Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   107032
Name   oriT_pNDM-CIT in_silico
Organism   Citrobacter freundii
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NC_019360 (101627..101910 [-], 284 nt)
oriT length   284 nt
IRs (inverted repeats)      183..188, 190..195  (AAAAGT..ACTTTT)
 45..50, 55..60  (TTTTAA..TTAAAA)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 284 nt

>oriT_pNDM-CIT
GTTATTGCCGCTTAATGCCGATAACGATTCGGGCTTTGCTATTTTTTTAAGCGATTAAAATTTCGTTAGCAAGCGCAGGGTTTTTTGATAAAATTCTGGTTAGTTTGGTCAAAAAGTGTTACAAGTAAGGCCAATGGATGAATGGTTAGTTTTAAGACTCAAATAGGCAATATTAAAATTCCAAAAGTTACTTTTCATCATTCAAAAACCAAACTTTAATTTCATGTAGAAGATTAGTACAATTGTATTGACGCAAGGACAATCCGCACATGTCAGAATCAGAT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   4642 GenBank   WP_015063004
Name   mobH_HTB29_RS00530_pNDM-CIT insolico UniProt ID   A0A706EP88
Length   1011 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1011 a.a.        Molecular weight: 112820.93 Da        Isoelectric Point: 4.5727

>WP_015063004.1 MULTISPECIES: MobH family relaxase [Enterobacteriaceae]
MNFRALFLSIQRVLGIFSSRENDVAELMMKDVSSLSPFAQIIGDQKYTVPDHPNLEVLKFIEYPTRPAGI
QTFNEQSILSLYRDKLHSISMMLAISDGDIREDAFTFTNLVLKPLIEYIRWIHLLPASENHHHNGIGGLL
SHSLEVAMISLKNANHSELRPIGYQDEEVIRRKVYLYAAFICGLVHDAGKVYDLDIVSLNLNETLTWAPS
SQSLLDWARENNVVEYEIHWRKRIHNQHNIWSSVFLERILDPVCMSFLDRVKKERVYAKMVTALNVYNDG
NDFLSKCVRTSDYYSTGTDLNVLRDPIMGLRSNDAAARAIGTIKHNFTSININNYKSKPMHIIIVNGEVY
LNENAFLDFVLSDFAAHKFNFPQGDAGKTVLVESLVQRGYVEPYDDERVVHYFIPGTYSENEIASIFRNG
IGKLEFYNLLKLRWIGLIFDSYKIPDSVPGLFSVNANKDFIYIDEQKTVTEYRRPVPGRESVTRVTDTVS
DAIEDTPQYGLKLVNGPDADSVNGKSSENTEAITESVEAAGTDKATDIIDPQVTTPTDTAGTGGLDEKER
VEEHEEQSQMRLVEQLHEMLLSAPLPHNAVINIDSVPYLNLDAAIALIPGIDEAAFCDGPFFQLTYRDGS
LDGMWIVRDVNNLRLIQLGDNCAGIQVSTSEPRTTSTLKSLFDTSMYQPLDIPESPSLNEAVSPPQTPLD
LPPARLNTPQAVEANSVAEQINAHSEPETVTASEYEQYGHLLEETLDSDSEAYSDFIVADNSVVEPPQPE
AKNSDVAEFHDETDQVVAPGKLNDPEDTREPPAPNTTGKEVILTSPVSSQDPIKSEPAGEKANHLSPALA
RLFAVNTQAEKKHENPPVTTPVKEAFNRSNSATVQAPIAVDQPGAEEKETLEDFTLLSGGEVTELEYVEI
ATMLHHILTKLSGSFKRKRKNRFMVLTQNTFFLTQSCVEKYGTQLNAPELFNQLPQYQVTSGAIVNTKCF
AFNMPTLVAASDRAKVDIELIINTLKDVGNL

  Protein domains


Predicted by InterproScan.

