Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   105921
Name   oriT_pYQ13422-IMP-4 in_silico
Organism   Enterobacter hormaechei strain YQ13422hy
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP098781 (38086..38186 [+], 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_pYQ13422-IMP-4
TATTTATTTTTTTATCTTTTAAATCAGTATGATAGCGTGATTTATCGCGCTGCGTTAGGTGTATAGCAGGTTAAGGGATAAAAAATCATCTTTTTTGGTAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   3995 GenBank   WP_012561166
Name   mobF_ND013_RS24015_pYQ13422-IMP-4 insolico UniProt ID   D7RU03
Length   1078 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1078 a.a.        Molecular weight: 120141.30 Da        Isoelectric Point: 6.5229

>WP_012561166.1 MULTISPECIES: MobF family relaxase [Gammaproteobacteria]
MLDITTITRQNVTSVVGYYSDAKDDYYSKDSSFTSWQGTGAEALGLSGDVESARFKELLVGEIDTFTHMQ
RHVGDAKKERLGYDLTFSAPKGVSMQALIHGDKTIIEAHEKAVAAAVREAEKLAQARTTRQGKSVTQNTN
NLVVATFRHETSRALDPDLHTHAFVMNMTQREDGQWRALKNDELMRNKMHLGDVYKQELALELTKAGYEL
RYNSKNNTFDMAHFSDEQIRAFSRRSEQIEKGLAAMGLTRETADAQTKSRVSMATREKKTEHSREEIHQE
WASRAKTLGIDFDNREWQGHGKPLEADIARNMAPDFTSPEVKADRAIQFAVKSLSERDASFERQKLIQIA
NKQVLGHATMADVEKAYLKAVQKGAIIEGEARYQSTLKVGASVMAETLTRKEWIDSLTNSGMRADKARFA
VDDGIKNGRLKKTSHRVTTVEGIRLERSILTIESRGRGQMPRQLTAEIAGQLLAGKTLKNEQMRAVTEIV
TSKDRFVAAHGYAGTGKSYMTMAAKELLESQGLKVTALAPYGTQKKALEDDGLPARTVAAFLKAKDKKLD
EKSVVFIDEAGVIPARQMKQLMEVIEKHNARAVFLGDTSQTKAVEAGKPFEQLIKAGMQTSYMKDIQRQK
NEVLLEAVKYAAEGNAARALKNITGVNELKEEAPRLAQLADRYLSLSSEQQDATLIISGTNASRKTLNDY
IRGNLGLAGTGETFTLLDRVDSTQAERRDSRYFSKGQIIIPEQDYKNGMKRGESYQVLDTGPGNKLTVES
SSGEQIAFSPRTHTKLSVYQAVSAELAPGDKVMVTRNDKTLDVANGDRFTVKTVEGEKLTLEDKKGRTVE
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 D7RU03


Auxiliary protein

ID   1770 GenBank   WP_001749975
Name   WP_001749975_pYQ13422-IMP-4 insolico UniProt ID   A0A5C2CVS6
Length   138 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 138 a.a.        Molecular weight: 15332.60 Da        Isoelectric Point: 5.9670

>WP_001749975.1 MULTISPECIES: hypothetical protein [Gammaproteobacteria]
MPIITAKVSDELLAYIDLVSGGNRSDYLRRCIEAGPGDRESGLKIVADRLSDVNRKLDYLFDRASDADFG
PLRDELKAITETLSGVKFPPAGQMMLHESLAIETLILLRSIAEPGKTKAAKAEVERNGYKVWEPKKER

  Protein domains



No domain identified.



  Protein structure


Source ID Structure
AlphaFold DB A0A5C2CVS6


T4CP

ID   4000 GenBank   WP_000342688
Name   t4cp2_ND013_RS24020_pYQ13422-IMP-4 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: 13777..24102

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
ND013_RS23850 9622..11055 - 1434 WP_001288432 DNA cytosine methyltransferase -
ND013_RS23855 11154..11426 + 273 Protein_11 IS1 family transposase -
ND013_RS23860 11437..11643 - 207 WP_001749967 hypothetical protein -
ND013_RS23865 11648..12295 - 648 WP_015344958 restriction endonuclease -
ND013_RS23870 12345..12656 - 312 WP_001452736 hypothetical protein -
ND013_RS23875 12692..13006 - 315 WP_001749965 TrbM/KikA/MpfK family conjugal transfer protein -
ND013_RS23880 13003..13347 - 345 WP_001749964 hypothetical protein -
ND013_RS23885 13363..13734 - 372 WP_011867773 H-NS family nucleoid-associated regulatory protein -
ND013_RS23890 13777..14511 + 735 WP_001749963 lytic transglycosylase domain-containing protein virB1
ND013_RS23895 14520..14801 + 282 WP_000440698 transcriptional repressor KorA -
ND013_RS23900 14811..15104 + 294 WP_001749962 hypothetical protein virB2
ND013_RS23905 15154..15471 + 318 WP_000496058 VirB3 family type IV secretion system protein virB3
ND013_RS23910 15603..18071 + 2469 WP_224743086 VirB4 family type IV secretion/conjugal transfer ATPase virb4
ND013_RS23915 18089..18802 + 714 WP_001749960 type IV secretion system protein virB5
ND013_RS23920 18810..19037 + 228 WP_001749959 IncN-type entry exclusion lipoprotein EexN -
ND013_RS23925 19053..20093 + 1041 WP_001749958 type IV secretion system protein virB6
ND013_RS24210 20194..20322 + 129 WP_071882546 conjugal transfer protein TraN -
ND013_RS23930 20312..21010 + 699 WP_104758599 type IV secretion system protein virB8
ND013_RS23935 21021..21905 + 885 WP_000735066 TrbG/VirB9 family P-type conjugative transfer protein virB9
ND013_RS23940 21905..23065 + 1161 WP_000101710 type IV secretion system protein VirB10 virB10
ND013_RS23945 23107..24102 + 996 WP_000128596 ATPase, T2SS/T4P/T4SS family virB11
ND013_RS23950 24102..24635 + 534 WP_000792636 phospholipase D family protein -
ND013_RS24215 24809..25096 - 288 Protein_32 DUF6710 family protein -
ND013_RS23960 25363..25542 + 180 Protein_33 helix-turn-helix domain-containing protein -
ND013_RS23965 25607..26311 + 705 WP_001067855 IS6-like element IS26 family transposase -
ND013_RS23970 26365..26996 - 632 Protein_35 transposase -
ND013_RS23975 27391..28047 + 657 WP_001516695 quinolone resistance pentapeptide repeat protein QnrS1 -
ND013_RS23980 28366..28980 - 615 WP_014839983 recombinase family protein -

Host bacterium

ID   6358 GenBank   NZ_CP098781
Plasmid name   pYQ13422-IMP-4 Incompatibility group   IncN
Plasmid size   52492 bp Coordinate of oriT [Strand]   38086..38186 [+]
Host baterium   Enterobacter hormaechei strain YQ13422hy

Cargo genes

Drug resistance gene   blaIMP-4, qnrS1
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -