Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   115448
Name   oriT_pSCW13-1 in_silico
Organism   Kluyvera cryocrescens strain SCW13
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_MN178639 (50241..50341 [+], 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_pSCW13-1
TATTTATTTTTTTATCTTTTAAATCAGTATGATAGCGTGATTTATCGCGCTGCGTTAGGTGTATAGCAGGTTAAGGGATAAAAAATCATCTTTTTTGGTAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   9891 GenBank   WP_012561166
Name   mobF_H5D42_RS00285_pSCW13-1 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   5796 GenBank   WP_001749975
Name   WP_001749975_pSCW13-1 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   11529 GenBank   WP_000342688
Name   t4cp2_H5D42_RS00290_pSCW13-1 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: 19967..30292

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
H5D42_RS00100 (KGCJEHFP_00023) 15812..17245 - 1434 WP_001288432 DNA cytosine methyltransferase -
H5D42_RS00105 (KGCJEHFP_00024) 17344..17616 + 273 Protein_21 IS1 family transposase -
H5D42_RS00110 (KGCJEHFP_00025) 17627..17833 - 207 WP_001749967 hypothetical protein -
H5D42_RS00115 (KGCJEHFP_00026) 17838..18485 - 648 WP_015344958 restriction endonuclease -
H5D42_RS00120 (KGCJEHFP_00027) 18535..18768 - 234 WP_001191790 hypothetical protein -
H5D42_RS00125 (KGCJEHFP_00028) 18882..19196 - 315 WP_001749965 TrbM/KikA/MpfK family conjugal transfer protein -
H5D42_RS00130 (KGCJEHFP_00029) 19193..19537 - 345 WP_001749964 hypothetical protein -
H5D42_RS00135 (KGCJEHFP_00030) 19553..19924 - 372 WP_011867773 H-NS family nucleoid-associated regulatory protein -
H5D42_RS00140 (KGCJEHFP_00031) 19967..20701 + 735 WP_001749963 lytic transglycosylase domain-containing protein virB1
H5D42_RS00145 (KGCJEHFP_00032) 20710..20991 + 282 WP_000440698 transcriptional repressor KorA -
H5D42_RS00150 (KGCJEHFP_00033) 21001..21294 + 294 WP_001749962 hypothetical protein virB2
H5D42_RS00155 (KGCJEHFP_00034) 21344..21661 + 318 WP_000496058 VirB3 family type IV secretion system protein virB3
H5D42_RS00160 (KGCJEHFP_00035) 21661..24261 + 2601 WP_001749961 VirB4 family type IV secretion/conjugal transfer ATPase virb4
H5D42_RS00165 (KGCJEHFP_00036) 24279..24992 + 714 WP_001749960 type IV secretion system protein virB5
H5D42_RS00170 (KGCJEHFP_00037) 25000..25227 + 228 WP_001749959 IncN-type entry exclusion lipoprotein EexN -
H5D42_RS00175 (KGCJEHFP_00038) 25243..26283 + 1041 WP_001749958 type IV secretion system protein virB6
H5D42_RS00180 26354..26512 + 159 WP_012561180 hypothetical protein -
H5D42_RS00185 (KGCJEHFP_00039) 26502..27200 + 699 WP_000646594 virB8 family protein virB8
H5D42_RS00190 (KGCJEHFP_00040) 27211..28095 + 885 WP_000735066 TrbG/VirB9 family P-type conjugative transfer protein virB9
H5D42_RS00195 (KGCJEHFP_00041) 28095..29255 + 1161 WP_000101710 type IV secretion system protein VirB10 virB10
H5D42_RS00200 (KGCJEHFP_00042) 29297..30292 + 996 WP_000128596 ATPase, T2SS/T4P/T4SS family virB11
H5D42_RS00205 (KGCJEHFP_00043) 30292..30825 + 534 WP_000792636 phospholipase D family protein -
H5D42_RS00355 30999..31322 - 324 WP_309353848 DUF6710 family protein -
H5D42_RS00220 (KGCJEHFP_00044) 31381..32085 + 705 WP_001067855 IS6-like element IS26 family transposase -
H5D42_RS00225 32139..32770 - 632 Protein_44 transposase -
H5D42_RS00230 (KGCJEHFP_00047) 33165..33821 + 657 WP_001516695 quinolone resistance pentapeptide repeat protein QnrS1 -
H5D42_RS00345 34140..34370 - 231 Protein_46 recombinase family protein -
H5D42_RS00235 (KGCJEHFP_00048) 34507..35052 + 546 WP_001493763 plasmid pRiA4b ORF-3 family protein -

Host bacterium

ID   15881 GenBank   NZ_MN178639
Plasmid name   pSCW13-1 Incompatibility group   IncN
Plasmid size   54815 bp Coordinate of oriT [Strand]   50241..50341 [+]
Host baterium   Kluyvera cryocrescens strain SCW13

Cargo genes

Drug resistance gene   dfrA14, qnrS1, blaCTX-M-3
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -