Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   104492
Name   oriT_SWHIN_116|unnamed3 in_silico
Organism   Shigella flexneri strain SWHIN_116
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP055078 (34712..34805 [+], 94 nt)
oriT length   94 nt
IRs (inverted repeats)      73..78, 84..89  (AAAAAA..TTTTTT)
 27..34, 37..44  (AGCGTGAT..ATCACGCT)
 13..19, 31..37  (TAAATCA..TGATTTA)
Location of nic site      55..56
Conserved sequence flanking the
  nic site    		  GGTGTATAGC
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 94 nt

>oriT_SWHIN_116|unnamed3
TTTTTTTTCTTTTAAATCATTTGGATAGCGTGATTTATCACGCTGCGTTAGGTGTATAGCAGGTTAAGGGATAAAAAATCATCTTTTTTGGTAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   3254 GenBank   WP_087751612
Name   mobF_HUZ90_RS24175_SWHIN_116|unnamed3 insolico UniProt ID   _
Length   1078 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1078 a.a.        Molecular weight: 120162.41 Da        Isoelectric Point: 6.7655

>WP_087751612.1 MULTISPECIES: MobF family relaxase [Enterobacteriaceae]
MLDITTITRQNVTSVVGYYSDAKDDYYSKDSSFTSWQGTGAETLGLSGDVESARFKELLVGEIDTFTQMQ
RHVGDAKKERLGYDLTFSAPKGVSMQALIHGDKAIIEAHEKAVAAAVREAEKLAQARTTHKGKSVTQNTN
NLVVATFRHETSRALDPDLHTHAFVMNMTQREDGQWRALKNDELMRNKMHLGDVYKQELALELTKAGYEL
RYNSKNNTFDMAHFSDDQIRAFSRRSEQIEKGLAAMGLTRETADAQTKSRVSMATREKKTEHSREEIHQE
WASRAKTLGIDFDNREWQGHGKPQEADIARNTAPDFTSPQVKADRAIQFAVKSLSERDASFERQKLIQIA
NKQVLGHASMADVEKAYLKAVQKGAIIEGEARYQSTLKVGASVMAETLTRKEWIDSLTNSGMRADKARFA
VDEGIKNGRLKKTSHRVTTVEGIRLERTILTIESRGRGQMPRQLTAEIAGQLLAGKTLKQEQMRAVTEIV
TSKDRFVAAHGYAGTGKSYMTMAAKELLESQGMKVTALAPYGTQKKALEDDGLPARTVAAFLKAKDKKLD
EKSVVFIDEAGVIPARQMKQLMEVIEKHNARAVFLGDTSQTKAVEAGKPFEQLIKAGMQTSYMKDIQRQK
NEVLLEAVKYAAEGNAARALKNITGVNELKDEAPRLAKLADRYLSLSSEQQDATLIISGTNASRKTLNDY
IRGNLGLAGTGETFTLLDRVDSTQAERRDSRYFSKGQIIIPEQDYKNGMKRGESYRVLDTGPGNKLTVES
TNGEQIAFSPRTHTKLSVYQAVSAELAPGDKVMVTRNDKTLDVANGDRFTVKTVEGEKLTLEDKKGRTVE
LDKKQASYLSYAYATTVHKSQGLTCDRVLFNIDTKSLTTSKDVFYVGISRARHEVEIFTDDKKSLASSVS
RDSPKTTAAEIDRFFGLEARFKDIGRDTSLETRSTEKGLPETTGASMAFNQKPDEHNMTTGTDFQPISNA
EDAFHLKQNPMDDSVGLRRHEAHESESELAHDYAAADDHQWSAQEYADYEHYAEAADYDFDSSIYEDYAM
PQASQAEQGHTGKDRNHEHEHEEGGHEI

  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



No available structure.




Auxiliary protein

ID   1440 GenBank   WP_032734202
Name   WP_032734202_SWHIN_116|unnamed3 insolico UniProt ID   _
Length   138 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 138 a.a.        Molecular weight: 15323.51 Da        Isoelectric Point: 5.9670

>WP_032734202.1 MULTISPECIES: hypothetical protein [Enterobacteriaceae]
MPTITAKVSDELLAYIDRVSGGNRSDYLRRCLEAGPGDRESGLKIVADQLGDVNRKLDYLFDRVSDADFG
SLRDELKAITETLSGVKFPPAGQMMLHESLAIETLILLRSIAEPGKTKAAKAEVERNGYKVWEPKKER

  Protein domains



No domain identified.



  Protein structure



No available structure.




T4CP

ID   3180 GenBank   WP_032734201
Name   t4cp2_HUZ90_RS24180_SWHIN_116|unnamed3 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: 57656.71 Da        Isoelectric Point: 9.7443

>WP_032734201.1 MULTISPECIES: type IV secretion system DNA-binding domain-containing protein [Enterobacteriaceae]
MDERERGLAFLFAITLPPIMVWFLVAKFTYGIDASTAKYLVPYLVKNTFSLWPLWSALIAGWVIGIGALI
GFIIYDNSRVFRGERFKKIYRGTELVRARTLADKTRQRGVSQLTVADIPIPVEAENLHFSIAGTTGTGKT
TIFNELLFKSIKRGGKNIVLDPNGGFLRNFYRPGDAILNAYDKRTKGWVFFNEIRRSYDYERLVNSIVQE
SPDMATEEWFGYGRLIFSEVSKKLHSLYSTVTMEEVIHWACNVDQKKLKEFLTGTPAEAIFSGSEKAVGS
ARFVLSKNLAPHLKMPEGNFSLRDWLDDGKPGTLFITWQEEMKKSLNPLISCWLDSIFSIVLGMGEKEGR
INVFIDELESLQYLPNLNDALTKGRKSGLCVFAGYQTFSQLVKVYGRDMAQTILANLRSNIVLGGSRLGE
DTLDHMSRSLGEIEGEVERKESDPQKPWIIRKRRDVKVVRAVTPTEISMLPNLTGYLALPGDMPVAKFKA
KYIKYQRKNPVPGIEQREI

  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: 17395..34137

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HUZ90_RS24060 (HUZ90_23830) 13372..14253 - 882 WP_032734178 replication protein RepA -
HUZ90_RS24065 (HUZ90_23835) 14256..14837 - 582 WP_032734179 recombinase family protein -
HUZ90_RS24070 (HUZ90_23840) 15331..15903 - 573 WP_050484097 restriction endonuclease -
HUZ90_RS24075 (HUZ90_23845) 15953..16264 - 312 WP_032734181 hypothetical protein -
HUZ90_RS24080 (HUZ90_23850) 16310..16624 - 315 WP_032734182 TrbM/KikA/MpfK family conjugal transfer protein -
HUZ90_RS24085 (HUZ90_23855) 16621..16965 - 345 WP_032734183 hypothetical protein -
HUZ90_RS24090 (HUZ90_23860) 16981..17352 - 372 WP_227502149 H-NS family nucleoid-associated regulatory protein -
HUZ90_RS24095 (HUZ90_23865) 17395..18129 + 735 WP_032734185 lytic transglycosylase domain-containing protein virB1
HUZ90_RS24100 (HUZ90_23870) 18138..18419 + 282 WP_032734186 transcriptional repressor KorA -
HUZ90_RS24105 (HUZ90_23875) 18429..18722 + 294 WP_032734187 hypothetical protein virB2
HUZ90_RS24110 (HUZ90_23880) 18772..19089 + 318 WP_032734188 VirB3 family type IV secretion system protein virB3
HUZ90_RS24115 (HUZ90_23885) 19089..21689 + 2601 WP_032734189 VirB4 family type IV secretion/conjugal transfer ATPase virb4
HUZ90_RS24120 (HUZ90_23890) 21707..22420 + 714 WP_032734190 type IV secretion system protein virB5
HUZ90_RS24125 (HUZ90_23895) 22428..22655 + 228 WP_032734191 IncN-type entry exclusion lipoprotein EexN -
HUZ90_RS24130 (HUZ90_23900) 22671..23723 + 1053 WP_032734192 type IV secretion system protein virB6
HUZ90_RS24135 (HUZ90_23905) 23806..23952 + 147 WP_001257173 conjugal transfer protein TraN -
HUZ90_RS24140 (HUZ90_23910) 23942..24640 + 699 WP_032734193 type IV secretion system protein virB8
HUZ90_RS24145 (HUZ90_23915) 24651..25535 + 885 WP_032734194 TrbG/VirB9 family P-type conjugative transfer protein virB9
HUZ90_RS24150 (HUZ90_23920) 25535..26695 + 1161 WP_032734195 type IV secretion system protein VirB10 virB10
HUZ90_RS24155 (HUZ90_23925) 26738..27733 + 996 WP_032734196 ATPase, T2SS/T4P/T4SS family virB11
HUZ90_RS24160 (HUZ90_23930) 27733..28266 + 534 WP_032734197 phospholipase D family protein -
HUZ90_RS24165 (HUZ90_23935) 28292..28543 + 252 WP_032734198 hypothetical protein -
HUZ90_RS24170 (HUZ90_23940) 28734..29372 - 639 WP_032734199 DUF6710 family protein -
HUZ90_RS24175 (HUZ90_23945) 29372..32608 - 3237 WP_087751612 MobF family relaxase -
HUZ90_RS24180 (HUZ90_23950) 32608..34137 - 1530 WP_032734201 type IV secretion system DNA-binding domain-containing protein virb4
HUZ90_RS24185 (HUZ90_23955) 34139..34555 - 417 WP_032734202 hypothetical protein -
HUZ90_RS24190 (HUZ90_23960) 35080..35514 + 435 WP_032734203 plasmid stabilization protein StbA -
HUZ90_RS24195 (HUZ90_23965) 35523..36239 + 717 WP_032734204 StbB family protein -
HUZ90_RS24200 (HUZ90_23970) 36241..36609 + 369 WP_032734205 plasmid stabilization protein StbC -
HUZ90_RS24205 (HUZ90_23975) 36804..37148 + 345 WP_032734206 hypothetical protein -
HUZ90_RS24210 (HUZ90_23980) 37188..37400 + 213 WP_032734207 hypothetical protein -
HUZ90_RS24215 (HUZ90_23985) 37487..37807 - 321 WP_032734208 hypothetical protein -
HUZ90_RS24220 (HUZ90_23990) 37862..38041 - 180 WP_032734209 hypothetical protein -

Host bacterium

ID   4931 GenBank   NZ_CP055078
Plasmid name   SWHIN_116|unnamed3 Incompatibility group   -
Plasmid size   38809 bp Coordinate of oriT [Strand]   34712..34805 [+]
Host baterium   Shigella flexneri strain SWHIN_116

Cargo genes

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