Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   113545
Name   oriT_ATCC 29903|unnamed2 in_silico
Organism   Shigella flexneri 2a strain ATCC 29903
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP026790 (88953..89237 [+], 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_ATCC 29903|unnamed2
GGTTATTGCTACTTAATGCCGATAACGACTCAGGCTTTGAGGTTTTTTTATACGGTTCACATTTCGTTAGCAAGGTCAGGGTTTTTTGATAAAATTCTGGTTAGTTTGGTTAAAAAGTGTTACAAGTAAGGGTAATGGCTGAAAGGTTAGTTTTAAGGTTCAAAGCGGCAGTATTAAAATTCCAAAAGTTACTTTTCATCCTTCAGAATCCAGACCTTAATTTCATGTAGAAGATTCGTACAATTGTATTGGCGCAAGGACAATCCGCACATGTCAGAATCAGAT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   8681 GenBank   WP_001011149
Name   mobH_C1P79_RS25130_ATCC 29903|unnamed2 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   10039 GenBank   WP_000167420
Name   traD_C1P79_RS25125_ATCC 29903|unnamed2 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: 77956.74 Da        Isoelectric Point: 8.7275

>WP_000167420.1 MULTISPECIES: conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MTKSKRTNLHAQENFYRPILEYRSASVLLICAVIMLVMGFRSDGVNIAPIILYTAVFLLLVCLYRCKTAH
PYLMAHWRVFQRQIMFISLKSLRTINKSNFFSNERKYRQLVQEYKKTNRPVPDRKTYFCNGFEWGPEHAD
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: 18364..27532

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
C1P79_RS24675 13878..15131 - 1254 WP_001048869 ParA family protein -
C1P79_RS24680 15889..16098 - 210 WP_124061980 hypothetical protein -
C1P79_RS24705 18364..21045 - 2682 WP_001255540 IncHI-type conjugal transfer ATPase TrhC virb4
C1P79_RS24710 21054..22004 - 951 WP_001022266 TraV family lipoprotein traV
C1P79_RS24715 22014..22766 - 753 WP_010892304 protein-disulfide isomerase HtdT -
C1P79_RS24720 22872..23384 - 513 WP_000429933 hypothetical protein -
C1P79_RS24725 23393..24751 - 1359 WP_000351840 IncHI-type conjugal transfer protein TrhB traB
C1P79_RS24730 24741..25181 - 441 WP_001224093 plasmid transfer protein HtdO -
C1P79_RS24735 25183..26415 - 1233 WP_000202110 type-F conjugative transfer system secretin TraK traK
C1P79_RS24740 26418..27203 - 786 WP_000771920 TraE/TraK family type IV conjugative transfer system protein traE
C1P79_RS24745 27215..27532 - 318 WP_000203871 type IV conjugative transfer system protein TraL traL
C1P79_RS24750 27584..27937 - 354 WP_000424121 hypothetical protein -
C1P79_RS25725 28500..28844 + 345 WP_153253765 hypothetical protein -
C1P79_RS24760 29291..30166 - 876 WP_001282731 RepB family plasmid replication initiator protein -
C1P79_RS24765 30701..31777 + 1077 WP_001015068 hypothetical protein -
C1P79_RS24770 31795..31995 + 201 WP_000357614 hypothetical protein -

Host bacterium

ID   13980 GenBank   NZ_CP026790
Plasmid name   ATCC 29903|unnamed2 Incompatibility group   IncHI1A
Plasmid size   165702 bp Coordinate of oriT [Strand]   88953..89237 [+]
Host baterium   Shigella flexneri 2a strain ATCC 29903

Cargo genes

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