Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   121710
Name   oriT_pNY0401-IMP in_silico
Organism   Enterobacter hormaechei strain NY0401
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP096924 (42764..42864 [+], 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_pNY0401-IMP
TATTTATTTTTTTATCTTTTAAATCAGTATGATAGCGTGATTTATCGCGCTGCGTTAGGTGTATAGCAGGTTAAGGGATAAAAAATCATCTTTTTTGGTAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   13701 GenBank   WP_012561166
Name   mobF_M2M22_RS23020_pNY0401-IMP 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   7547 GenBank   WP_001749975
Name   WP_001749975_pNY0401-IMP 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   16010 GenBank   WP_000342688
Name   t4cp2_M2M22_RS23025_pNY0401-IMP 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: 22916..42197

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
M2M22_RS22890 (M2M22_22880) 18761..20194 - 1434 WP_001288432 DNA cytosine methyltransferase -
M2M22_RS22895 (M2M22_22885) 20293..20565 + 273 Protein_23 IS1 family transposase -
M2M22_RS22900 (M2M22_22890) 20576..20782 - 207 WP_001749967 hypothetical protein -
M2M22_RS22905 (M2M22_22895) 20787..21434 - 648 WP_015344958 restriction endonuclease -
M2M22_RS22910 (M2M22_22900) 21484..21795 - 312 WP_001452736 hypothetical protein -
M2M22_RS22915 (M2M22_22905) 21831..22145 - 315 WP_001749965 TrbM/KikA/MpfK family conjugal transfer protein -
M2M22_RS22920 (M2M22_22910) 22142..22486 - 345 WP_001749964 hypothetical protein -
M2M22_RS22925 (M2M22_22915) 22502..22873 - 372 WP_011867773 H-NS family nucleoid-associated regulatory protein -
M2M22_RS22930 (M2M22_22920) 22916..23650 + 735 WP_001749963 lytic transglycosylase domain-containing protein virB1
M2M22_RS22935 (M2M22_22925) 23659..23940 + 282 WP_000440698 transcriptional repressor KorA -
M2M22_RS22940 (M2M22_22930) 23950..24243 + 294 WP_001749962 hypothetical protein virB2
M2M22_RS22945 (M2M22_22935) 24293..24610 + 318 WP_000496058 VirB3 family type IV secretion system protein virB3
M2M22_RS22950 (M2M22_22940) 24742..27210 + 2469 WP_270094212 VirB4 family type IV secretion/conjugal transfer ATPase virb4
M2M22_RS22955 (M2M22_22945) 27228..27941 + 714 WP_001749960 type IV secretion system protein virB5
M2M22_RS22960 (M2M22_22950) 27949..28176 + 228 WP_001749959 IncN-type entry exclusion lipoprotein EexN -
M2M22_RS22965 (M2M22_22955) 28192..29232 + 1041 WP_001749958 type IV secretion system protein virB6
M2M22_RS23160 29333..29461 + 129 WP_071882546 conjugal transfer protein TraN -
M2M22_RS22970 (M2M22_22960) 29451..30149 + 699 WP_000646594 virB8 family protein virB8
M2M22_RS22975 (M2M22_22965) 30160..31044 + 885 WP_000735066 TrbG/VirB9 family P-type conjugative transfer protein virB9
M2M22_RS22980 (M2M22_22970) 31044..32204 + 1161 WP_000101710 type IV secretion system protein VirB10 virB10
M2M22_RS22985 (M2M22_22975) 32246..33241 + 996 WP_000128596 ATPase, T2SS/T4P/T4SS family virB11
M2M22_RS22990 (M2M22_22980) 33241..33774 + 534 WP_000792636 phospholipase D family protein -
M2M22_RS23165 33948..34235 - 288 Protein_44 DUF6710 family protein -
M2M22_RS23000 (M2M22_22990) 34376..34921 + 546 WP_001493763 plasmid pRiA4b ORF-3 family protein -
M2M22_RS23005 (M2M22_22995) 35058..35630 + 573 WP_001493762 recombinase family protein -
M2M22_RS23010 (M2M22_23000) 35667..37058 + 1392 WP_014839878 ISKra4-like element ISKpn19 family transposase -
M2M22_RS23015 (M2M22_23005) 37022..37432 - 411 WP_224256499 DUF6710 family protein -
M2M22_RS23020 (M2M22_23010) 37432..40668 - 3237 WP_012561166 MobF family relaxase -
M2M22_RS23025 (M2M22_23015) 40668..42197 - 1530 WP_000342688 type IV secretion system DNA-binding domain-containing protein virb4
M2M22_RS23030 (M2M22_23020) 42199..42615 - 417 WP_001749975 hypothetical protein -
M2M22_RS23035 (M2M22_23025) 43106..43525 + 420 WP_001749974 plasmid stabilization protein StbA -
M2M22_RS23040 (M2M22_23030) 43534..44250 + 717 WP_001749973 StbB family protein -
M2M22_RS23045 (M2M22_23035) 44252..44620 + 369 WP_000414913 plasmid stabilization protein StbC -
M2M22_RS23050 (M2M22_23040) 44802..45146 + 345 WP_000999874 hypothetical protein -
M2M22_RS23055 (M2M22_23045) 45257..45577 - 321 WP_001749971 protein CcgAII -
M2M22_RS23060 (M2M22_23050) 45632..45811 - 180 WP_000214483 protein CcgAI -
M2M22_RS23065 (M2M22_23055) 46538..47047 - 510 WP_000129958 antirestriction protein ArdA -

Host bacterium

ID   22137 GenBank   NZ_CP096924
Plasmid name   pNY0401-IMP Incompatibility group   IncN
Plasmid size   55933 bp Coordinate of oriT [Strand]   42764..42864 [+]
Host baterium   Enterobacter hormaechei strain NY0401

Cargo genes

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