Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   120456
Name   oriT_pRHBSTW-00446_4 in_silico
Organism   Citrobacter sp. RHBSTW-00446
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP056511 (48352..50057 [-], 1706 nt)
oriT length   1706 nt
IRs (inverted repeats)      655..664, 672..681  (TTTTTTAAAA..TTTTAAAAAA)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 1706 nt

>oriT_pRHBSTW-00446_4
GCCGTATGAATGACATTTATTTCCGTCCAATCCATCGCAATCAATATTTTGAGGAAATGAAAGCATGATAAAGAAACTTAAAGTAATCATGTTGGCGGCAATAGTTACCGGATGTTCATCGCCACCGCCTCCCGTTCCTGTAGAGTGGGATAAAGCCGCTGAGCCATTAAATACCAGTTTACCGCAATGGAGTGACAATAACGTTATAGTCCCTTCCCCGACAGTTAACGGTAAATGGACATCATCAATCAGCGCACAAAGTTTCCACGATACAATATGGACTCCAGCAGTATTTTACGCAGCCGCCCATTCAACACGAATTGTCGTCACTGCACAATCCGGTACTGATTTCTTTAATGCTAAAAACTGGCTTCGCCAGAATGGCGCAAAAGGTGTTATTGAATACCAGCCCGTCTTTAATTGTCTGACATGCAGAGAAACCACTATTTATTTCTCTCGCCAATCCATTTAATCAACACAATCTAATAAGGATTTACCATGAAAAAAACCGTTATCACGGCGGCTGTATTATGCCTGACCGCAGGAACGCCGATTTATTCATTTGCCGCTGACCCATGCGAAGTTGTTCTTTGCATGTACGGAAAAGCAACGGGTAATAGTGGTGGGAGTGAATGCAGTTCAGCAGAACGCGCATTTTTTAAAATCAACGCTTTTAAAAAACACCATCGTTTTAATCCGGGTAAAACATTCGATATGCGAAAAGAATTTTTAGGCGAATGTAAAGCCGCAGACCCTGAATCAATAAGCAAAATCCTTTCAAAATTTGGCAGAGTGAAAGGATAACTGACATATCCATTTTGATATGAGAGGTTCGAAATGATAAACGAAGATTTATTCATTAAGAATATACACTCAAAAAATCAGGACGGAATATCTGTAGCCCTGGTATATGACACGTTATCAAAAGAAGCCCACAGAGGTTGTGGGCTGTATTATGAAATATACGAAAGCTGTTTTATAGGCCTTTTGCGCGATCATCTTTCAGAACTTAATGAAGCCGACGCAAATAAATTAACGAGGTACGCAGAAAGTAAAGGCACGAAAATTGATGATGTGTCCTACAGTGAAGCACTGGAAGCTGAAAGGGAGTGCAGAGCTGAAATATACCGCGAGCAGATGTAATCACACAAAACAAAAGTGTATTGTACAATACACAGACTAACAGGCGGCGGGATTTTAAGGCTTCATTATTTTTGGCTTCAATTTCGAAGAAATTGTTAAGACGAAAAATAATGAAGTGGTACGCGGAAAGAAAATTCAATTTCGAAGAAATTGCTAATTTTCAGGAAACGCGCCCACCTGCGAACATTCGCCCACAGCGAATTGAGCAGGCCGGGGGGAGCCGCAAAAATTTTGCCGCCCCAGCGAGCAAAAAGGCACGCCCACGTGCCGTTTTTTGTGGGGGGCTTGCCCCGCACACCGTCGCAGCCAGGTAATATAACCCGCCCCAGCGGGGGATATTACCGATTAGGCGCGACCAACCCCTTTAAAGCAGCGTTCCGATTTTTTCGAGCTTGCGAGGAAAAATAGGCTAAACGCAGCGTCTTAAAGGGGTTGGTCGCGCGTAGCGCAAGACGGTGTGCCGCCTTTGACCCTGGGGGTTTTGGCTCGGCGTCCAGCCGGGACATTACCCCCATGTGTCATGCAGTGAGGGCGTCCAGCCCGAACGTAATGGCACACGCCGT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


