Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   103897
Name   oriT_pHCM1 in_silico
Organism   Salmonella enterica subsp. enterica serovar Typhi strain 311189_217186
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP029645 (198924..199208 [-], 285 nt)
oriT length   285 nt
IRs (inverted repeats)      184..189, 191..196  (AAAAGT..ACTTTT)
Location of nic site      109..110
Conserved sequence flanking the
  nic site    		  TTTGGTTAAA
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 285 nt

>oriT_pHCM1
GGTTATTGCTACTTAATGCCGATAACGACTCAGGCTTTGAGGTTTTTTTATACGGTTCACATTTCGTTAGCAAGGTCAGGGTTTTTTGATAAAATTCTGGTTAGTTTGGTTAAAAAGTGTTACAAGTAAGGGTAATGGCTGAAAGGTTAGTTTTAAGGTTCAAAGCGGCAGTATTAAAATTCCAAAAGTTACTTTTCATCCTTCAGAATCCAGACCTTAATTTCATGTAGAAGATTCGTACAATTGTATTGGCGCAAGGACAATCCGCACATGTCAGAATCAGAT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2899 GenBank   WP_001011149
Name   mobH_SM217186_RS01160_pHCM1 insolico UniProt ID   A0A0G3BA46
Length   1011 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1011 a.a.        Molecular weight: 113023.00 Da        Isoelectric Point: 4.5108

>WP_001011149.1 MULTISPECIES: MobH family relaxase [Enterobacterales]
MNFRALFLSMQRVFGIFSRRENDVSELMMKDAANFSPFAQIIGEQKYTVPDHPNPEVLKFIEYPTRPAGI
QTFNEQSILSLYRDKLHSISMMLAISDGDIREDAYTFTNLVLKPLIEYIRWIHLLPASENHHHNGIGGLL
SHSLEVAMISLKNANHSELRPIGYQDEEVVRRKVYLYAAFICGLVHDAGKVYDLDIVSLNLSETLTWAPS
SQSLLDWARENNVVEYEIHWRKRIHNQHNIWSSVFLERILDPVCMSFLDRVKKERVYAKMVTALNVYNDG
NDFLSKCVRTSDYYSTGTDLNVLRDPIMGLRSNDAAARAIGTIKHNFTSININNYKTKPMHIIIVNGEVY
LNENAFLDFVLSDFAAHKFNFPQGDAGKTVLVESLVQRGYVEPYDDERVVHYFIPGTYSENEIASIFRNG
IGKLEFYNLLKLRWIGLIFDSYKIPDSVPGLFSVNANKDFIYIDEQKTVTEYRRPVPGRESVTRVTDTVN
DAIENTPQYGLQLVNGPDADSNNIISSENTESITDSLEESGADISNEIFETQVVTAIDTAETVNADEPEQ
VEEHDDRSQIHLVEQLHEMLLSAPLPHHAVINIDSVPYLDLDAAIALIPGIDEAAFCNGPFFQLTYRDGS
LDGMWIVRDVNNLRLIQLGDNCAGMQVSTSEPRNTSSLKSLFDTSMYQPLDIPEAPSVNEAASPPQTPLE
LPQPRLNAPVAEEASSVAEQTNAHSEPDSVIATEYEQYGHLLEETLDSDGEAYSDLIASDSTEAEYPATD
PQSSDFAQLPRETALSVAPGDLDYSEGAIKPPAPDATGKETILTSPEPAEDVRETVAAVEKASHLSPALA
RLFAVSTHAEKKHEKTQEPSPVKEVKNPTSSTTVKAPISIEPPGAEEKEAVEEFTLLNDGEVTELEYVEI
ATMLHQILTKLSGSFKRKRKNRFMVLTQNTFYLTQSCIEKYGTQLNAPELFNQLPQYQVTSGAVVNTKCI
AFNIPTLVAASDRAKVDIELIINKLKEVGNL

  Protein domains


Predicted by InterproScan.