Putative helicase (TraI_2)

(106-301)


  Protein structure


Source ID Structure
AlphaFold DB A0A706EP88


T4CP

ID   4738 GenBank   WP_015063005
Name   traD_HTB29_RS00535_pNDM-CIT insolico UniProt ID   _
Length   694 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 694 a.a.        Molecular weight: 77900.52 Da        Isoelectric Point: 8.5005

>WP_015063005.1 MULTISPECIES: conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MAKSKRTNLHAQENFYRPILEYRSASVLLICAIIMLFMGFRSDGLNIAPIILYTAAFMLLVCLYRCKTAY
PYLMAHWRVFQRQIMFISLKSLRSINKSNFFSNERKYRQLVQEYKKSNRQVPDRKTYFCNGFEWGPEHAD
RAYQIANLSSDKREIALPFALNPIARHFEAMARSMGGSNAIFAVDKRAPIFVTEDNWFGHTLITGNVGTG
KTVLQRLLSISMLHLGHVIVVIDPKNDADWRQSLMDEAAELGLPFYKFHPAQPSSSVCIDVCNAYTNVSD
LTSRLLSLVSVPGEVNPFVQYAEALVSTVITGLSYTDKKPSIYLIHKNMKSHMAILNLTVKVLECCYARH
YGPDVWMEKVKYSSNDTLQVRFKRLVEWFSAHFLNYEGAEPIDWIDTVGRLVDYSLSDPEHMSKMTAGIM
PLFSRLTEQPLNELLSPSPNSLTSREIVTSDGIFSTGGVLYISLDGLSNPESARAISQLIMSDLTSCAGS
RYNSDDGDMSSHSRISIFVDEAHSAINNSMINLLAQGRAAQIALFICTQTISDFIAAANVETANRITGLC
NNYISLRVNDTPTQTLVVENFGKSPISTNMVTYTTGSETTLPHNNFSGSISERKQTTLEESIPKELLGQV
PKFHIVARLQDGRKVVGQIPIAVSENSMRPNTTLLEMFLKPAGKVTLRQNVGLDYLNKHLRKLH

  Protein domains


Predicted by InterproScan.

TraM recognition site of TraD and TraG (TraG-D_C)

(505-627)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 223059..232230

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HTB29_RS01230 (D726_p093) 218420..218620 - 201 WP_015063096 hypothetical protein -
HTB29_RS01235 (D726_p094) 218638..219711 - 1074 WP_058658219 hypothetical protein -
HTB29_RS01240 (D726_p205) 220253..221128 + 876 WP_015063098 RepB family plasmid replication initiator protein -
HTB29_RS01245 222179..222364 + 186 WP_032610388 hypothetical protein -
HTB29_RS01250 (D726_p207) 222654..223007 + 354 WP_015063100 hypothetical protein -
HTB29_RS01255 (D726_p208) 223059..223376 + 318 WP_022652151 type IV conjugative transfer system protein TraL traL
HTB29_RS01260 (D726_p209) 223388..224173 + 786 WP_022652152 TraE/TraK family type IV conjugative transfer system protein traE
HTB29_RS01265 (D726_p210) 224176..225414 + 1239 WP_015063103 type-F conjugative transfer system secretin TraK traK
HTB29_RS01270 (D726_p211) 225416..225856 + 441 WP_015063104 plasmid transfer protein HtdO -
HTB29_RS01275 (D726_p212) 225846..227207 + 1362 WP_015063105 IncHI-type conjugal transfer protein TrhB traB
HTB29_RS01280 (D726_p213) 227216..227722 + 507 WP_015063106 hypothetical protein -
HTB29_RS01285 (D726_p214) 227828..228580 + 753 WP_193216073 protein-disulfide isomerase HtdT -
HTB29_RS01290 (D726_p215) 228590..229540 + 951 WP_015063108 TraV family lipoprotein traV
HTB29_RS01295 (D726_p216) 229549..232230 + 2682 WP_015063109 IncHI-type conjugal transfer ATPase TrhC virb4
HTB29_RS01305 (D726_p217) 234581..235834 + 1254 WP_015063110 ParA family protein -
HTB29_RS01310 (D726_p218) 235831..236835 + 1005 WP_015063111 ParB family protein -

Host bacterium

ID   7468 GenBank   NC_019360
Plasmid name   pNDM-CIT Incompatibility group   IncHI1B
Plasmid size   288920 bp Coordinate of oriT [Strand]   101627..101910 [-]
Host baterium   Citrobacter freundii

Cargo genes

Drug resistance gene   catA1, dfrA12, aadA2, qacE, sul1, blaNDM-1, armA, msr(E), mph(E)
Virulence gene   -
Metal resistance gene   arsC, arsB, arsR, arsH, terE, terD, terC, terB, terA, terZ, terW
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -