Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100515
Name   oriT_pN-Cit in_silico
Organism   Citrobacter freundii
Sequence Completeness      intact
NCBI accession of oriT (coordinates [strand])   NC_020122 (17167..17521 [+], 355 nt)
oriT length   355 nt
IRs (inverted repeats)      IR1: 145..155, 161..171  (ATATGTAATAC..GTATTACATAT)
  IR2: 208..218, 223..233  (GCATTTACGAT..ATCGTAATTGC)
  IR3: 336..344, 347..355  (CTTTCATGC..GCATGAAAG)
Location of nic site      242..243
Conserved sequence flanking the
  nic site    		  GGTGT|ATAGC
Note   predicted by the oriTfinder

  oriT sequence  


Download         Length: 355 nt

>oriT_pN-Cit
ACTCCGATACGTTGCCCTCCGAACGGTATTCAAGGTCGATTTTTTGCGCTTCGGTCACTCTTAAACTGATAGATGGCATAGGTTTCCTTTGTGTAATACCGATGTAATACATACAAATCTAGCATAGATGCGGCTTAATTCCACATATGTAATACGCTGTGTATTACATATTAAAACACAAATTAGAATAATTTGTTTTGTTTTCAAGCATTTACGATGAAAATCGTAATTGCGTATGGTGTATAGCCATTAAGGGATACCATAACACGCCTTTTTTAAGGGAGAAACAGCTCTTACACACGCATTAAACGCTCAAAAAGCGTTCACATTCACCACTTTCATGCTTGCATGAAAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   586 GenBank   YP_007354951
Name   TraI_pN-Cit insolico UniProt ID   L7SYL3
Length   967 a.a. PDB ID   
Note   putative relaxase

  Relaxase protein sequence


Download         Length: 967 a.a.        Molecular weight: 108240.28 Da        Isoelectric Point: 9.7636

>YP_007354951.1 TraI (plasmid) [Citrobacter freundii]
MLNITTITRQRVDKVVDYYADGADDYYAKDGNAMQWQGAGAEELGLTGEVEQKRFAKLLDGKVTDDISVM
RKTANSESKERLGYDLTFSAPKGVTLQALVNGDKRIIEAHDRAVTKAIEEAERLALGRFTVNKKTHVENT
NKLIVGKFRHETSRELDPDLHTHAFVMNLTKTSDGKWRSLTNDGIVNSLTLLGNVYKSELARELELAGYN
LRYDRNGTFDLAHFSQEQIAQFSQRSQQIEAELAKNGLSRETASHEQKNAAALKTRKSKGEVDRDVLYEG
WKNRAKELQIDFDSREWKGAANDDIARNTQPAALEKPIEYQADKVMTFAIRSLTERQSVITERELMDVAM
KHGYGRLTLDDIRAARERAITSGNLIKEEATYAAATTNKKQQNVAMTREQWVTELVKAGRNKDEARKLVD
KGITNGRLVQQKPRFTTQLAQQRERNILKMEREGRGKIQTPYTREFSEGWLASRTLKPEQLKAVMGIIHT
PNQFISVHGFAGTGKSYMTKSAADFLKEQGVHVTSLAPYGSQVKALQAEGLESRTLQSFLRASDKKIGPG
SVVFIDEAGVIPARQMEETMRVIRDAGARAVFLGDTKQTKAVEAGKPFEQLIKAGMETAYMKDIQRQKDP
ELLKAALNAAEGKIKASLTHVTSIVEEKNHDQRYRRIVGDYVAMPPTDRANALIITGTNDSRKKINAYIQ
AELGLKGQGINYPLLNRLDTTQAQRQHSKYYEKGAVIIPERDYSNGLKRGAVYTVLDTGPGNKLTVSDGS
GDTIAFSPARFSKLSVYSVEKTELAVGDQVRITRNDAHLDLANGDRFKVKGVQSGEVLLENEKGRLVKID
ANKPMYLGLAYASTVHSAQGLTCDKVFINMDTRSLTTAKDVYYVAVTRAKHEAVIYTDDEKKLDKAASRE
GFKTAALELEQLKRYAKEQQHDAREKGRDKTEPTQEKDNAKRKGHDKNNDERAFTSL

  Protein domains


Predicted by InterproScan.

AAA domain (AAA_30)

(475-649)

UvrD-like helicase C-terminal domain (UvrD_C_2)

(850-896)

TrwC relaxase (TrwC)

(14-287)


  Protein structure


Source ID Structure
AlphaFold DB L7SYL3


T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 507..16905

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HS982_RS00010 208..444 - 237 WP_000089855 H-NS histone family protein -
HS982_RS00015 (D726_p4001) 507..1247 + 741 WP_000815895 lytic transglycosylase domain-containing protein virB1
HS982_RS00020 (D726_p4002) 1270..1587 + 318 WP_001267114 hypothetical protein -
HS982_RS00025 (D726_p4003) 1571..1861 + 291 WP_015345248 TrbC/VirB2 family protein virB2
HS982_RS00030 (D726_p4004) 1914..2228 + 315 WP_024249950 VirB3 family type IV secretion system protein virB3
HS982_RS00035 (D726_p4005) 2228..4858 + 2631 WP_024249951 VirB4 family type IV secretion/conjugal transfer ATPase virb4
HS982_RS00040 (D726_p4006) 4868..5575 + 708 WP_015345224 type IV secretion system protein virB5
HS982_RS00045 5579..5815 + 237 WP_000733633 EexN family lipoprotein -
HS982_RS00050 (D726_p4007) 5834..6877 + 1044 WP_000885742 type IV secretion system protein virB6
HS982_RS00055 6927..7142 + 216 WP_087871672 hypothetical protein -
HS982_RS00060 (D726_p4008) 7145..7861 + 717 WP_000914645 type IV secretion system protein virB8
HS982_RS00065 (D726_p4009) 7864..8751 + 888 WP_000744355 TrbG/VirB9 family P-type conjugative transfer protein virB9
HS982_RS00070 (D726_p4010) 8748..9902 + 1155 WP_015345225 type IV secretion system protein VirB10 virB10
HS982_RS00075 (D726_p4011) 9895..10926 + 1032 WP_000138004 P-type DNA transfer ATPase VirB11 virB11
HS982_RS00080 (D726_p4012) 10889..11443 + 555 WP_000616063 phospholipase D family protein -
HS982_RS00085 (D726_p4013) 11444..11938 + 495 WP_015345227 GNAT family protein -
HS982_RS00090 11950..12144 + 195 WP_024249955 hypothetical protein -
HS982_RS00095 (D726_p4014) 12422..15325 - 2904 WP_015345228 MobF family relaxase -
HS982_RS00100 (D726_p4015) 15328..16905 - 1578 WP_001001035 type IV secretion system DNA-binding domain-containing protein virb4
HS982_RS00105 (D726_p4016) 16898..17278 - 381 WP_015345229 hypothetical protein -
HS982_RS00110 (D726_p4017) 17732..18166 + 435 WP_015345230 hypothetical protein -
HS982_RS00115 (D726_p4018) 18179..18889 + 711 WP_000686338 StbB family protein -
HS982_RS00120 (D726_p4019) 18891..19259 + 369 WP_015345231 plasmid stabilization protein StbC -
HS982_RS00125 (D726_p4020) 19451..20221 + 771 WP_015345232 SprT-like domain-containing protein -
HS982_RS00130 20262..20450 - 189 WP_001001010 hypothetical protein -
HS982_RS00135 20455..20712 - 258 WP_021536820 hypothetical protein -
HS982_RS00140 20785..20940 - 156 WP_021536821 hypothetical protein -
HS982_RS00145 21140..21382 - 243 WP_024249959 hypothetical protein -
HS982_RS00150 21437..21724 - 288 WP_001098466 hypothetical protein -

Host bacterium

ID   976 GenBank   NC_020122
Plasmid name   pN-Cit Incompatibility group   _
Plasmid size   34826 bp Coordinate of oriT [Strand]   17167..17521 [+]
Host baterium   Citrobacter freundii

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -