Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   108772
Name   oriT_X14|3 in_silico
Organism   Nitrobacter hamburgensis X14
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NC_007961 (13..46 [+], 34 nt)
oriT length   34 nt
IRs (inverted repeats)      19..24, 29..34  (CGTCGC..GCGACG)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 34 nt

>oriT_X14|3
TCCAAGGGCGCAGTTATACGTCGCTGACGCGACG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   5882 GenBank   WP_011505201
Name   traA_NHAM_RS23140_X14|3 insolico UniProt ID   Q1QF79
Length   1107 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1107 a.a.        Molecular weight: 123275.44 Da        Isoelectric Point: 10.3283

>WP_011505201.1 Ti-type conjugative transfer relaxase TraA [Nitrobacter hamburgensis]
MAITHFTVQIVSRGTGGSAVLSAAYRHCARMDYEAEARVVDYSNKRNLAHEDFVLPPDAPAWVRAMIADR
SVSGASETFWNYVEAFETRSDAQFAREAIIALPVELTREQNIALMRAFVTQEILPRGQVADWVYHNEPGN
PHVHLMTTLRPLIESGFGGKKVAVTGEDGKPLRTQAGKIRYALWAGDTPDFLAQRARWIDLQNQHLALAG
LDVRVEGRSYAERGIAIVPTTHIGVATKAIDRRKAKRQGGTQRLDRLAVFEENRAENARRIQRRPEIVLE
LVSREKSVFDERDIAKVLHRYVDDSGTFQNLLTRILQLPEVIRLQAESIDFATGGRAPARYTVRELIRCE
AEMARRAIHLSGSTTFPVKASVIAGVSARHANLSAEQRTAIEHLSSGERIAAVVGRAGAGKTTMMRAARE
MWEEAGYRVVGGALAGKAAEGLEKEAGIAARTLASWELGWKNGRDDLDDKTVFVLDEAGMVASRQMALVV
ETASKAGAKIVLVGDPEQLQPIEAGAAFRSIVERIGYAELETIYRQREQWMRDASLDLARGRTAQALSAY
RQHGRVLGSELKAQAIDSLIADWNRDYDPSKSTLILAHLRRDVRALNDMARAKLVERGLVEEGHVFGTED
GERRFAVGDQIVFLKNEGSLGVKNGMIGKVVDAAPGRLVAEIGDGQGSVENRRRVAVEQRFYRNVDHGYA
TTVHKAQGATVDRVKVLATLSLDKHLTYVALTRHREEVTLYYGRRSFQFAGGLIPILSQRRAKETTLDYE
RGALYRDALRFAANRGLHIVRVARTLINDRRRWTLRQKQRLVDAGRRLRALGERLGLVDSHKPVISTARK
EAKPMVAGVTTFLKSFTDTIEDRILADPAIKKQWKEVSTRFRLVFADPERAFRAVNFDAMLKDSAAAVST
IQQLAANPESFGALRGKTGLLAGKADKQERQRAEANVPALKSDIERYLRLRAEAEHKHEAEERAIRHSVA
IDIPALSRDAHRVLERVRDAIDRNDLPSALEFALADRMVKAEIDGFNKAIAERFGDRTFLPNAAREAKGQ
AFEKAAAGMDPARREQLKEAWPAMRTAQRLAAGERTAQALKQVESQRMMQRQGQTLK

  Protein domains


Predicted by InterproScan.

MobA/MobL family (MobA_MobL)

(18-243)

Viral (Superfamily 1) RNA helicase (Viral_helicase1)

(697-741)

AAA domain (AAA_30)

(383-566)

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

(863-959)


  Protein structure


Source ID Structure
AlphaFold DB Q1QF79


T4CP

ID   6321 GenBank   WP_011505221
Name   t4cp2_NHAM_RS23270_X14|3 insolico UniProt ID   _
Length   817 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 817 a.a.        Molecular weight: 91398.84 Da        Isoelectric Point: 5.4984

>WP_011505221.1 conjugal transfer protein TrbE [Nitrobacter hamburgensis]
MVALRSFRHPSPSFADLVPHAGLVANGIVLLKDGSLMAGWYFAGPDSESSTDAERNEVSRQINTILSRLG
SGWMIQVEAVRVPTTDYPARQDCHFPDPVTRAIDDERRARFEAERGHFESRHAIILTWRPPERRRAGLAR
YIYSDVESRSASYADTAIETFQNAIREIEQYLASVLSIQRMETREVDERDGTRVARYDELFQFIRFCITG
ENHPVRLPDIPMYLDWLATAELQHGLSPMVENRFLGVVAIDGFPAESWPGILNSLDLMPLTYRWSSRFMF
LDDQDARQKLERTRKKWQQKVRPFIDQLFQTQSRSIDQDAAAMVAETEDAIAEASSQLVAYGYYTPVIVL
FDDNSTRLQEKTEAVRRLIQAEGFGARIETLNATEAFLGSLPGNWYANIREPLINTRNLADLIPLNAVWS
GSPTAPCPFYPPNSPPLMQVASGSTPFRMNLHVDDVGHTLVFGPTGSGKSTLLALIAAQFRRYAGAQIFA
FDKGRSMMPLTLAAGGDHYEIGGDDADGSAALAFCPLSDLSTDTDRAWASEWIETLVAVQGVTITPDHRN
AISRQIGLMAEARGRSLSDFVSGVQMREIKDALHHYTVDGPMGQLLDAESDGLELGSFQTFEIEQLMNMG
ERNLVPVLTYLFRRIEKRLTGAPSLIILDEAWLMLGHPVFRDKIREWLKVLRKANCAVLLATQSISDAER
SGIIDVLKESCPTKICLPNGAAREPGTRKFYERIGFNDRQIEIVATAVPKREYYVASPEGRRLFNMALGP
VALSFVGASGKDDLKRILALKKDSTDWPVYWLKERGIGHAETLLADS

  Protein domains


Predicted by InterproScan.

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

(189-400)

  Protein structure



No available structure.



ID   6322 GenBank   WP_011505305
Name   traG_NHAM_RS23775_X14|3 insolico UniProt ID   _
Length   641 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 641 a.a.        Molecular weight: 68992.73 Da        Isoelectric Point: 9.2301

>WP_011505305.1 Ti-type conjugative transfer system protein TraG [Nitrobacter hamburgensis]
MKARKIALAIAPAILMAVLCLATTGAESWLARFGTTPGGRMLLGRIGLALPYALPAAAAVIFLFAAAGAN
AIRAAGWGVVTGGCLVVVIAASREIARLHSFADAVPAGERLLAYADPSTIGGATIAALVAAFGLRVAMRG
NAAFAAAAPRRIRGRRAIHGESDWMAMTEAARLFAEAGGIVVGERYRVDQDAVADRAFRADEADTWGAGG
KSPLLCFDASFGSSHAIVFAGSGGFKTTSVTVPTALKWGGGLVVLDPSNEVAPMVLTHRRNAGRQAFVLD
PRSPEGGFNVLDWVGQHGATKEEDIAAVASWIMTDNPRQGSARDDFFRASALQLLTALVADICLSGHTEK
KDQHLRQVRANLSEPEPKLRQRLQAIYDNSASGFVKENVAPFIAMTPETFSGVYANAAKETHWLSYANYA
ALVSGSSFTTAELADGQTDIFINLDLKTLENHPGLARVIIGSLLNAIYNRNGEVSGHTLFLLDEVARLGY
LRILETARDAGRKYGITLLMLYQSIGQMREAYGGRDATSKWFESASWISFSAINDPETADYISKRCGDTT
VEADQLSRSSQMSGSSRTRSKQLARRPLIMPHEVLRMRTDEQIVFTAGNPPLRCGRAIWFRRRDMKACTG
QDPYHRSEAVR

  Protein domains


Predicted by InterproScan.

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

(163-632)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 15988..25519

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
NHAM_RS27830 11327..11581 - 255 WP_011504828 hypothetical protein -
NHAM_RS23215 (Nham_4554) 11777..11944 + 168 WP_157043862 hypothetical protein -
NHAM_RS23220 (Nham_4555) 11949..12368 + 420 WP_011505210 hypothetical protein -
NHAM_RS23225 (Nham_4556) 13055..14200 - 1146 WP_011505211 IS110 family transposase -
NHAM_RS28730 14494..14670 - 177 WP_245270143 hypothetical protein -
NHAM_RS23230 (Nham_4558) 14844..15548 - 705 WP_011505213 autoinducer binding domain-containing protein -
NHAM_RS23235 (Nham_4559) 15988..17289 - 1302 WP_011505214 IncP-type conjugal transfer protein TrbI virB10
NHAM_RS23240 (Nham_4560) 17300..17752 - 453 WP_011505215 conjugal transfer protein TrbH -
NHAM_RS23245 (Nham_4561) 17755..18594 - 840 WP_011505216 P-type conjugative transfer protein TrbG virB9
NHAM_RS23250 (Nham_4562) 18612..19274 - 663 WP_011505217 conjugal transfer protein TrbF virB8
NHAM_RS23255 (Nham_4563) 19317..20471 - 1155 WP_011505218 P-type conjugative transfer protein TrbL virB6
NHAM_RS27835 (Nham_4564) 20484..20669 - 186 WP_011505219 entry exclusion protein TrbK -
NHAM_RS23265 (Nham_4565) 20666..21463 - 798 WP_011505220 P-type conjugative transfer protein TrbJ virB5
NHAM_RS23270 (Nham_4566) 21435..23888 - 2454 WP_011505221 conjugal transfer protein TrbE virb4
NHAM_RS23275 (Nham_4567) 23898..24197 - 300 WP_011505222 conjugal transfer protein TrbD virB3
NHAM_RS23280 (Nham_4568) 24190..24546 - 357 WP_086008386 TrbC/VirB2 family protein virB2
NHAM_RS23285 (Nham_4569) 24551..25519 - 969 WP_041359818 P-type conjugative transfer ATPase TrbB virB11
NHAM_RS23290 (Nham_4570) 25537..26160 - 624 WP_011505225 acyl-homoserine-lactone synthase -
NHAM_RS23295 (Nham_4571) 26576..27790 + 1215 WP_011505226 plasmid partitioning protein RepA -
NHAM_RS23300 (Nham_4572) 27787..28818 + 1032 WP_011505227 plasmid partitioning protein RepB -
NHAM_RS23305 (Nham_4573) 29095..30420 + 1326 WP_011505228 plasmid replication protein RepC -

Host bacterium

ID   9207 GenBank   NC_007961
Plasmid name   X14|3 Incompatibility group   -
Plasmid size   121408 bp Coordinate of oriT [Strand]   13..46 [+]
Host baterium   Nitrobacter hamburgensis X14

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   -
Degradation gene   RPYSC3_16500
Symbiosis gene   -
Anti-CRISPR   AcrIF11