Putative helicase (TraI_2)

(106-301)


  Protein structure


Source ID Structure
AlphaFold DB A0A0G3BA46


T4CP

ID   2744 GenBank   WP_000167418
Name   traD_SM217186_RS01165_pHCM1 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: 77969.74 Da        Isoelectric Point: 8.7275

>WP_000167418.1 MULTISPECIES: conjugative transfer system coupling protein TraD [Enterobacterales]
MTKSKRTNLHAQENFYRPILEYRSASVLLICAVIMLVMGFRSDGVNIAPIILYTAVFLLLVCLYRCKTAH
PYLMAHWRVFQRQIMFISLKSLRTINKSNFFSNERKYRQLVQEYKKNNRPVPDRKTYFCNGFEWGPEHAD
RAYQIANLSSDKREIALPFVLSPIARHFETMARSMGGNNAIFAVDRRAPIFVTEDNWFGHTLITGNVGTG
KTVLQRLLSISMLHLGHVIVVIDPKNDAEWRQSLMDEASELGLPFYKFHPAQPSSSVCIDVCNAYTNVSD
LTSRLLSLVSVPGEVNPFVQYAEALVSTVITGLSYTDKKPSIYLIHKNMKSHMSVVNLTIKVMECCFARH
YGPDVWMEKVKYASNDTLQVRFKRLTEWFNAHFLNYEGAEPIEWIDTVGRLVDYSMSDPEHMSKMTAGIM
PLFSRLTEQPLNELLSPSPNTLTSREIVTSDGMFSTGGVLYISLDGLSNPESARAISQLIMSDLTSCAGS
RYNADDGDMSSHSRISIFVDEAHSAINNSMINLLAQGRAAQIALFICTQTISDFIAAANAETANRITGLC
NNYISLRVNDTPTQTLVVENFGKSPISTNMVTYTTGSETTLPHNNFSGSISERKQTTLEESIPKELLGQV
PKFHIVARLQDGRKVVGQIPIAVSEKAMKPNTTLLEMFLKPAGKVTLRQNVGLSYLNKYLRKLH

  Protein domains


Predicted by InterproScan.

AAA-like domain (AAA_10)

(199-245)

Type IV secretion-system coupling protein DNA-binding domain (TrwB_AAD_bind)

(410-638)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 42872..52040

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
SM217186_RS00250 38321..38521 - 201 WP_000357614 hypothetical protein -
SM217186_RS00255 (SM217186_07286) 38539..39615 - 1077 WP_001015069 hypothetical protein -
SM217186_RS00260 (SM217186_07287) 40150..41025 + 876 WP_001282731 RepB family plasmid replication initiator protein -
SM217186_RS26455 41472..41816 - 345 WP_153253765 hypothetical protein -
SM217186_RS00270 (SM217186_07294) 42467..42820 + 354 WP_000424121 hypothetical protein -
SM217186_RS00275 (SM217186_07296) 42872..43189 + 318 WP_000203871 type IV conjugative transfer system protein TraL traL
SM217186_RS00280 (SM217186_07499) 43201..43986 + 786 WP_000771920 TraE/TraK family type IV conjugative transfer system protein traE
SM217186_RS00285 (SM217186_07290) 43989..45221 + 1233 WP_000202110 type-F conjugative transfer system secretin TraK traK
SM217186_RS00290 (SM217186_07299) 45223..45663 + 441 WP_001224093 plasmid transfer protein HtdO -
SM217186_RS00295 (SM217186_07495) 45653..47011 + 1359 WP_000351840 IncHI-type conjugal transfer protein TrhB traB
SM217186_RS00300 (SM217186_07295) 47020..47532 + 513 WP_000429933 hypothetical protein -
SM217186_RS00305 (SM217186_07269) 47638..48390 + 753 WP_010892304 protein-disulfide isomerase HtdT -
SM217186_RS00310 (SM217186_07293) 48400..49350 + 951 WP_001022266 TraV family lipoprotein traV
SM217186_RS00315 (SM217186_07301) 49359..52040 + 2682 WP_001255540 IncHI-type conjugal transfer ATPase TrhC virb4
SM217186_RS00325 (SM217186_07482) 53084..55081 + 1998 WP_001541890 choline BCCT transporter BetT -
SM217186_RS00330 (SM217186_07303) 55144..56439 + 1296 WP_000625666 DUF2254 domain-containing protein -

Host bacterium

ID   4337 GenBank   NZ_CP029645
Plasmid name   pHCM1 Incompatibility group   IncHI1B
Plasmid size   216963 bp Coordinate of oriT [Strand]   198924..199208 [-]
Host baterium   Salmonella enterica subsp. enterica serovar Typhi strain 311189_217186

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   corA, merR, merT, merP, merA, merD, merE
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -