Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   109981
Name   oriT_STLIN_11|unnamed3 in_silico
Organism   Shigella flexneri strain STLIN_11
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP058774 (48240..48340 [+], 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_STLIN_11|unnamed3
TATTAATTTTTTTATCTTTTAAATCAGTATGATAGCGTGATTTATCGCGCTGCGTTAGGTGTATAGCAGGTTAAGGGTTAAAAAATCATCTTTTTTGGTAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   6589 GenBank   WP_058818671
Name   mobF_HZS97_RS25095_STLIN_11|unnamed3 insolico UniProt ID   A0A6G8F840
Length   1078 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1078 a.a.        Molecular weight: 120149.39 Da        Isoelectric Point: 6.5766

>WP_058818671.1 MULTISPECIES: MobF family relaxase [Enterobacteriaceae]
MLDITTITRQNVTSVVGYYSDAKDDYYSKDSSFTSWQGTGAEALGLSGDVESARFKELLVGEIDTFTHMQ
RHVGDAKKERLGYDLTFSAPKGVSMQALIHGDKTIIEAHEKAVAAAVREAEKLAQARTTRQGKSVTQNTN
NLVVATFRHETSRALDPDLHTHAFVMNMTQREDGQWRALKNDELMRNKMHLGDVYKQELALELTKAGYEL
RYNSKNNTFDMAHFSDEQIRAFSRRSEQIEKGLAAMGLTRETADAQTKSRVSMATREKKTEHSREEIHQE
WASRAKTLGIDFDNREWQGHGKPLEADIARNMAPDFTSPEVKADRAIQFAVKSLSERDASFERQKLIQIA
NKQVLGHATIADVEKAYLKAVQKGAIIEGEARYQSTLKVGASVMAETLTRKEWIDSLTNSGMRADKARFA
VDDGIKNGRLKKTSHRVTTVEGIRLERSILTIESRGRGQMPRQLTAEIAGQLLAGKTLKKEQMRAVTEIV
TSKDRFVAAHGYAGTGKSYMTMAAKELLESQGLKVTALAPYGTQKKALEDDGLPARTVAAFLKAKDKKLD
EKSVVFIDEAGVIPARQMKQLMEVIEKHNARAVFLGDTSQTKAVEAGKPFEQLIKAGMQTSYMKDIQRQK
NEVLLEAVKYAAEGNAARALKNITGVNELKEEAPRLAQLADRYLSLSSEQQDATLIISGTNASRKTLNDY
IRGNLGLAGTGETFTLLDRVDSTQAERRDSRYFSKGQIIIPEQDYKNGMKRGESYQVLDTGPGNKLTVES
SSGEQIAFSPRTHTKLSVYQAVSAELAPGDKVMVTRNDKTLDVANGDRFTVKIVEGEKLTLEDKKGRTVE
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 A0A6G8F840


Auxiliary protein

ID   3539 GenBank   WP_000706094
Name   WP_000706094_STLIN_11|unnamed3 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   7276 GenBank   WP_000342688
Name   t4cp2_HZS97_RS25100_STLIN_11|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: 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: 19781..30106

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HZS97_RS24930 (HZS97_24545) 14782..15834 + 1053 WP_239613368 alpha/beta fold hydrolase -
HZS97_RS24935 (HZS97_24550) 15776..16117 - 342 Protein_12 AraC family transcriptional regulator -
HZS97_RS24940 (HZS97_24555) 16150..16755 - 606 WP_000509966 recombinase family protein -
HZS97_RS24945 (HZS97_24560) 16850..19747 + 2898 WP_001553819 Tn3-like element Tn5403 family transposase -
HZS97_RS24950 (HZS97_24565) 19781..20776 - 996 WP_012561144 ATPase, T2SS/T4P/T4SS family virB11
HZS97_RS24955 (HZS97_24570) 20818..21978 - 1161 WP_032334995 type IV secretion system protein VirB10 virB10
HZS97_RS24960 (HZS97_24575) 21978..22862 - 885 WP_000735066 TrbG/VirB9 family P-type conjugative transfer protein virB9
HZS97_RS24965 (HZS97_24580) 22873..23571 - 699 WP_000646594 type IV secretion system protein virB8
HZS97_RS24970 (HZS97_24585) 23561..23707 - 147 WP_001257173 conjugal transfer protein TraN -
HZS97_RS24975 (HZS97_24590) 23790..24830 - 1041 WP_001749958 type IV secretion system protein virB6
HZS97_RS24980 (HZS97_24595) 24846..25073 - 228 WP_001749959 IncN-type entry exclusion lipoprotein EexN -
HZS97_RS24985 (HZS97_24600) 25081..25794 - 714 WP_001749960 type IV secretion system protein virB5
HZS97_RS24990 (HZS97_24605) 25812..28412 - 2601 WP_012561149 VirB4 family type IV secretion/conjugal transfer ATPase virb4
HZS97_RS24995 (HZS97_24610) 28412..28729 - 318 WP_000496058 VirB3 family type IV secretion system protein virB3
HZS97_RS25000 (HZS97_24615) 28779..29072 - 294 WP_001749962 hypothetical protein virB2
HZS97_RS25005 (HZS97_24620) 29082..29363 - 282 WP_032335136 transcriptional repressor KorA -
HZS97_RS25010 (HZS97_24625) 29372..30106 - 735 WP_196320807 lytic transglycosylase domain-containing protein virB1
HZS97_RS25015 (HZS97_24630) 30149..30520 + 372 WP_206695657 H-NS family nucleoid-associated regulatory protein -
HZS97_RS25020 (HZS97_24635) 30536..30880 + 345 WP_032335138 hypothetical protein -
HZS97_RS25025 (HZS97_24640) 30877..31191 + 315 WP_001749965 TrbM/KikA/MpfK family conjugal transfer protein -
HZS97_RS25030 (HZS97_24645) 31227..31538 + 312 WP_001452736 hypothetical protein -
HZS97_RS25035 (HZS97_24650) 31588..32235 + 648 WP_015344958 restriction endonuclease -
HZS97_RS25040 (HZS97_24655) 32240..32446 + 207 WP_001749967 hypothetical protein -
HZS97_RS25045 (HZS97_24660) 32457..32729 - 273 Protein_34 IS1 family transposase -
HZS97_RS25050 (HZS97_24665) 32828..34261 + 1434 WP_001288432 DNA cytosine methyltransferase -
HZS97_RS25055 (HZS97_24670) 34295..34963 - 669 Protein_36 type II site-specific deoxyribonuclease -

Host bacterium

ID   10416 GenBank   NZ_CP058774
Plasmid name   STLIN_11|unnamed3 Incompatibility group   IncN
Plasmid size   61566 bp Coordinate of oriT [Strand]   48240..48340 [+]
Host baterium   Shigella flexneri strain STLIN_11

Cargo genes

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