Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100285
Name   oriT_pMAK3 in_silico
Organism   Salmonella enterica subsp. enterica serovar Dublin
Sequence Completeness      intact
NCBI accession of oriT (coordinates [strand])   NC_009982 (15955..16356 [+], 402 nt)
oriT length   402 nt
IRs (inverted repeats)      IR1: 135..141, 148..154  (TGTAGTG..CACTACA)
  IR2: 177..184, 192..199  (AAGTCATT..AATGACTT)
 IR3: 203..208, 213..218  (CGCACC..GGTGCG)
 IR4: 317..326, 330..339  (CCCAATGCGC..GCGCATTGGG)
Location of nic site      226..227
Conserved sequence flanking the
  nic site    		  TGTCT|ATAGC
Note   predicted by the oriTfinder

  oriT sequence  


Download         Length: 402 nt

>oriT_pMAK3
CCGCCTCGTCCTCCAAAAGTGCCTGCTTTTCCGGGCTTAGCCGTACTTGGATGGGGTCGCCTAGTGCCATGTCCTCTCCCGTAGTGTTACTGTAGTGGTTCAATCCTAGCATTTACAAGGGGTTGCGGCAATATTGTAGTGGCATAACACTACACAGGTTTTCGTCCTTGGCGTGGAAGTCATTGTAAATCAATGACTTACGCGCACCGAAAGGTGCGTATTGTCTATAGCCCAGATTTAAGGATACCAACCCGGCTTTTAAGGACGGAAACCATGCGATAACGCCAGCGTGACCCTAAAGAGGGTCAAAACTGCTCCCAATGCGCTATGCGCATTGGGTTATCGTGCAGCAATGATGCAACTATAATGCTATGATGGTGCTACAATGATGCAGAAAATGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   356 GenBank   YP_001552064
Name   TrwC_pMAK3 insolico UniProt ID   A8R760
Length   966 a.a. PDB ID   
Note   putative relaxase

  Relaxase protein sequence


Download         Length: 966 a.a.        Molecular weight: 107446.77 Da        Isoelectric Point: 9.8804

>YP_001552064.1 trwC protein (plasmid) [Salmonella enterica subsp. enterica serovar Dublin]
MLSHMVLTRQDIGRAASYYEDGADDYYAKDGDASEWQGKGAEELGLSGEVDSKRFRELLAGNIGEGHRIM
RSATRQDSKERIGLDLTFSAPKSVSLQALVAGDAEIIKAHDRAVARTLEQAEARAQARQKIQGKTRIETT
GNLVIGKFRHETSRERDPQLHTHAVILNMTKRSDGQWRALKNDEIVKATRYLGAVYNAELAHELQKLGYQ
LRYGKDGNFDLAHIDRQQIEGFSKRTEQIAEWYAARGLDPNSVSLEQKQAAKVLSRAKKTSVDREALRAE
WQATAKELGIDFSRREWSGREKGGSEKQAHSFMPSDEAAKRAVRYAINHLTERQSVMDERELVDTAMKHA
VGAARLEDIQKELLRQTETGYLIREAPRYRPGGQTGPTDEPGKTRAEWVAELAAKGMKQGAARERVDNAI
KTGGLVPIEPRYTTQTALEREKRILQIERDGRGAVAPVIAAEAARERLASTNLNQGQREAAELIVSAANR
VVGVQGFAGTGKSHMLDTAKQMIEGEGYHVRALAPYGSQVKALRELNVEANTLASFLRAKDKNIDSRTVL
VIDEAGVVPTRLMEQTLKLAEKAGARVVLMGDTAQTKAIEAGRPFDQLQAAGMQTAHMREIQRQKNPELK
IAVELAAAGKASSSLERIKDVTEIKNHHERRAAVAEAYIALKPDERDRTLIVSGTNEARREINQIVREGL
GTAGKGIEFDTLVRVDTTQAERRHSKNYQVGHVIQPERDYAKTGLQRGELYRVVETGPGNRLTVIGEHDG
QRIQFSPMTHTKISVYQPERAELAVGDTIRITRNDKHLDLANGDRMKVVAVEDRKVTVTDGKRNVELPTD
KPLHVDHAYATTVHSSQGLTSDRVLIDAHAESRTTAKDVYYVAISRARFEARVFTNDRGKLPAAIARENI
KSAAHDLARDRGGRSAAAERQREQQREAERNRQTQQPAHDRQKAAREAERGMEAGR

  Protein domains


Predicted by InterproScan.

AAA domain (AAA_30)

(473-657)

TrwC relaxase (TrwC)

(13-287)


  Protein structure


Source ID Structure
AlphaFold DB A8R760


T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 1020..15657

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HXC03_RS00005 (MAK3.01c) 1..288 - 288 WP_012414174 H-NS histone family protein -
HXC03_RS00010 (MAK3.02) 437..1018 + 582 WP_012196419 hypothetical protein -
HXC03_RS00015 (MAK3.03) 1020..1718 + 699 WP_012443549 lytic transglycosylase domain-containing protein virB1
HXC03_RS00020 (MAK3.04) 1840..2136 + 297 WP_012196420 KorA family transcriptional regulator -
HXC03_RS00025 (MAK3.05) 2102..2407 + 306 WP_031942907 VirB2 family type IV secretion system major pilin TrwL virB2
HXC03_RS00030 (MAK3.06) 2420..2734 + 315 WP_012196422 VirB3 family type IV secretion system protein virB3
HXC03_RS00035 (MAK3.07) 2737..5208 + 2472 WP_012196423 VirB4 family type IV secretion/conjugal transfer ATPase virb4
HXC03_RS00040 (MAK3.08) 5205..5894 + 690 WP_012196424 P-type DNA transfer protein VirB5 virB5
HXC03_RS00045 (MAK3.09) 5891..6121 + 231 WP_012196425 EexN family lipoprotein -
HXC03_RS00050 (MAK3.10) 6135..7163 + 1029 WP_012196426 type IV secretion system protein virB6
HXC03_RS00055 (MAK3.12) 7416..8111 + 696 WP_012196428 VirB8/TrbF family protein virB8
HXC03_RS00060 (MAK3.13) 8122..8922 + 801 WP_012196429 P-type conjugative transfer protein VirB9 virB9
HXC03_RS00065 (MAK3.14) 8922..10109 + 1188 WP_012196430 type IV secretion system protein VirB10 virB10
HXC03_RS00070 (MAK3.15) 10075..11151 + 1077 WP_012196431 P-type DNA transfer ATPase VirB11 virB11
HXC03_RS00075 (MAK3.16c) 11234..14122 - 2889 WP_065164176 MobF family relaxase -
HXC03_RS00080 (MAK3.17c) 14134..15657 - 1524 WP_012196433 type IV secretion system DNA-binding domain-containing protein virb4
HXC03_RS00085 (MAK3.18c) 15659..16024 - 366 WP_012196434 hypothetical protein -
HXC03_RS00090 (MAK3.19) 16478..16903 + 426 WP_012196435 hypothetical protein -
HXC03_RS00095 (MAK3.20) 16900..17595 + 696 WP_012196436 StbB family protein -
HXC03_RS00100 (MAK3.21) 17609..17995 + 387 WP_012196437 hypothetical protein -
HXC03_RS00105 (MAK3.22c) 18149..18400 - 252 WP_012196438 hypothetical protein -
HXC03_RS00110 (MAK3.23c) 18548..19201 - 654 WP_012196439 hypothetical protein -
HXC03_RS00115 (MAK3.24c) 19217..19561 - 345 WP_012196440 hypothetical protein -
HXC03_RS00120 (MAK3.26c) 20254..20577 - 324 WP_012196442 TrfB-related DNA-binding protein -

Host bacterium

ID   747 GenBank   NC_009982
Plasmid name   pMAK3 Incompatibility group   IncW
Plasmid size   39924 bp Coordinate of oriT [Strand]   15955..16356 [+]
Host baterium   Salmonella enterica subsp. enterica serovar Dublin

Cargo genes

Drug resistance gene   aac(6')-Iae, aadA2, qacE, sul1, floR
Virulence gene   trwM, trwK, trwH1, trwG, trwF, trwD
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -