Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100472
Name   oriT_pVQS1 in_silico
Organism   Salmonella enterica subsp. enterica serovar Virchow
Sequence Completeness      intact
NCBI accession of oriT (coordinates [strand])   NC_019124 (12527..13164 [-], 638 nt)
oriT length   638 nt
IRs (inverted repeats)      IR1: 198..207, 211..220  (ATTAGGTGTT..AATACCTAAT)
 IR2:319..324, 330..335  (AAAAAA..TTTTTT)
  IR3: 393..402, 405..414  (GTATTCATGC..GCATGAATAC)
Location of nic site      301..302
Conserved sequence flanking the
  nic site    		  GGTGT|ATAGC
Note   predicted by the oriTfinder

  oriT sequence  


Download         Length: 638 nt

>oriT_pVQS1
AGCGCCGCAGATAATCTGACCGATTACCTCCTGAAACCAGGTCTATATAGGCCAAAAGTTCATCTGATACTTTTGCGGTTATTATTGGCATTCAGTCCTCACATTGTGCATTTCTTAAACAAAAGATTGGGATCTAACAAGCTGAAATCTTAGTATTACCAAAGTAATAAAGCAAACTCATTATAAAACAATGAGTTATTAGGTGTTTTTAATACCTAATTATTACCGAATATTGACGCTATTTATTTTTTTATTTTTTAAATCAGTGTGATAGCGTGATTTATCGCGCTGCGTTAGGTGTATAGCAGGTTAAGGGATAAAAAATCATCTTTTTTGGTAGGAGCGATCTACGTAGGTTAAGGACTAACTGACTAAAAAGCGTTCAATATTCCGTATTCATGCTTGCATGAATACCAGTACAACACTATTACAACAAAAGTACATCAAAAGTACATCACTTGAAGGTTGACAGTACAACAGAATTACATCATTATCTGGTCATGAGGTAGCCAGTACAACAAAAGTACATCAAAAATACATCATAAATACATCAGAAATACATCAAAATTACATCATTCTAAATGAGGGTACTATGAAGCCCAAAAGTATCAGGGCGGCACTTCAGTTGATGTTGCCGG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   543 GenBank   YP_006957340
Name   TraI_pVQS1 insolico UniProt ID   I2E140
Length   1078 a.a. PDB ID   
Note   putative relaxase

  Relaxase protein sequence


Download         Length: 1078 a.a.        Molecular weight: 120179.41 Da        Isoelectric Point: 6.5766

>YP_006957340.1 traI (plasmid) [Salmonella enterica subsp. enterica serovar Virchow]
MLDITTITRQNVTSVVGYYSDAKDDYYSKDSSFTSWQGTGAEALGLSGDVESARFKELLVGEIDTFTHMQ
RHVGDAKKERLGYDLTFSAPKGVSMQALIHGDKTIIEAHEKAVAAAVREAEKLAQARTTRQGKSVTQNTN
NLVVATFRHETSRALDPDLHTHAFVMNMTQREDGQWRALKNDELMRNKMHLGDVYKQELALELTKAGYEL
RYNSKNNTFDMAHFSDEQIRAFSRRSEQIEKGLAAMGLTRETADAQTKSRVSMATREKKTEHSREEIHQE
WASRAKTLGIDFDNREWQGHGKPLEADIARNMAPDFTSPEVKADRAIQFAVKSLSERDASFERQKLIQIA
NKQVLGHATIADVEKAYLKAVQKGAIIEGEARYQSTLKVGASVMAETLTRKEWIDSLTNSGMRADKARFA
VDDGIKNGRLKKTSHRVTTVEGIRLERSILTIESRGRGQMPRQLTAEIAGQLLSGKTLKKEQMRAVTEIV
TSKDRFVAAHGYAGTGKSYMTMAAKELLESQGLKVTALAPYGTQKKALEDDGLPARTVAAFLKAKDKKLD
EKSVVFIDEAGVIPARQMKQLMEVIEKHNARAVFLGDTSQTKAVEAGKPFEQLIKAGMQTSYMKDIQRQK
NEVLLEAVKYAAEGNAARALKNITGVNELKEEAPRLAQLADRYLSLSSEQQDATLIISGTNASRKTLNDY
IRGNLGLAGTGETFTLLDRVDSTQAERRDSRYFSKGQIIIPEQDYKNGMKRGESYQVLDTGPGNKLTVES
ISGEQIAFSPRTHTKLSVYQAVSAELAPGDKVMVTRNDKTLDVANGDRFTVKTVEGEKLTLEDKKGRTVE
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 I2E140


T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 13492..29915

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HTA22_RS00055 (D645_p9028) 8526..9035 + 510 WP_000129958 antirestriction protein ArdA -
HTA22_RS00060 (D645_p9027) 9867..10046 + 180 WP_000214483 protein CcgAI -
HTA22_RS00065 (D645_p9026) 10101..10421 + 321 WP_000211833 protein CcgAII -
HTA22_RS00070 (D645_p9037) 10532..10876 - 345 WP_015059326 hypothetical protein -
HTA22_RS00075 (D645_p9025) 11058..11426 - 369 WP_000414913 plasmid stabilization protein StbC -
HTA22_RS00080 (D645_p9024) 11428..12144 - 717 WP_000861577 StbB family protein -
HTA22_RS00245 12153..12572 - 420 WP_000802909 plasmid stabilization protein StbA -
HTA22_RS00090 (D645_p9022) 13074..13490 + 417 WP_001532083 hypothetical protein -
HTA22_RS00095 (D645_p9021) 13492..15021 + 1530 WP_000342688 type IV secretion system DNA-binding domain-containing protein virb4
HTA22_RS00100 (D645_p9020) 15021..18257 + 3237 WP_011407157 MobF family relaxase -
HTA22_RS00105 (D645_p9019) 18257..18883 + 627 WP_000434930 DUF6710 family protein -
HTA22_RS00110 (D645_p9018) 19057..19590 - 534 WP_000731968 phospholipase D family protein -
HTA22_RS00115 (D645_p9017) 19590..20585 - 996 WP_000128596 ATPase, T2SS/T4P/T4SS family virB11
HTA22_RS00120 (D645_p9016) 20627..21787 - 1161 WP_000101711 type IV secretion system protein VirB10 virB10
HTA22_RS00125 (D645_p9015) 21787..22671 - 885 WP_000735067 TrbG/VirB9 family P-type conjugative transfer protein virB9
HTA22_RS00130 (D645_p9014) 22682..23380 - 699 WP_000646594 type IV secretion system protein virB8
HTA22_RS00135 (D645_p9013) 23370..23528 - 159 WP_012561180 hypothetical protein -
HTA22_RS00140 (D645_p9012) 23599..24639 - 1041 WP_000886022 type IV secretion system protein virB6
HTA22_RS00145 (D645_p9010) 24655..24882 - 228 WP_000734973 IncN-type entry exclusion lipoprotein EexN -
HTA22_RS00150 (D645_p9011) 24890..25603 - 714 WP_000749362 type IV secretion system protein virB5
HTA22_RS00155 (D645_p9004) 25621..28221 - 2601 WP_001200711 VirB4 family type IV secretion/conjugal transfer ATPase virb4
HTA22_RS00160 (D645_p9003) 28221..28538 - 318 WP_000496058 VirB3 family type IV secretion system protein virB3
HTA22_RS00165 (D645_p9009) 28588..28881 - 294 WP_000209137 TrbC/VirB2 family protein virB2
HTA22_RS00170 (D645_p9008) 28891..29172 - 282 WP_000440698 transcriptional repressor KorA -
HTA22_RS00175 (D645_p9007) 29181..29915 - 735 WP_000033783 lytic transglycosylase domain-containing protein virB1
HTA22_RS00180 (D645_p9005) 29958..30329 + 372 WP_011867773 H-NS family nucleoid-associated regulatory protein -
HTA22_RS00185 (D645_p9038) 30345..30722 + 378 WP_000504251 hypothetical protein -
HTA22_RS00190 (D645_p9006) 30685..30999 + 315 WP_000734776 TrbM/KikA/MpfK family conjugal transfer protein -
HTA22_RS00195 (D645_p9039) 31113..31346 + 234 WP_001191790 hypothetical protein -
HTA22_RS00200 (D645_p9040) 31402..32043 + 642 WP_001694850 restriction endonuclease -
HTA22_RS00205 (D645_p9041) 32048..32245 + 198 WP_000844102 hypothetical protein -
HTA22_RS00210 (D645_p9042) 32446..33306 - 861 WP_000027057 broad-spectrum class A beta-lactamase TEM-1 -
HTA22_RS00215 (D645_p9043) 33489..34046 - 558 WP_001235713 recombinase family protein -

Host bacterium

ID   933 GenBank   NC_019124
Plasmid name   pVQS1 Incompatibility group   IncN
Plasmid size   40995 bp Coordinate of oriT [Strand]   12527..13164 [-]
Host baterium   Salmonella enterica subsp. enterica serovar Virchow

Cargo genes

Drug resistance gene   blaTEM-1B, qnrS1
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -