Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   107796
Name   oriT_pNGR234b in_silico
Organism   Sinorhizobium fredii NGR234
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NC_012586 (1013789..1013817 [+], 29 nt)
oriT length   29 nt
IRs (inverted repeats)      14..19, 24..29  (CGTCGC..GCGACG)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 29 nt

>oriT_pNGR234b
AGGGCGCAATATACGTCGCTGTCGCGACG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   5234 GenBank   WP_015887153
Name   traA_NGR_RS05005_pNGR234b insolico UniProt ID   C3KR00
Length   1537 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1537 a.a.        Molecular weight: 170863.77 Da        Isoelectric Point: 9.5089

>WP_015887153.1 Ti-type conjugative transfer relaxase TraA [Sinorhizobium fredii]
MAIMFVRAQVISRGAGRSIVSAAAYRHRSRMMDEQAGASFSYRGGAAELVHEELALPDDIPAWLRSTIDG
RSVAGASEVLWNAVDAFEKRADAQLARELIIALPEELTRAENIALVREFVRDNFTSHGMIADWVFHDKNA
NPHIHLMTALRPLMEKGFGPKKVPVLGEDGEPLRVATPDRPNGKIVYKLWAGDKETMKEWKIAWADTANR
HLTLAGHEIRLDGRSYAEQGLDGIAQKHLGPDKAALARKGVEMYFAPADLARRQKMADRLIADPELLLKQ
LGNERSTFDERDIARALHRYVDDPVDFANIRARLMASDDMVLLKPQEVDAETGKATEPAIFTTREILRIE
FDMAQSAEVLSMRKGFGPSGTQVSAAVRKVERADPEKSFRLDAEQVAAVRHVTGNDAIAAVTGLAGAGKS
TLLAAARVAWEGEGRRVIGAALAGKAAEGLEDSSGIRSRTLASWELAWAGGREQLNRGDVLVIDEAGMIS
SQQMARVLRIVEEAEAKVVLVGDPMQLQPIQAGAAFRAITERIGFAELAGVRRQRELWARDASRLFARGK
VEEGLDAYAREGRIVEAETRAEIIDRIVVDWTDARRTQLQKSAAGENPGRLRGEELLVLAHTNENVRKLN
DSLRKVMIDEGALTGAREFRTERGLREFAAGDRIIFLENARFLEPRARRLGSQYVKNGMLGSVVSTGDKR
GESLLTVRLDNGRHVVISEDSYRNVDHGYAATIHKSQGATVDRAFVLATGMMDQHLVYVAMTRHRDRADL
YAAKEDFEPKLKWRRKPRVDHSAGVTGEVVEVGQARFRPNDADADESPYADVKSDDGTVHRLWGVSLPKA
LEDAGVSDGDTVTLRKDGVERVKVQVPVVDEKTGQKRFEEREVDRNVWTAKQIEAAEARQERIERESHRP
DLFNELVERLGRSGAKTTTLDFESAEGYRAHARDFARRRGIDTLAEVAAGMEKGAARRLAWIAEKRERLA
KLWERASVALGFAIERERRVSYNEERTESLSTGIGGKYLIPPTTEFARSIEEDARRTQLASDRWREREAI
LRPVLAQIYRDPDDALSALNALASDATIEPRKLAEDLGSASDRLGRLRGSDLMVDGRAARDERSATTAAL
SELLPLARAHAAEFRRQAERFGIREQQRRAHMSLSVPALSKQAMARLVEIEAARDRGGTDAYKTAFAYAV
EDRLLVQEVKAVNEALSARFGWSAFTTKADAIAERNMLERMPEDLDPERREKLTRLFAVIRRFAEEQHLV
EKKDRSNVVAGASVEAEKETVPMLPMLAAVTEFKAPIEEEARERALAVPYYANRRSALVETAVRIWRDPA
SAVAKIEDLVVKGFAAERIAAAVTNDPAAFGALRGSDRIIDKLLAAGRERKGAIQAVQEAASRARSLGAS
YASALDAETRAVTEERKRMAVAIPGLSRAADEALRRLTAEMKKKGSKLDWVAGSLDPDIRQQFTAVSRAL
DERFGRSAILRGEKDVINRVPPSQRRALEAMQERLKLLQRILRIDSNQKSVSKRREHAINRMRDVDR

  Protein domains


Predicted by InterproScan.

AAA domain (AAA_30)

(391-578)

MobA/MobL family (MobA_MobL)

(17-249)

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

(1307-1396)


  Protein structure



No available structure.




T4CP

ID   5478 GenBank   WP_015887150
Name   traG_NGR_RS04990_pNGR234b insolico UniProt ID   _
Length   637 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 637 a.a.        Molecular weight: 70421.20 Da        Isoelectric Point: 9.3354

>WP_015887150.1 Ti-type conjugative transfer system protein TraG [Sinorhizobium fredii]
MAVKGKRHPNLLLILVPVTVTAFAAYVVGWRWQELAAGMSGKTAYWFLRAAPVPALLFGPLAGLVSVWAL
PLYRRRPVAIASLACFLVVVGFYALREYGRLVPSVESGAVTWDRALSYLDLLVVVGAVIGFLAVAVSARI
SVVVPEPVRRARRGTFGDADWLPMSAAARLFPEDGEIVVGERYRVDKQIIHELPFDPNDRSTWGQGGKAA
LLTYKQDFDSTHMLFFAGSGGYKTTSNVVPTALRYTGPLICLDPSTEVAPMVVEHRTCALGREVMVLDPT
NPIIGFNVLDGIENSTHKEEEIVGIAHMLLSESARFESSSGAYFQNQAHNLLTGLLAHVMLSPEYAGRRH
LRSLRQIVSEPEPSVLAMLRDIQEHSASAFIRETLGVFTNMTEQTFSGVYSTASKDTQWLSLDSYAALAC
GNAFKSTDIVTGNKDVFLNIPASILRSYPGIGRVIIGSLINAMIGADGRFKRRALFMLDEVDLLGYMRVL
EEARDRGRKYGLTMMLMYQSLGQLERHFGKDGATSWIESCAFASYAAVKALDTARNVSAQCGEMTVEVRS
QSRNVSWDTKAGGSRKSESVNYQRRPLIMAHEITQSMRKDEQIIIVQGHSPIRCGRAIYFRRNEMNRAAK
PSRFVKY

  Protein domains


Predicted by InterproScan.

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

(166-631)

  Protein structure



No available structure.



ID   5479 GenBank   WP_164924122
Name   tcpA_NGR_RS10360_pNGR234b insolico UniProt ID   _
Length   920 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 920 a.a.        Molecular weight: 99152.46 Da        Isoelectric Point: 4.6325

>WP_164924122.1 FtsK/SpoIIIE domain-containing protein [Sinorhizobium fredii]
MRIPRTNFSTAAFHDADVADDFELPQPGAPVESHVQTNRASAQDHLFEAPEAPRRGTDDTGYTGRAARLY
GHGSAYAPAQVTASTRDPLPTLAEITGQSDEDGWESHFFLSPNVRFTRTPEREFMKRRPPVADENDTEVE
AVAAESAEPEVVAEAAPADAAPAAIEPEAPAHSPSELLRVLIQQLPSWRPAQMRNAEPAADAAAVAVGRS
SVAAEVSTPAVSALEVALGVPDGLEATPDAYDIVTGNETNARLSYLSDHAFFEFMPLEIAAAPQAAVEPV
KQPVKPPAQIAPAPKPVAMPVEIRRQPPTAITSMFRVVECRPAATAFAAPVPAETRDAKEDAGPATAAAP
AETVEPVVAVKAEEIAPVPDSPVTKAAITMPAVVQRSSSPFPPIGGGDRLQVGDAYEFPAKELLQEPPQG
QGFFMTQEQLEQNAGLLESVLEDFGVKGEIIHVRPGPVVTLYEFEPAPGVKSSRVIGLADDIARSMSALS
ARVAVVPGRNVIGIELPNATRETVYFRELIESNDFQRTGCKLALCLGKTIGGEPVIAELAKMPHLLVAGT
TGSGKSVAINTMILSLLYRLKPEECRLIMVDPKMLELSVYDGIPHLLTPVVTDPKKAVMALKWAVREMED
RYRKMSRLGVRNIDGYNQRAAAAREKGEPILATVQTGFEKGTGEPLFEQQEMDLAPMPYIVVIVDEMADL
MMVAGKEIEGAIQRLAQMARAAGIHLIMATQRPSVDVITGTIKANFPTRISFQVTSKIDSRTILGEQGAE
QLLGQGDMLHMAGGGRIARVHGPFVSDLEVEHVVAHLKTQGRPEYLETVTADEEEEEEEEDQGAVFDKSA
IAAEDGNELYEQAVKVMLRDKKCSTSYIQRRLGIGYNRAASLVERMEKEGLVGPANHVGKREIIHGNRDH
AVKPDDGDMD

  Protein domains


Predicted by InterproScan.

FtsK alpha domain (FtsK_alpha)

(408-508)

FtsK/SpoIIIE family (FtsK_SpoIIIE)

(517-735)

Ftsk gamma domain (FtsK_gamma)

(845-904)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 990745..1000237

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
NGR_RS04845 986036..986273 - 238 Protein_986 type II toxin-antitoxin system prevent-host-death family antitoxin -
NGR_RS04850 (NGR_b10200) 987211..988569 - 1359 WP_015887115 IS5-like element ISRsp18 family transposase -
NGR_RS04855 (NGR_b10210) 988791..989033 - 243 WP_015887120 hypothetical protein -
NGR_RS04860 (NGR_b10220) 989253..989612 - 360 WP_015887121 hypothetical protein -
NGR_RS04865 (NGR_b10230) 989757..990134 - 378 WP_015887122 MarR family transcriptional regulator -
NGR_RS32980 (NGR_b10240) 990224..990745 + 522 WP_015887123 hypothetical protein -
NGR_RS04870 (NGR_b10250) 990745..991359 + 615 WP_015887124 transglycosylase SLT domain-containing protein virB1
NGR_RS04875 (NGR_b10260) 991356..991658 + 303 WP_015887125 TrbC/VirB2 family protein virB2
NGR_RS04880 (NGR_b10270) 991663..992001 + 339 WP_015887126 type IV secretion system protein VirB3 virB3
NGR_RS04885 (NGR_b10280) 991976..994351 + 2376 WP_193377876 VirB4 family type IV secretion system protein virb4
NGR_RS04890 (NGR_b10290) 994351..995046 + 696 WP_015887128 P-type DNA transfer protein VirB5 virB5
NGR_RS04895 (NGR_b10300) 995043..995276 + 234 WP_015887129 EexN family lipoprotein -
NGR_RS04900 (NGR_b10310) 995281..996195 + 915 WP_015887130 type IV secretion system protein virB6
NGR_RS04905 (NGR_b10320) 996195..996524 + 330 WP_015887131 VirB7 type IV secretion related protein -
NGR_RS04910 (NGR_b10330) 996528..997199 + 672 WP_015887132 virB8 family protein virB8
NGR_RS04915 (NGR_b10340) 997223..998065 + 843 WP_015887133 P-type conjugative transfer protein VirB9 virB9
NGR_RS04920 (NGR_b10350) 998062..999228 + 1167 WP_015887134 type IV secretion system protein VirB10 virB10
NGR_RS04925 (NGR_b10360) 999242..1000237 + 996 WP_015887135 P-type DNA transfer ATPase VirB11 virB11
NGR_RS32985 1000530..1000874 + 345 Protein_1004 hypothetical protein -
NGR_RS04930 (NGR_b10380) 1000996..1002186 + 1191 WP_015887137 hypothetical protein -
NGR_RS04935 (NGR_b10390) 1002491..1003681 - 1191 WP_015887138 DUF1173 domain-containing protein -
NGR_RS04940 (NGR_b10400) 1003976..1004167 + 192 WP_164923884 hypothetical protein -
NGR_RS04945 (NGR_b10410) 1004182..1005219 + 1038 WP_015887140 toprim domain-containing protein -

Host bacterium

ID   8231 GenBank   NC_012586
Plasmid name   pNGR234b Incompatibility group   -
Plasmid size   2430033 bp Coordinate of oriT [Strand]   1013789..1013817 [+]
Host baterium   Sinorhizobium fredii NGR234

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   actP, arsC
Degradation gene   bphC
Symbiosis gene   fixB, fixA
Anti-CRISPR   AcrVIB, AcrIIC2