Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100113
Name   oriT_pIE321 in_silico
Organism   Salmonella enterica subsp. enterica serovar Dublin
Sequence Completeness      intact
NCBI accession of oriT (coordinates [strand])   NC_010716 (8038..8368 [-], 331 nt)
oriT length   331 nt
IRs (inverted repeats)      IR1: 105..112, 120..127  (AAGTCATT..AATGACTT)
  IR2: 131..136, 141..146  (CGCACC..GGTGCG)
  IR3: 246..255, 259..268  (CCCAATGCGC..GCGCATTGGG)
Location of nic site      154..155
Conserved sequence flanking the
  nic site    		  TGTCT|ATAGC
Note   _

  oriT sequence  


Download         Length: 331 nt

>oriT_pIE321
CCTCTCCTGTAGTGTTTCCGTAGTGGTTCAATCCTAGCATTTACAAGGCTTTCCGCCAATATTGTAGTAGTCGAACACTACAGCGGTTTTCGTCCTTTGCGTGGAAGTCATTGTAAATCAATGACTTACGCGCACCGAAAGGTGCGTATTGTCTATAGCCCAGATTTAAGGATACCAACCCTGCTTTTAAGGACGAAAACCATGCCGATAACGCCAGCGTGACCCTAAAGAGGGTCAAAACTGCTCCCAATGCGCTATGCGCATTGGGTTATCGCGCAACAATGATGCACTTATAATGCTATGATAGTGCTACGATGATGCAGAAAATGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file

  Reference


[1] Revilla C et al. (2008) Different pathways to acquiring resistance genes illustrated by the recent evolution of IncW plasmids. Antimicrob Agents Chemother. 52(4):1472-80. [PMID:18268088]


Relaxase

ID   108 GenBank   YP_001911166
Name   TrwC_pIE321 experimental UniProt ID   A7KZU5
Length   966 a.a. PDB ID   
Note   conjugative relaxase

  Relaxase protein sequence


Download         Length: 966 a.a.        Molecular weight: 107579.95 Da        Isoelectric Point: 9.8802

>YP_001911166.1 TrwC (plasmid) [Salmonella enterica subsp. enterica serovar Dublin]
MLSHMVLTRQDIGRAASYYEDGADDYYAKDGDASEWQGKGAEELGLSGEVDSKRFRELLAGNIGEGHRIM
RSATRQDSKERIGLDLTFSAPKSVSLQALVAGDAEIIKAHDRAVARTLEQAEARAQARQKIQGKTRIETT
GNLVIGKFRHETSRERDPQLHTHAVILNMTKRSDGQWRALKNDEIVKATRYLGAVYNAELAHELQKLGYQ
LRYGKDGNFDLAHIDRQQIEGFSKRTEQIAEWYAARGLDPNSVSLEQKQAAKVLSRAKKTSVDREALRAE
WQATAKELGIDFSRREWSGREKGGSEKQAHSFMPSDEAAKRAVRYAINHLTERQSVMDERELVDTAMKHA
VRAARLEDIQKELLRQTETGYLIREAPRYRPGGQTGPTDEPGKTRAEWVAELAAKGMKQGAARERVDNAI
KTGGLVPIEPRYTTQTALEREKRILQIERDGRGAVAPVIAAEVARERLASTNLNQGQREAAELIVSAANR
VVGVQGFAGTGKSHMLDTAKQMIEGEGYHVRALAPYGSQVKALRELNVEANTLASFLRAKDKNIDSRTVL
VIDEAGVVPTRLMEQTLKLAEKAGARVVLMGDTAQTKAIEAGRPFDQLQAAGMQTAHMREIQRQKNPELK
VAVELAASGKASSSLERIKDVTEIKDHHERRAAVAEAYIALKPDERDRTLIVSGTNEARREINQMVREGL
GTAGKGIEFDTLVRVDTTQAERRHSKNYQVGHVIQPERDYAKTGLQRGELYRVVDTGPGNRLTVVGERDG
QRIQFSPMTHTKISVYQPERAELAVGDMVRITRNDKDLDLANGDRMKVVAVEDRKVTVTDGKRNVELPTD
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 A7KZU5

  Reference


[1] Revilla C et al. (2008) Different pathways to acquiring resistance genes illustrated by the recent evolution of IncW plasmids. Antimicrob Agents Chemother. 52(4):1472-80. [PMID:18268088]


Auxiliary protein

ID   164 GenBank   YP_001911164
Name   TrwA_pIE321 experimental UniProt ID   A7KZU3
Length   120 a.a. PDB ID   _
Note   relaxosome accessory protein

  Auxiliary protein sequence


Download         Length: 120 a.a.        Molecular weight: 13242.20 Da        Isoelectric Point: 4.8464

>YP_001911164.1 TrwA (plasmid) [Salmonella enterica subsp. enterica serovar Dublin]
MALGDPIQVRLSPEKQALLEDEAARKGKRLATYLRELLEGENDLQGELAAIRREVASLHHMIEDLADAGP
RGQAEPGTNPVQIETLLLLRAIAGPERMKPVKGEMKRLGIDVWTPEGKED

  Protein domains



No domain identified.