T4CP

ID   15130 GenBank   WP_047502583
Name   t4cp2_HV199_RS28150_pRHBSTW-00446_4 insolico UniProt ID   _
Length   578 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 578 a.a.        Molecular weight: 65654.85 Da        Isoelectric Point: 7.4566

>WP_047502583.1 MULTISPECIES: type IV secretory system conjugative DNA transfer family protein [Enterobacteriaceae]
MGSHLMQRLNAFADAFSFFLLWLQNSPVILSLLAGLTLPFIFHLPREERKNAPFWLKSVACVSIFFFIFG
TISPLTIQGLSYFFKSLDNNILFRVPLWIMTIIFTAAGLIFHIAARRLLAGEIDNLKHRMIKKSKLERNT
RTDVRKVKELLPDSIEYNPLDYIDLKKGVFIGLNKDDQPQYITIKEFKTQHAAIIGTTGSGKGVTATVLL
YQAILLGEAVFVEDPKDDEWAPHVLREACKKAGKKFTLINLNKLNFQLDLLADISHEQLEELFNAGFSLA
KKGEASDFYRISDRRAARNTSAIYEKGMTLRDLFNADFVQSLREDVPAFCGELEEIALVNSINAKNGFSL
KEVFDDGGCCYIIGSTRNQKIISAQRMILTRLIQIAETRDRINSTPRTVAIFLDELKYHLSRPALEGLGT
SRDKGVHIFMAFQAIDDLRDCPSDLNGDSVIGAIIENAKFKLIYKIQNPETAEWAAKMTGSILVDDEMRK
VRTDLSLTEKVDTDRMIRQAESYYVDSNMFLNLPEKVGFVFTSTELPRATKMFQVQVKKENIELLSFEYK
QATPEKNENQEHKPSINL

  Protein domains


Predicted by InterproScan.

TraM recognition site of TraD and TraG (TraG-D_C)

(399-490)

Helicase HerA, central domain (DUF87)

(174-314)

  Protein structure



No available structure.



ID   15131 GenBank   WP_047502599
Name   t4cp2_HV199_RS28205_pRHBSTW-00446_4 insolico UniProt ID   _
Length   912 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 912 a.a.        Molecular weight: 103124.05 Da        Isoelectric Point: 7.6337

>WP_047502599.1 MULTISPECIES: VirB3 family type IV secretion system protein [Enterobacteriaceae]
MAKLLKAMKRPAALWGVPMVPLLAVTGVTIIVAIWTSVALLFLLPVQFLVMKSLTRNEPMRFNLIAVWLR
AKGKPVANRLFGATTFMPVEHDDVDIKEFLDAMKLNQCATIRKYIPYSSHIHQHVVRSPKSDLYCTWELM
GTPFDCESDESLQFGTNQLHGLIRSFEGMPVTFYIHNDRNTFTDNLHKDSGNPYADEVSRLYYASVGLFR
RNRLFLTVCYRPFVSLEKAERKRMKDSQKLKELDGALLEMLEIKSTLDTALSRYGARPLGTFTEGSAVFS
SQLAFYEYLLTHQWRKVRVTRTPAYDVMGAAALFFSAESGQINHANGTQYFRGLEVKEFSEETATGMMDS
LLYAPCDYVITQSYTCMSREEAKKAIKRTRRLLMSADDDAVSQRLDLDVALDLLTSGKIAYGKHHFSIMV
YSPSLESLVADTNEISNALNNIGITPVPAEISLSAAYMAQLPGNYNLRPRKGELSSQNFVELAALHNFYP
GKRDKAPWGDAMALLRTPSGDGYYINLHNTLADKDEFNEKNPASTCILGTNGSGKTMLMTFFEIMQQKYG
REDSFSPDAKTKRLTTVYLDKDRGAEMNIRALGGRYWRVISGESTGWNPFSLPATKRNINFIKQLMKILC
SRNGSTISPRDERRLSDAVNAVMNDEPQYRVYGITRMLENLPEPATKEAQENGLSIRLSQWAQGGEFGWV
FDNQSDTFDISNCDNFGIDGTEFLDDASVCAPISFYLLYRITSLLDGRRLVIFMDEFWKWLRDPVFKDFA
YNKLKTIRKLNGMLVVGTQSPAEIIKDDIAPAVIEQCGTQILAANPNADRAHYVDGMKFEQEVFDVVKGL
DPQARQYVVVKNQFKRGDTKRFAARVTLDLSGIGRYTKVMSGDAPNLEIFESIYREGMQPHEWLDTYLAK
AL

  Protein domains


Predicted by InterproScan.

Type IV secretory pathway, VirB3-like protein (VirB3)

(3-79)

CagE, TrbE, VirB family, component of type IV transporter system (CagE_TrbE_VirB)

(269-470)

TraG P-loop domain (P-loop_TraG)

(535-813)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 46399..59945

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HV199_RS28115 (HV199_28125) 42084..42833 + 750 Protein_43 SprT-like domain-containing protein -
HV199_RS28120 (HV199_28130) 42953..43600 + 648 WP_004178130 ParA family protein -
HV199_RS28125 (HV199_28135) 43641..43874 + 234 WP_004178129 hypothetical protein -
HV199_RS28130 (HV199_28140) 44055..44486 - 432 WP_052138047 hypothetical protein -
HV199_RS28135 (HV199_28145) 44723..45064 - 342 WP_032442697 hypothetical protein -
HV199_RS28140 (HV199_28150) 45125..45598 - 474 WP_047502580 thermonuclease family protein -
HV199_RS28145 (HV199_28155) 45635..46390 - 756 WP_032442693 MobC family replication-relaxation protein -
HV199_RS28150 (HV199_28160) 46399..48135 - 1737 WP_047502583 type IV secretory system conjugative DNA transfer family protein virb4
HV199_RS28155 (HV199_28165) 48915..49220 - 306 WP_047502586 hypothetical protein -
HV199_RS28160 (HV199_28170) 49254..49559 - 306 WP_032722794 conjugal transfer protein -
HV199_RS28165 (HV199_28175) 49586..49993 - 408 WP_072034110 cag pathogenicity island Cag12 family protein -
HV199_RS28170 (HV199_28180) 49990..51015 - 1026 WP_032442691 P-type DNA transfer ATPase VirB11 virB11
HV199_RS28175 (HV199_28185) 51005..52273 - 1269 WP_047502589 VirB10/TraB/TrbI family type IV secretion system protein virB10
HV199_RS28180 (HV199_28190) 52320..53228 - 909 WP_102063339 P-type conjugative transfer protein VirB9 virB9
HV199_RS28185 (HV199_28195) 53225..53908 - 684 WP_004178111 type IV secretion system protein virB8
HV199_RS28190 (HV199_28200) 54130..55203 - 1074 WP_047502593 type IV secretion system protein virB6
HV199_RS28195 (HV199_28205) 55207..55449 - 243 WP_047502596 EexN family lipoprotein -
HV199_RS28200 (HV199_28210) 55457..56164 - 708 WP_039109365 type IV secretion system protein -
HV199_RS28205 (HV199_28215) 56182..58920 - 2739 WP_047502599 VirB3 family type IV secretion system protein virb4
HV199_RS28210 (HV199_28220) 58933..59238 - 306 WP_191233349 TrbC/VirB2 family protein virB2
HV199_RS28215 (HV199_28225) 59235..59945 - 711 WP_004178175 lytic transglycosylase domain-containing protein virB1
HV199_RS28220 (HV199_28230) 60063..60281 - 219 WP_004178172 hypothetical protein -
HV199_RS28225 (HV199_28235) 60286..60501 - 216 WP_004178170 hypothetical protein -
HV199_RS28230 (HV199_28240) 60573..61028 - 456 WP_009309974 transcription termination/antitermination NusG family protein -
HV199_RS28235 (HV199_28245) 61318..61656 + 339 WP_306460784 helix-turn-helix domain-containing protein -

Host bacterium

ID   20885 GenBank   NZ_CP056511
Plasmid name   pRHBSTW-00446_4 Incompatibility group   IncFII
Plasmid size   62128 bp Coordinate of oriT [Strand]   48352..50057 [-]
Host baterium   Citrobacter sp. RHBSTW-00446

Cargo genes

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