraG)

(411-682)

  Protein structure



No available structure.



ID   15636 GenBank   WP_231198707
Name   virD4_SmelRRI128_RS33850_pRRI128_4 insolico UniProt ID   _
Length   685 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 685 a.a.        Molecular weight: 75844.37 Da        Isoelectric Point: 5.5596

>WP_231198707.1 type IV secretion system ATPase VirD4 [Sinorhizobium meliloti]
MDGSTTRKLNTLLFAFLLSLITGLLFASIYASFYRHGISRETINRFDIFSFWYETPLYVGYVTPVFLRGL
TIAVSTAVIATMAGAIVILKKPHHHGTARWAARQELQRVGYIRPFRNITGPIFGKTVGPRWPGQYLTNGE
QPHSLVVAPTRAGKGVGVVIPTLLTFNGSILALDVKGELFELTSRARVTRGDRVFKFAPLDGAGRTHSYN
PVLDIVNMPPERRFSETRRLAVNLIVAKGKGSEGFIDGARDLFVAGILACIERGTPTIGAVYDLFAQPGE
KYKLFAQLAEETQNQEAQRIFDNMAGNDTKILTSYTSVLGDGGLNLWADPLIKAATTTSDFSIYDLRRDP
TSIFLCVSPNDLEVIAPLIRLFFQQVVSILQRTLPKKDEIFEVLFLLDEFKHLGKLEAIETAVTTIAGYK
GRFMFIIQSLSALTGAYEEFGKENFLSNTGIQIFMATADDETPNYISKAIGDYTFRARSTSFSQRNIFDT
NIQLSDQGAPLLRPEQVRLIDDDMEIVLIKGQPPLRLKKVKYYSDRVLKRIFDSQSGALPEPERLHLATT
YVQAPATLLVTAESQPDGAKLEDAVQAALPDFDDVPVEDQAFSDFPAGGATSSDAVGEYADVEHAHDVYG
PNRVSDDHLSEEELQARAAQRALLDRIIDLQRRTNAWQTGELAPGAMHSDDTVLE

  Protein domains


Predicted by InterproScan.

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

(99-540)

  Protein structure



No available structure.



ID   15637 GenBank   WP_231198736
Name   t4cp2_SmelRRI128_RS34145_pRRI128_4 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: 91133.51 Da        Isoelectric Point: 5.7135

>WP_231198736.1 conjugal transfer protein TrbE [Sinorhizobium meliloti]
MVDLRTFRSTGPSFADLVPYAGLVDNGILLLKDGSLMAGWYFAGPDSESATDFERNELSRQINSILSRLG
TGWMIQVEAVRVPTKEYPSAERSHFPDAVTLLIDDERRRHFGQERGHFESRHALVLTYRPPERRRSGLTR
YIYSDTESRSAKYADTALDTFRRSIREIEQYLSNILSVQRMQTREVPEREGARVARYDELFQFIRFAITG
ENHPVRLPEVPMYLDWLATAELEHGLTPRVESRFLGVIAIDGLPAESWPGILNSLNLMPLTYRWSSRFIF
LDAEEAKQRLERTRKKWQQKVRPFFDQLFQTQSRSVDQDAMAMVAETEDAIAEASSQMVAYGYYTPVIIL
FDESRSALQEKAEAVRRLIQAEGFGARIETLNATDAFLGSLPGNWYCNIREPLINTRNLADLVPLNSVWS
GQPSAPCPFYPPDAPPLMQVASGSTPFRLNLHVDDVGHTLIFGPTGSGKSTLLALIAAQFCRYEKAQVFA
FDKGNSMLPLTLGAGGDHYEIGGESGEGASLAFCPLSELSTDADRAWASEWIETLVSLQGVTIAPDHRNA
ISRQIGLMASAPGRSLSDFVSGVQMREIKDALHHYTVDGPMGQLLDAEKDGLTLGRFQCFEIEQLMNMGE
RNLVPVLTYLFRRIEKRLDGSPSLIVLDEAWLMLGHPVFRDKIREWLKVLRKANCAVILATQSISDAERS
GIIDVLKESCPTKICLPNGAARESGTREFYERIGFNERQIEIVANAIPKREYYVTSPDGRRLFDMSLGPV
TLSFVGASGKADLARIRALSSTHGHEWPGQWLIERGIDRYE

  Protein domains


Predicted by InterproScan.

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

(190-400)

Helicase HerA, central domain (DUF87)

(457-492)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 84047..93222

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
SmelRRI128_RS33640 (SmelRRI128_33640) 79578..80537 - 960 Protein_87 transposase -
SmelRRI128_RS33645 (SmelRRI128_33645) 80557..80862 - 306 WP_011971014 hypothetical protein -
SmelRRI128_RS33650 (SmelRRI128_33650) 80862..82426 - 1565 Protein_89 IS66 family transposase -
SmelRRI128_RS33655 (SmelRRI128_33655) 82498..82845 - 348 WP_011971016 IS66 family insertion sequence element accessory protein TnpB -
SmelRRI128_RS33660 (SmelRRI128_33660) 83313..83504 - 192 Protein_91 IS5/IS1182 family transposase -
SmelRRI128_RS33665 (SmelRRI128_33665) 83448..83834 + 387 WP_231198775 DDE-type integrase/transposase/recombinase -
SmelRRI128_RS33670 (SmelRRI128_33670) 84047..85048 - 1002 WP_231198768 P-type DNA transfer ATPase VirB11 virB11
SmelRRI128_RS33675 (SmelRRI128_33675) 85045..86241 - 1197 WP_231198769 TrbI/VirB10 family protein virB10
SmelRRI128_RS33680 (SmelRRI128_33680) 86435..87217 - 783 WP_231198770 TrbG/VirB9 family P-type conjugative transfer protein virB9
SmelRRI128_RS33685 (SmelRRI128_33685) 87245..87919 - 675 WP_231198771 virB8 family protein virB8
SmelRRI128_RS33690 (SmelRRI128_33690) 88149..89261 - 1113 WP_231198772 type IV secretion system protein virB6
SmelRRI128_RS33695 (SmelRRI128_33695) 89266..90066 - 801 WP_231198695 type IV secretion system protein -
SmelRRI128_RS33700 (SmelRRI128_33700) 90197..92491 - 2295 WP_231198696 DUF87 domain-containing protein virb4
SmelRRI128_RS33705 (SmelRRI128_33705) 92550..92828 - 279 WP_018009845 VirB3 family type IV secretion system protein virB3
SmelRRI128_RS33710 (SmelRRI128_33710) 92911..93222 - 312 WP_093041803 TrbC/VirB2 family protein virB2
SmelRRI128_RS33715 (SmelRRI128_33715) 93262..94242 - 981 WP_231198697 lytic transglycosylase domain-containing protein -
SmelRRI128_RS33720 (SmelRRI128_33720) 94569..94690 - 122 Protein_103 IS256 family transposase -
SmelRRI128_RS33725 (SmelRRI128_33725) 94797..95042 - 246 Protein_104 IS6 family transposase -
SmelRRI128_RS33730 (SmelRRI128_33730) 95093..95275 + 183 Protein_105 transposase -
SmelRRI128_RS33735 (SmelRRI128_33735) 95412..97175 - 1764 WP_231198698 hypothetical protein -
SmelRRI128_RS33740 (SmelRRI128_33740) 97515..97772 - 258 Protein_107 transposase -

Region 2: 162661..177888

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
SmelRRI128_RS34065 (SmelRRI128_34065) 160923..161489 + 567 WP_231198723 conjugative transfer signal peptidase TraF -
SmelRRI128_RS34070 (SmelRRI128_34070) 161479..162645 + 1167 WP_231198724 conjugal transfer protein TraB -
SmelRRI128_RS34075 (SmelRRI128_34075) 162661..163278 + 618 WP_231198725 TraH family protein virB1
SmelRRI128_RS34080 (SmelRRI128_34080) 163300..163857 - 558 WP_231198726 hypothetical protein -
SmelRRI128_RS34085 (SmelRRI128_34085) 163895..164059 + 165 WP_231198727 hypothetical protein -
SmelRRI128_RS34090 (SmelRRI128_34090) 164212..165237 - 1026 WP_231198728 RcgR family putative quorum lactone hydrolase -
SmelRRI128_RS34095 (SmelRRI128_34095) 165227..166846 - 1620 WP_231198729 RcgA family putative transporter -
SmelRRI128_RS34100 (SmelRRI128_34100) 167135..167839 + 705 WP_026160825 autoinducer binding domain-containing protein -
SmelRRI128_RS34105 (SmelRRI128_34105) 167840..168139 - 300 WP_231198730 transcriptional repressor TraM -
SmelRRI128_RS34110 (SmelRRI128_34110) 168341..169639 - 1299 WP_231198731 IncP-type conjugal transfer protein TrbI virB10
SmelRRI128_RS34115 (SmelRRI128_34115) 169655..170101 - 447 WP_146721842 conjugal transfer protein TrbH -
SmelRRI128_RS34120 (SmelRRI128_34120) 170105..170935 - 831 WP_268934220 P-type conjugative transfer protein TrbG virB9
SmelRRI128_RS34125 (SmelRRI128_34125) 170951..171613 - 663 WP_231198732 conjugal transfer protein TrbF virB8
SmelRRI128_RS34130 (SmelRRI128_34130) 171635..172816 - 1182 WP_231198733 P-type conjugative transfer protein TrbL virB6
SmelRRI128_RS34135 (SmelRRI128_34135) 172810..173013 - 204 WP_231198734 entry exclusion protein TrbK -
SmelRRI128_RS34140 (SmelRRI128_34140) 173010..173810 - 801 WP_231198735 P-type conjugative transfer protein TrbJ virB5
SmelRRI128_RS34145 (SmelRRI128_34145) 173803..176238 - 2436 WP_231198736 conjugal transfer protein TrbE virb4
SmelRRI128_RS34150 (SmelRRI128_34150) 176249..176548 - 300 WP_146721836 conjugal transfer protein TrbD virB3
SmelRRI128_RS34155 (SmelRRI128_34155) 176541..176933 - 393 WP_231198737 TrbC/VirB2 family protein virB2
SmelRRI128_RS34160 (SmelRRI128_34160) 176923..177888 - 966 WP_231198738 P-type conjugative transfer ATPase TrbB virB11

Host bacterium

ID   21568 GenBank   NZ_CP088117
Plasmid name   pRRI128_4 Incompatibility group   -
Plasmid size   178254 bp Coordinate of oriT [Strand]   75492..75528 [-]
Host baterium   Sinorhizobium meliloti strain RRI128

Cargo genes

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