Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100218
Name   oriT_R7K in_silico
Organism   Providencia rettgeri
Sequence Completeness      core
NCBI accession of oriT (coordinates [strand])   NC_010643 (9136..9174 [-], 39 nt)
oriT length   39 nt
IRs (inverted repeats)      9..14, 19..24  (CGCACC..GGTGCG)
Location of nic site      32..33
Conserved sequence flanking the
  nic site    		  TGTCT|ATAGC
Note   _

  oriT sequence  


Download         Length: 39 nt

>oriT_R7K
GACTTACGCGCACCGAAAGGTGCGTATTGTCTATAGCCC

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   211 GenBank   YP_001874877
Name   TrwC_R7K experimental UniProt ID   B2G2P0
Length   966 a.a. PDB ID   
Note   conjugative relaxase

  Relaxase protein sequence


Download         Length: 966 a.a.        Molecular weight: 107460.80 Da        Isoelectric Point: 9.8804

>YP_001874877.1 mobilisation protein (plasmid) [Providencia rettgeri]
MLSHMVLTRQDIGRAASYYEDGADDYYAKDGDASEWQGKGAEELGLSGEVDSKRFRELLAGNIGEGHRIM
RSATRQDSKERIGLDLTFSAPKSVSLQALVAGDAEIIKAHDRAVARTLEQAEARAQARQKIQGKTRIETT
GNLVIGKFRHETSRERDPQLHTHAVILNMTKRSDGQWRALKNDEIVKATRYLGAVYNAELAHELQKLGYQ
LRYGKDGNFDLAHIDRQQIEGFSKRTEQIAEWYAARGLDPNSVSLEQKQAAKVLSRAKKTSVDREALRAE
WQATAKELGIDFSRREWSGREKGGSEKQAHSFMPSDEAAKRAVRYAINHLTERQSVMDERELVDTAMKHA
VGAARLEDIQKELLRQTETGYLIREAPRYRPGGQTGPTDEPGKTRAEWIAELAAKGMKQGAARERVDNAI
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 B2G2P0

  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   297 GenBank   YP_001874875
Name   TrwA_R7K experimental UniProt ID   B2G2N8
Length   121 a.a. PDB ID   _
Note   mobilisation protein

  Auxiliary protein sequence


Download         Length: 121 a.a.        Molecular weight: 13473.38 Da        Isoelectric Point: 5.0435

>YP_001874875.1 mobilisation protein (plasmid) [Providencia rettgeri]
MALGEPIKFRLTPEKHAQYEDEAARLGKPLGTYLRERLEADDAVRDELAALRREVVSLHHVIEDLADTGL
RSDQSGPGPNAVQIETLLLLRAIAGPERMKPVKGELKRLGIEVWTPEGKED

  Protein domains



No domain identified.



  Protein structure


Source ID Structure
AlphaFold DB B2G2N8

  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   211 GenBank   YP_001874876
Name   TrwB_R7K insolico UniProt ID   B2G2N9
Length   507 a.a. PDB ID   _
Note   Type IV secretion-system coupling protein

  T4CP protein sequence


Download         Length: 507 a.a.        Molecular weight: 56287.02 Da        Isoelectric Point: 9.9420

>YP_001874876.1 mobilisation protein (plasmid) [Providencia rettgeri]
MHPDDQRKVSAGIVIVLPLIFWITAVQKTEVLGSPKLLALWELMKLTPQKPILLLSALGGLAVGVLFVWL
LNSVGQGEFGGAPFKRFLRGTRIVSGGKLKRMTREKAKQVTVAGVPMPRDAEPRHLLVNGATGTGKSVLL
RELAYTGLLRGDRMVIVDPNGDMLSKFGRDKDVILNPYDKRTKGWSFFNEIRNDYDWQRYALSVVPRGKT
DEAEEWASYGRLLLRETAKKLALIGTPSMRELFHWTTIATFDDLRGFLEGTLAESLFAGSNEASKALTSA
RFVLSDKLPEHVTMPDGDFSIRSWLEDPNGGNLFITWREDMGPALRPLISAWVDVVCTSILSLPEEPKRR
LWLFIDELASLEKLASLADALTKGRKAGLRVVAGLQSTSQLDDVYGVKEAQTLRASFRSLVVLGGSRTDP
KTNEDMSLSLGEHEVERDRYSKNTGKHHSTGRALERVRERVVMPVEIANLPDLTAYVGFAGNRPIAKVPL
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 B2G2N9


T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 9667..24301

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HXE96_RS00035 6438..6773 + 336 WP_181408544 stable inheritance protein -
HXE96_RS00040 (R7K_007) 6921..7172 + 252 WP_012196438 hypothetical protein -
HXE96_RS00045 (R7K_008) 7327..7713 - 387 WP_012196437 hypothetical protein -
HXE96_RS00050 (R7K_009) 7727..8422 - 696 WP_012414157 StbB family protein -
HXE96_RS00055 (R7K_010) 8419..8844 - 426 WP_012196435 hypothetical protein -
HXE96_RS00060 (R7K_011) 9300..9665 + 366 WP_012414158 hypothetical protein -
HXE96_RS00065 (R7K_012) 9667..11190 + 1524 WP_012414159 type IV secretion system DNA-binding domain-containing protein virb4
HXE96_RS00070 (R7K_013) 11202..14090 + 2889 WP_238838742 MobF family relaxase -
HXE96_RS00075 (R7K_014) 14173..15249 - 1077 WP_012196431 P-type DNA transfer ATPase VirB11 virB11
HXE96_RS00080 (R7K_015) 15215..16402 - 1188 WP_012414162 type IV secretion system protein VirB10 virB10
HXE96_RS00085 (R7K_016) 16402..17202 - 801 WP_012414163 P-type conjugative transfer protein VirB9 virB9
HXE96_RS00090 (R7K_017) 17214..17909 - 696 WP_012196428 VirB8/TrbF family protein virB8
HXE96_RS00220 (R7K_018) 17914..18048 - 135 Protein_18 TrwH protein -
HXE96_RS00095 (R7K_019) 18161..19189 - 1029 WP_012414166 type IV secretion system protein virB6
HXE96_RS00100 (R7K_020) 19203..19433 - 231 WP_012196425 EexN family lipoprotein -
HXE96_RS00105 (R7K_021) 19430..20119 - 690 WP_012414167 P-type DNA transfer protein VirB5 virB5
HXE96_RS00110 (R7K_022) 20116..22587 - 2472 WP_012414168 VirB4 family type IV secretion/conjugal transfer ATPase virb4
HXE96_RS00115 (R7K_023) 22590..22901 - 312 WP_181408538 VirB3 family type IV secretion system protein virB3
HXE96_RS00120 (R7K_024) 22914..23219 - 306 WP_181408539 VirB2 family type IV secretion system major pilin TrwL virB2
HXE96_RS00125 (R7K_025) 23185..23481 - 297 WP_012414171 KorA family transcriptional regulator -
HXE96_RS00130 (R7K_026) 23603..24301 - 699 WP_012414172 lytic transglycosylase domain-containing protein virB1
HXE96_RS00135 (R7K_027) 24303..24689 - 387 WP_238838740 hypothetical protein -
HXE96_RS00140 (R7K_028) 25033..25320 + 288 WP_012414174 H-NS histone family protein -
HXE96_RS00145 (R7K_029) 25356..25769 + 414 WP_012414175 hypothetical protein -
HXE96_RS00150 (R7K_030) 25921..26577 + 657 WP_012414176 recombinase family protein -
HXE96_RS00155 (R7K_031) 26570..27541 + 972 WP_012414177 replication protein RepA -
HXE96_RS00160 (R7K_032) 28255..28884 + 630 WP_181408540 DNA-binding protein -

Host bacterium

ID   211 GenBank   NC_010643
Plasmid name   R7K Incompatibility group   IncW
Plasmid size   39792 bp Coordinate of oriT [Strand]   9136..9174 [-]
Host baterium   Providencia rettgeri

Cargo genes

Drug resistance gene   blaTEM-1D, aph(6)-Id, aph(3'')-Ib, aadA13
Virulence gene   trwD, trwF, trwG, trwK, trwM
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -