Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   115804
Name   oriT_S378P in_silico
Organism   Serratia marcescens strain S378
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_MZ643942 (36112..36212 [+], 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_S378P
TATTTATTTTTTTATCTTTTAAATCAGTATGATAGCGTGATTTATCGCGCTGCGTTAGGTGTATAGCAGGTTAAGGGATAAAAAATCATCTTTTTTGGTAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   10124 GenBank   WP_012561166
Name   mobF_K6M17_RS00215_S378P 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   5960 GenBank   WP_001749975
Name   WP_001749975_S378P 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   11827 GenBank   WP_000342688
Name   t4cp2_K6M17_RS00220_S378P 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: 12859..23184

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
K6M17_RS00050 8704..10137 - 1434 WP_001288432 DNA cytosine methyltransferase -
K6M17_RS00055 10236..10508 + 273 Protein_10 IS1 family transposase -
K6M17_RS00060 10519..10725 - 207 WP_001749967 hypothetical protein -
K6M17_RS00065 10730..11377 - 648 WP_015344958 restriction endonuclease -
K6M17_RS00070 11427..11660 - 234 WP_001191790 hypothetical protein -
K6M17_RS00075 11774..12088 - 315 WP_001749965 TrbM/KikA/MpfK family conjugal transfer protein -
K6M17_RS00080 12085..12429 - 345 WP_001749964 hypothetical protein -
K6M17_RS00085 12445..12816 - 372 WP_011867773 H-NS family nucleoid-associated regulatory protein -
K6M17_RS00090 12859..13593 + 735 WP_001749963 lytic transglycosylase domain-containing protein virB1
K6M17_RS00095 13602..13883 + 282 WP_000440698 transcriptional repressor KorA -
K6M17_RS00100 13893..14186 + 294 WP_001749962 hypothetical protein virB2
K6M17_RS00105 14236..14553 + 318 WP_000496058 VirB3 family type IV secretion system protein virB3
K6M17_RS00110 14553..17153 + 2601 WP_001749961 VirB4 family type IV secretion/conjugal transfer ATPase virb4
K6M17_RS00115 17171..17884 + 714 WP_001749960 type IV secretion system protein virB5
K6M17_RS00120 17892..18119 + 228 WP_001749959 IncN-type entry exclusion lipoprotein EexN -
K6M17_RS00125 18135..19175 + 1041 WP_001749958 type IV secretion system protein virB6
K6M17_RS00130 19246..19404 + 159 WP_012561180 hypothetical protein -
K6M17_RS00135 19394..20092 + 699 WP_000646594 virB8 family protein virB8
K6M17_RS00140 20103..20987 + 885 WP_000735066 TrbG/VirB9 family P-type conjugative transfer protein virB9
K6M17_RS00145 20987..22147 + 1161 WP_000101710 type IV secretion system protein VirB10 virB10
K6M17_RS00150 22189..23184 + 996 WP_000128596 ATPase, T2SS/T4P/T4SS family virB11
K6M17_RS00155 23184..23717 + 534 WP_000792636 phospholipase D family protein -
K6M17_RS00330 23891..24178 - 288 Protein_31 DUF6710 family protein -
K6M17_RS00170 24445..24624 + 180 Protein_32 helix-turn-helix domain-containing protein -
K6M17_RS00175 24629..25260 - 632 Protein_33 transposase -
K6M17_RS00180 25655..26311 + 657 WP_001516695 quinolone resistance pentapeptide repeat protein QnrS1 -
K6M17_RS00185 26630..27244 - 615 WP_014839983 recombinase family protein -
K6M17_RS00190 27406..27588 + 183 Protein_36 DUF4158 domain-containing protein -

Host bacterium

ID   16237 GenBank   NZ_MZ643942
Plasmid name   S378P Incompatibility group   IncN
Plasmid size   48780 bp Coordinate of oriT [Strand]   36112..36212 [+]
Host baterium   Serratia marcescens strain S378

Cargo genes

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