  Protein structure


Source ID Structure
AlphaFold DB A7KZU3

  Reference


[1] Revilla C et al. (2008) Different pathways to acquiring resistance genes illustrated by the recent evolution of IncW plasmids. Antimicrob Agents Chemother. 52(4):1472-80. [PMID:18268088]


T4CP

ID   108 GenBank   YP_001911165
Name   TrwB _pIE321 insolico UniProt ID   A7KZU4
Length   507 a.a. PDB ID   _
Note   coupling protein

  T4CP protein sequence


Download         Length: 507 a.a.        Molecular weight: 56306.97 Da        Isoelectric Point: 9.8647

>YP_001911165.1 TrwB (plasmid) [Salmonella enterica subsp. enterica serovar Dublin]
MHPDDQRKVSAGIIIVLPFIFWITAVQKTEVLGSPKLLALWELMKLTPQKPILLLSALGGLAVGVLFVWL
LNSVGQGEFGGAPFKRFLRGTRIVSGGKLKRMTREKAKQVTVAGVPMPRDAEPRHLLVNGATGTGKSVLL
RELAYTGLLRGDRMVIVDPNGDMLSKFGRDKDVILNPYDKRTKGWSFFNEIRNDYDWQRYALSVVPRGKT
DEAEEWASYGRLLLRETAKKLALIGTPSMRELFHWTTIATFDDLRAFLEGTLAESLFAGSNEASKALTSA
RFVLSDKLPEHVTMPDGDFSIRSWLENPDGGNLFITWREDMGPALRPLISAWVDVVCTSILSLPEEPNRR
LWLFIDELASLEKLASLADALTKGRKAGLRVVAGLQSTSQLDDVYGVKEAQTLRASFRSLVVLGGSRTDP
KTNEDMSLSLGEHEVERDRYSKNTGKHHSTGRALERVRERVVMPAEIANLPDLTAYVGFAGNRPIAKVPL
EIKQFANRQPAFVEGTI

  Protein domains


Predicted by InterproScan.

Type IV secretion-system coupling protein DNA-binding domain (TrwB_AAD_bind)

(110-490)

  Protein structure


Source ID Structure
AlphaFold DB A7KZU4


T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 8737..23376

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HS501_RS00030 (pIncW_005) 4113..4505 - 393 WP_001351729 isochorismatase family cysteine hydrolase -
HS501_RS00035 (pIncW_006) 4509..6260 + 1752 Protein_6 Tn3-like element TnAs1 family transposase -
HS501_RS00040 (pIncW_007) 6399..6770 - 372 WP_181409690 hypothetical protein -
HS501_RS00045 (pIncW_008) 6799..7494 - 696 WP_012443534 StbB family protein -
HS501_RS00055 (pIncW_010) 8329..8733 + 405 WP_238839073 mobilization protein -
HS501_RS00060 (pIncW_011) 8737..10260 + 1524 WP_012443537 type IV secretion system DNA-binding domain-containing protein virb4
HS501_RS00065 (pIncW_012) 10272..13160 + 2889 WP_238839075 MobF family relaxase -
HS501_RS00070 (pIncW_013) 13243..14257 - 1015 Protein_12 P-type DNA transfer ATPase VirB11 -
HS501_RS00075 (pIncW_014) 14287..15474 - 1188 WP_012443540 type IV secretion system protein VirB10 virB10
HS501_RS00080 (pIncW_015) 15474..16274 - 801 WP_012414163 P-type conjugative transfer protein VirB9 virB9
HS501_RS00085 (pIncW_016) 16286..16981 - 696 WP_012443541 VirB8/TrbF family protein virB8
HS501_RS00090 (pIncW_018) 17235..18263 - 1029 WP_012443542 type IV secretion system protein virB6
HS501_RS00095 (pIncW_019) 18275..18505 - 231 WP_012443543 EexN family lipoprotein -
HS501_RS00100 (pIncW_020) 18502..19191 - 690 WP_012443544 P-type DNA transfer protein VirB5 virB5
HS501_RS00105 (pIncW_021) 19188..21659 - 2472 WP_012443545 VirB4 family type IV secretion/conjugal transfer ATPase virb4
HS501_RS00110 (pIncW_022) 21662..21976 - 315 WP_012443546 VirB3 family type IV secretion system protein virB3
HS501_RS00115 (pIncW_023) 21989..22294 - 306 WP_119529903 VirB2 family type IV secretion system major pilin TrwL virB2
HS501_RS00120 (pIncW_024) 22260..22556 - 297 WP_012443548 KorA family transcriptional regulator -
HS501_RS00125 (pIncW_025) 22678..23376 - 699 WP_012443549 lytic transglycosylase domain-containing protein virB1
HS501_RS00130 (pIncW_026) 23378..23764 - 387 WP_181409688 hypothetical protein -
HS501_RS00135 (pIncW_027) 24108..24395 + 288 WP_012414174 H-NS histone family protein -
HS501_RS00140 24431..24727 + 297 WP_181409689 hypothetical protein -
HS501_RS00145 (pIncW_029) 24992..25648 + 657 WP_012443522 recombinase family protein -
HS501_RS00150 (pIncW_030) 25641..26612 + 972 WP_012196453 replication protein RepA -
HS501_RS00155 (pIncW_031) 27345..27974 + 630 WP_012443523 DNA-binding protein -

Host bacterium

ID   108 GenBank   NC_010716
Plasmid name   pIE321 Incompatibility group   IncW
Plasmid size   38150 bp Coordinate of oriT [Strand]   8038..8368 [-]
Host baterium   Salmonella enterica subsp. enterica serovar Dublin

Cargo genes

Drug resistance gene   tet(A), aph(3'')-Ib, aph(6)-Id
Virulence gene   trwF, trwG, trwH1, trwK, trwM
Metal resistance gene   _
Degradation gene   _
Symbiosis gene   -
Anti-CRISPR   -