Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   113540
Name   oriT_1205p3 in_silico
Organism   Shigella flexneri 4c strain 1205
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP012143 (13271..13371 [-], 101 nt)
oriT length   101 nt
IRs (inverted repeats)      80..85, 91..96  (AAAAAA..TTTTTT)
 20..26, 38..44  (TAAATCA..TGATTTA)
Location of nic site      62..63
Conserved sequence flanking the
  nic site    		  GGTGTATAGC
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 101 nt

>oriT_1205p3
TATTTATTTTTTTATTTTTTAAATCAGTGTGATAGCGTGATTTATCGCGCTGCGTTAGGTGTATAGCAGGTTAAGGGATAAAAAATCATCTTTTTTGGTAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   8677 GenBank   WP_000884352
Name   mobF_AD871_RS28090_1205p3 insolico UniProt ID   A8R732
Length   1078 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1078 a.a.        Molecular weight: 120163.41 Da        Isoelectric Point: 6.5766

>WP_000884352.1 MULTISPECIES: MobF family relaxase [Enterobacterales]
MLDITTITRQNVTSVVGYYSDAKDDYYSKDSSFTSWQGTGAEALGLSGDVESARFKELLVGEIDTFTHMQ
RHVGDAKKERLGYDLTFSAPKGVSMQALIHGDKTIIEAHEKAVAAAVREAEKLAQARTTRQGKSVTQNTN
NLVVATFRHETSRALDPDLHTHAFVMNMTQREDGQWRALKNDELMRNKMHLGDVYKQELALELTKAGYEL
RYNSKNNTFDMAHFSDEQIRAFSRRSEQIEKGLAAMGLTRETADAQTKSRVSMATREKKTEHSREEIHQE
WASRAKTLGIDFDNREWQGHGKPLEADIARNMAPDFTSPEVKADRAIQFAVKSLSERDASFERQKLIQIA
NKQVLGHATIADVEKAYLKAVQKGAIIEGEARYQSTLKVGASVMAETLTRKEWIDSLTNSGMRADKARFA
VDDGIKNGRLKKTSHRVTTVEGIRLERSILTIESRGRGQMPRQLTAEIAGQLLAGKTLKKEQMRAVTEIV
TSKDRFVAAHGYAGTGKSYMTMAAKELLESQGLKVTALAPYGTQKKALEDDGLPARTVAAFLKAKDKKLD
EKSVVFIDEAGVIPARQMKQLMEVIEKHNARAVFLGDTSQTKAVEAGKPFEQLIKAGMQTSYMKDIQRQK
NEVLLEAVKYAAEGNAARALKNITGVNELKEEAPRLAQLADRYLSLSSEQQDATLIISGTNASRKTLNDY
IRGNLGLAGTGETFTLLDRVDSTQAERRDSRYFSKGQIIIPEQDYKNGMKRGESYQVLDTGPGNKLTVES
ISGEQIAFSPRTHTKLSVYQAVSAELAPGDKVMVTRNDKTLDVANGDRFTVKTVEGEKLTLEDKKGRTVE
LDKKQASYLSYAYATTVHKSQGLTCDRVLFNIDTKSLTTSKDVFYVGISRARHEVEIFTDDKKSLASSVS
RDSPKTTAAEIDRFFGLEARFKDIGRDTSLETRSAEKGLPEATGESMAFNQKPDEHNMTTGTDYQPVSNA
EDAFHLKQNPMDDSVGLRRHEAQQNDAELAHDYAAADDQQWSAQEYADYEHYAEASDYDFDSSIYDDYAM
PQTSQAEQSHTGKEHTHEHEHEEGGHEI

  Protein domains


Predicted by InterproScan.

UvrD-like helicase C-terminal domain (UvrD_C_2)

(851-895)

TrwC relaxase (TrwC)

(16-287)

AAA domain (AAA_30)

(477-653)


  Protein structure


Source ID Structure
AlphaFold DB A8R732


Auxiliary protein

ID   5067 GenBank   WP_000706094
Name   WP_000706094_1205p3 insolico UniProt ID   B6UZ32
Length   96 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 96 a.a.        Molecular weight: 10829.54 Da        Isoelectric Point: 8.5040

>WP_000706094.1 MULTISPECIES: hypothetical protein [Enterobacterales]
MKIVADRLSDVNRKLDYLFDRASDADFGPLRDELKAITETLSGVKFPPAGQMMLHESLAIETLILLRSIA
EPGKTKAAKAEVERNGYKVWEPKKER

  Protein domains



No domain identified.



  Protein structure


Source ID Structure
AlphaFold DB B6UZ32


T4CP

ID   10034 GenBank   WP_000342688
Name   t4cp2_AD871_RS28085_1205p3 insolico UniProt ID   _
Length   509 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 509 a.a.        Molecular weight: 57762.87 Da        Isoelectric Point: 9.6551

>WP_000342688.1 MULTISPECIES: type IV secretion system DNA-binding domain-containing protein [Enterobacterales]
MDDRERGLAFLFAITLPPVMVWFLVAKFTYGIDPSTAKYLIPYLVKNTFSLWPLWSALIAGWFIGVGGLI
AFIIYDKSRVFKGERFKKIYRGTELVRARTLADKTRERGVNQLTVANIPIPTYAENLHFSIAGTTGTGKT
TIFNELLFKSIIRGGKNIALDPNGGFLKNFYRPGDVILNAYDKRTEGWVFFNEIRRSYDYERLVNSIVQE
SPDMATEEWFGYGRLIFSEVSKKLHSLYSTVTMEEVIHWACNVDQKKLKEFLMGTPAEAIFSGSEKAVGS
ARFVLSKNLAPHLKMPEGNFSLRDWLDDGKPGTLFITWQEEMKRSLNPLISCWLDSIFSIVLGMGEKESR
INVFIDELESLQFLPNLNDALTKGRKSGLCVYAGYQTYSQLVKVYGRDMAQTILANMRSNIVLGGSRLGD
ETLDQMSRSLGEIEGEVERKESDPQKPWIVRKRRDVKVVRAVTPTEISMLPNLTGYLALPGDMPVAKFKA
KHVKYHRKNPVPGIELREI

  Protein domains


Predicted by InterproScan.

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

(113-489)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 13938..30361

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
AD871_RS28045 (AD871_28235) 8985..9494 + 510 WP_000129958 antirestriction protein ArdA -
AD871_RS28050 (AD871_28240) 10322..10501 + 180 WP_000214483 protein CcgAI -
AD871_RS31060 (AD871_28245) 10556..10871 + 316 Protein_13 CcgAII protein -
AD871_RS28060 (AD871_28250) 10981..11244 - 264 WP_252904095 hypothetical protein -
AD871_RS30885 11708..11869 - 162 WP_252904096 hypothetical protein -
AD871_RS30890 11871..12029 - 159 WP_158667468 hypothetical protein -
AD871_RS30895 (AD871_28260) 12026..12247 - 222 WP_252904097 hypothetical protein -
AD871_RS30900 (AD871_28265) 12336..12581 - 246 WP_252904098 plasmid stabilization protein -
AD871_RS30905 (AD871_28270) 12585..13007 - 423 WP_252904099 plasmid stabilization protein StbA -
AD871_RS28080 (AD871_28275) 13646..13936 + 291 WP_000706094 hypothetical protein -
AD871_RS28085 (AD871_28280) 13938..15467 + 1530 WP_000342688 type IV secretion system DNA-binding domain-containing protein virb4
AD871_RS28090 (AD871_28285) 15467..18703 + 3237 WP_000884352 MobF family relaxase -
AD871_RS28095 (AD871_28290) 18703..19329 + 627 WP_000434930 DUF6710 family protein -
AD871_RS28100 (AD871_28295) 19503..20036 - 534 WP_000731968 phospholipase D family protein -
AD871_RS28105 (AD871_28300) 20036..21031 - 996 WP_000128596 ATPase, T2SS/T4P/T4SS family virB11
AD871_RS28110 (AD871_28305) 21073..22233 - 1161 WP_000101711 type IV secretion system protein VirB10 virB10
AD871_RS28115 (AD871_28310) 22233..23117 - 885 WP_000735067 TrbG/VirB9 family P-type conjugative transfer protein virB9
AD871_RS28120 (AD871_28315) 23128..23826 - 699 WP_000646594 virB8 family protein virB8
AD871_RS28125 (AD871_28320) 23816..23962 - 147 WP_001257173 conjugal transfer protein TraN -
AD871_RS28130 (AD871_28325) 24045..25085 - 1041 WP_000886022 type IV secretion system protein virB6
AD871_RS28135 (AD871_28330) 25101..25328 - 228 WP_000734973 IncN-type entry exclusion lipoprotein EexN -
AD871_RS28140 (AD871_28335) 25336..26049 - 714 WP_000749362 type IV secretion system protein virB5
AD871_RS28145 (AD871_28340) 26067..28535 - 2469 WP_225303560 VirB4 family type IV secretion/conjugal transfer ATPase virb4
AD871_RS28150 (AD871_28345) 28667..28984 - 318 WP_000496058 VirB3 family type IV secretion system protein virB3
AD871_RS28155 (AD871_28350) 29034..29327 - 294 WP_000209137 TrbC/VirB2 family protein virB2
AD871_RS28160 (AD871_28355) 29337..29618 - 282 WP_000440698 transcriptional repressor KorA -
AD871_RS28165 (AD871_28360) 29627..30361 - 735 WP_000033783 lytic transglycosylase domain-containing protein virB1
AD871_RS28170 (AD871_28365) 30425..30775 + 351 WP_024129965 H-NS family nucleoid-associated regulatory protein -
AD871_RS28175 (AD871_28370) 30791..31168 + 378 WP_000504251 hypothetical protein -
AD871_RS28180 (AD871_28375) 31131..31445 + 315 WP_000734776 TrbM/KikA/MpfK family conjugal transfer protein -
AD871_RS28185 (AD871_28380) 31481..31792 + 312 WP_001452736 hypothetical protein -
AD871_RS28190 (AD871_28385) 31980..32489 + 510 WP_000893479 restriction endonuclease -
AD871_RS28195 (AD871_28390) 32494..32691 + 198 WP_000844102 hypothetical protein -
AD871_RS29920 32711..32872 - 162 WP_260630687 IS1 family transposase -
AD871_RS28200 (AD871_28395) 32981..33526 + 546 WP_001493763 plasmid pRiA4b ORF-3 family protein -
AD871_RS28205 (AD871_28400) 33663..34235 + 573 WP_001493762 recombinase family protein -

Host bacterium

ID   13975 GenBank   NZ_CP012143
Plasmid name   1205p3 Incompatibility group   IncN
Plasmid size   42002 bp Coordinate of oriT [Strand]   13271..13371 [-]
Host baterium   Shigella flexneri 4c strain 1205

Cargo genes

Drug resistance gene   qnrS1, aac(3)-IId
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -