Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   114457
Name   oriT_pLN126_33 in_silico
Organism   Shigella sp. LN126
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NC_019256 (110..458 [-], 349 nt)
oriT length   349 nt
IRs (inverted repeats)      134..140, 154..160  (AAAATAT..ATATTTT)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 349 nt

>oriT_pLN126_33
ACTGCGATGCAGGATAGGGCAAACGCCGCAAAATGACGTCTCTGACGCCATTCCGCAACGTTTGCCCGGTGACCTACAGTCGGTTCTTGTTGGAGAATTTTATGAAATATTTGGTCAAAGAGTTTATTAACGAAAAATATACTAAGGCTGTTAATATTTTAAAGGATAACCTTAAAGAACACTATCATGTTTTTTATTGTGTGAGATTAAGTGAGATTCTTTTTCCTGCCAGTGAATATGGAACTGAACAGTTTTTTAGTGATTTTGAAAAGATAAACTCCATTTCATTACCTGTCTTAGTGTTTGATCTCAAAGAGGGTGTTCCTGTGATTGTCATTAGTCTTGATGA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   9269 GenBank   WP_000539530
Name   mobP1_HXG23_RS00075_pLN126_33 insolico UniProt ID   A0A611DMI3
Length   388 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 388 a.a.        Molecular weight: 44497.84 Da        Isoelectric Point: 10.5286

>WP_000539530.1 MULTISPECIES: MobP1 family relaxase [Enterobacteriaceae]
MGVYVDKEHRVKRKSSENGRKSAFAHKVKNGGKNYSRNVQERINRKGASKEVVVKISGGAVTRQGIRNSI
DYMSRESELPVMSESGRVWTGDEILEAKEHMIDRANDPQHVMNDKGKENKKITQNIVFSPPVSAKVKPED
LLESVRKTMQKKYPNHRFVLGYHCDKKEHPHVHVVFRIRDNDGKRADIRKKDLREIRTGFCEELKLKGYD
VKATHKQQHGLNQSVKDAHNTAPKRQKGVYEVVDIGYDHYQNDKTKSKQHFIKLKTLNKGVEKTYWGADF
GDLCSRESVKAGDLVRLKKLGQKEVKIPALDKNGVQHGWKTVHRNEWQLENLGVKGVDRTPSASKELVLN
SPDMLLKQQQRMAQFTQQKASTLQSEQKLKTGIKFFNI

  Protein domains


Predicted by InterproScan.

Relaxase/Mobilisation nuclease domain (Relaxase)

(70-228)


  Protein structure


Source ID Structure
AlphaFold DB A0A611DMI3


T4CP

ID   10748 GenBank   WP_015060504
Name   t4cp2_HXG23_RS00110_pLN126_33 insolico UniProt ID   _
Length   395 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 395 a.a.        Molecular weight: 45208.65 Da        Isoelectric Point: 6.1890

>WP_015060504.1 hypothetical protein [Shigella sp. LN126]
MTTEHQNFFGKNPTLGHTEILGTSNVGKTVLLMTKAFAAQQFGTPESFPANRKLKKLTTVFFDKDRAGEV
GIRAMGGSYYRVKEGEPTGWNPAALPPTKRNIAFMKDLVRLLCTLNSEPLDDYQNSLISDAVERLMQRSD
RSYPISKLRPLIQEPDDTETKRHGLKARLKPWTQGEEFGWVFDNREDTFDVDNLDVFGIDGTEFLDNKVL
ASAASFYLIYRVTMLADGRRLLIYMDEFWQWINNEAFRDFVYNKLKTGRKLDMVLVVATQSPDELIKSPI
AAAVREQCATHIYLANPKAKRSEYVDGLQVRELYFDKIKAIDPLSRQFLVVKNPQRKGESDDFAAFARLE
LGKAAYYLPVLSASKPQLELFDEIWKEGMKPEEWLDTYLEQANLI

  Protein domains


Predicted by InterproScan.

TraG P-loop domain (P-loop_TraG)

(166-294)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 8763..16322

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HXG23_RS00035 (pLN126_33_07) 4086..4331 + 246 WP_000356546 hypothetical protein -
HXG23_RS00040 (pLN126_33_08) 4321..4536 + 216 WP_001180116 hypothetical protein -
HXG23_RS00045 (pLN126_33_09) 4629..4958 + 330 WP_000866648 hypothetical protein -
HXG23_RS00050 (pLN126_33_10) 5001..5180 + 180 WP_000439078 hypothetical protein -
HXG23_RS00055 (pLN126_33_11) 5202..5399 + 198 WP_001675595 hypothetical protein -
HXG23_RS00060 (pLN126_33_12) 5412..5684 + 273 WP_000160399 hypothetical protein -
HXG23_RS00070 (pLN126_33_14) 6010..6555 + 546 WP_015060502 DNA distortion polypeptide 1 -
HXG23_RS00075 (pLN126_33_15) 6558..7724 + 1167 WP_000539530 MobP1 family relaxase -
HXG23_RS00080 (pLN126_33_16) 8070..8588 + 519 WP_001446885 transcription termination/antitermination NusG family protein -
HXG23_RS00085 8518..8730 + 213 WP_032312290 hypothetical protein -
HXG23_RS00090 (pLN126_33_17) 8763..9278 + 516 WP_001690148 lytic transglycosylase domain-containing protein virB1
HXG23_RS00230 9284..9409 + 126 WP_001722382 hypothetical protein -
HXG23_RS00095 (pLN126_33_18) 9387..9683 + 297 WP_000916182 TrbC/VirB2 family protein virB2
HXG23_RS00100 (pLN126_33_19) 9702..11279 + 1578 WP_255430356 VirB3 family type IV secretion system protein virb4
HXG23_RS00110 (pLN126_33_22) 12045..13232 + 1188 WP_015060504 hypothetical protein virb4
HXG23_RS00115 (pLN126_33_23) 13243..13992 + 750 WP_000744202 type IV secretion system protein -
HXG23_RS00120 (pLN126_33_24) 14007..14291 + 285 WP_000748128 EexN family lipoprotein -
HXG23_RS00125 (pLN126_33_25) 14303..15364 + 1062 WP_000796673 type IV secretion system protein virB6
HXG23_RS00235 (pLN126_33_26) 15491..15619 + 129 WP_001328099 hypothetical protein -
HXG23_RS00130 (pLN126_33_27) 15609..16322 + 714 WP_000394613 type IV secretion system protein virB8
HXG23_RS00135 (pLN126_33_28) 16327..17127 + 801 Protein_28 TrbG/VirB9 family P-type conjugative transfer protein -
HXG23_RS00140 (pLN126_33_29) 17161..17766 - 606 WP_000509966 recombinase family protein -
HXG23_RS00145 (pLN126_33_30) 17861..20758 + 2898 WP_001553819 Tn3-like element Tn5403 family transposase -
HXG23_RS00150 20791..20925 + 135 Protein_31 conjugal transfer protein -

Host bacterium

ID   14892 GenBank   NC_019256
Plasmid name   pLN126_33 Incompatibility group   IncX1
Plasmid size   32533 bp Coordinate of oriT [Strand]   110..458 [-]
Host baterium   Shigella sp. LN126

Cargo genes

Drug resistance gene   -
Virulence gene   mrkA, mrkB, mrkC, mrkD, mrkF
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -