Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   121158
Name   oriT_pYUSHP29-4 in_silico
Organism   Leclercia adecarboxylata strain SH19PE29
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP087284 (4722..6427 [-], 1706 nt)
oriT length   1706 nt
IRs (inverted repeats)     _
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 1706 nt

>oriT_pYUSHP29-4
GCCGTATGAATGACATTTATTTCCGTCCAATTCATCGAAACCAGTATTTTGAGGAAATGAAAGCATGATAAAGAAACTTAAAGTAATCATGTTAGCGGCAATAGTTACCGGATGTTCATCGCCGCCGCCTCCCGTTCCTGTAGAGTGGGATAAAGCCGCCGCCCCATTAAACACCAGTTTACCGCAATGGAGTGACAATAACGTTATAGTTCCTTCCCCGACAGTTAACGGTAAATGGACATCATCAATCAGCGCACAAAGTTTCTACGATACAATATGGACTCCAGCAGTATTTTACGCAGTCGCCCATTCAACACGAATTGTCGTCACTGCACAATCCGGTACTGCTTTCTTTAATGCCAAAAACTGGCTTCGCCAGAATGGTGCAAAAGGTGTTATTGAATACCAGCCCGTCTTTAATTGCCTGACATGCAGAGAAACCACCATTTATTTATCTCGCTAATCCATTTAAACAATACAATCTAATAAGGATTTACCATGAAAAAAACCGTTATCGCGGCGGCTGTATTATGCCTGACCGCAGGAACACCGTTTTATTCCTTTGCCGCTGACCCGTGCGAAGTTGTTCTTTGCATGTACGGAAAAGCTACGGGTAATAGTGGTGGGAGTGAATGCAGTTCAGCAGAACGCGCATTTTTTAAAATCAACGCCTTTAAAAAACACCATCGTTTTAATCCGGGTAAAACATTCGATATGCGAAAAGAATTTTTAGGCGAATGTAAAGCCGCAGACCCTGAATCAATAAGCAAAATCCTTTCAAAGTTTGGCAGAGTGAAAGGATAACTGACATATCCATTTTGATATGAGAGGTTCGAAATGATAAACGAAGATTTATTCATTAATAATCTACACTCAAAAAATCAGGACAGAATATCTGTAGCCCTGGTATATGACACGTTATCAAAAGAAGCCCACAGAGGTTGTGGGCTGTATTACGAAATATACGAAAGCTGTTTTATCGGTCTTTTGCGCGATCATCTTTCAGAACTTAATGAAGCTGACGCAAATAAATTACGACGCTATGCCGAAAGCAAAGGCACGAAAATTGATGATGCGTCCTACAGTGAAGCACTGGAAGCTGAAAGGGAGTGCAGGGCTGAAATATACCGCGAGCAAATGTAATCACACAAAACAAATGTGTATTGTACAATACACAGACTAACAGGCGACGGGACTTTAAGGCTTCATTATTTTTGGCTTCAATTTCGAAGAAATTGTTAAGACGAAAAATAATGAAGTGGTACGCGGAAAGAAAATTCAATTTCGAAGAAATTGCTAATTTTCAGGAACCGCGCCCACCTGCGAACATTCGCCCACAGCGAATTGAGCAGGCCGGGGGGAGCCGCAAAAATTTTGCCGCCCCAGCGAGCAAAAAGGCACGCCCACGTGCCGTTTTTTGTGGGGGGCTTGCCCCGCACACCGTCGCAGCCAGGTAATATAACCCGCCCCAGCGGGGGATATTACCGATTAGGCGCGACCAACCCCTTTAAAGCAGCGTTCCGATTTTTTCGAGCTTGCGAGGAAAAATAGGCTAAACGCAGCGTCTTAAAGGGGTTGGTCGCGCGTAGCGCAAGACGGTGTGCCGCCTTTGACCTTGGGGGTTTTGGCTCGGCGTCCAGCCGGGACATTACCCCCATGTGTCATGCAGTGAGGGCGTCCAGCCCGAACGTAATGGCACACGCCGT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


T4CP

ID   15647 GenBank   WP_045895973
Name   t4cp2_LO739_RS24395_pYUSHP29-4 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: 65609.81 Da        Isoelectric Point: 7.4566

>WP_045895973.1 MULTISPECIES: type IV secretory system conjugative DNA transfer family protein [Enterobacterales]
MGSHLMQRLNAFADAFSFFLLWLQNSPVILSLLAGLTLPFIFHLPREERKNAPFWLKSVACVSIFFFIFG
TISPLTIQGLSYFFKSLDNNILFRVTLWIMTIIFTAAGLIFHIAARRLLAGEIDNLKHRMIKKSKLERNT
RTDVRKVKELLPDPIEYNPLDYIDLKKGVFIGLNKDDQPQYITIKEFKTQHAAIIGTTGSGKGVTATVLL
YQAILLGEAVFVEDPKDDEWAPHVLREACKKAGKKFTLINLNKLNSQLDLLADISHEQLEELFNAGFSLA
KKGEASDFYRISDRRAARNTSAIYEKGMTLRDLFNTDFVQSLREDVPAFCGELEEIALVNSINAKNGFSL
KEVFDEGGCCYIIGSTRNQKIISAQRMILTRLIQIAETRDRINSTPRTVAIFLDELKYHLSRPALEGLGT
ARDKGVHIFMAFQAIDDLRDCPSDLNGDSVIGAIIENAKFKLIYKIQNPETAEWAAKMTGSILVDDEMRK
VRTDLSLTEKVDTDRMIRQAESYYVDSNMFLNLPEKVGFVFTSTELPRATKMFQVQVKKENIELLSFEYK
QATPEKNESQEHKPSINL

  Protein domains


Predicted by InterproScan.

Helicase HerA, central domain (DUF87)

(174-260)

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

(399-490)

  Protein structure



No available structure.



ID   15648 GenBank   WP_012457110
Name   t4cp2_LO739_RS24450_pYUSHP29-4 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: 103056.99 Da        Isoelectric Point: 7.4625

>WP_012457110.1 MULTISPECIES: VirB3 family type IV secretion system protein [Enterobacterales]
MAKLLKAMKRPAALWGVPMVPLLAVTGVTIIVAIWTSVALLFLLPVQFLVMKSLTRNEPMRFNLIAVWLR
AKGKPVANRLFGATTFMPVEHDDVDIKEFLDAMKLNQCATIKKYIPYSSHIHQHVVRSPKSDLYCTWELM
GTPFDCESDESLQFGTNQLHGLIRSFEGMPVTFYIHNDRNTFTDNLHKDSGNPYADEVSRLYYASVGLFR
RNRLFLTVCYRPFVSLEKAERKRMKDSQKLKELDGALLEMLEIKSTLDTALSRYGARPLGTFTEGSAVFS
SQLAFYEYLLTHQWRKVRVTRTPAYDVMGAAALFFSAESGQINHANGTQYFRGLEVKEFSEETATGMMDS
LLYAPCDYVITQSYTCMSREEAKKAIKRTRRLLMSADDDAVSQRLDLDVALDLLTSGKIAYGKHHFSIMV
YSPSLESLVADTNEISNALNNIGITPVPAEISLSAAYMAQLPGNYNLRPRKGELSSQNFVELAALHNFYP
GKRDKAPWGDAMALLRTPSGDGYYINLHNTLADKDEFNEKNPASTCILGTNGSGKTMLMTFFEIMQQKYG
REDSFSPDAKTKRLTTVYLDKDRGAEMNIRALGGRYYRVISGESTGWNPFSLPATKRNINFIKQLMKILC
TRNGSTISPRDERRLSDAVNAVMNDEPQYRVYGITRMLENLPEPATKEAQENGLSIRLSQWAQGGEFGWV
FDNESDTFDISNCDNFGIDGTEFLDDASVCAPISFYLLYRITSLLDGRRLVIFMDEFWKWLRDPVFKDFA
YNKLKTIRKLNGMLVVGTQSPAEIIKDDIAPAVIEQCGTQILAANPNADRAHYVDGMKFEPEVFDVVKGL
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: 2769..16292

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
LO739_RS24370 (LO739_24365) 134..781 + 648 WP_045895980 ParA family protein -
LO739_RS24375 (LO739_24370) 822..1055 + 234 WP_004178129 hypothetical protein -
LO739_RS24380 (LO739_24375) 1093..1389 - 297 WP_223283641 hypothetical protein -
LO739_RS24385 (LO739_24380) 1495..1968 - 474 WP_045895976 thermonuclease family protein -
LO739_RS24390 (LO739_24385) 2005..2760 - 756 WP_023316386 MobC family replication-relaxation protein -
LO739_RS24395 (LO739_24390) 2769..4505 - 1737 WP_045895973 type IV secretory system conjugative DNA transfer family protein virb4
LO739_RS24400 (LO739_24395) 5285..5590 - 306 WP_059321833 hypothetical protein -
LO739_RS24405 (LO739_24400) 5624..5929 - 306 WP_045895969 conjugal transfer protein -
LO739_RS24410 (LO739_24405) 5965..6363 - 399 WP_071687791 cag pathogenicity island Cag12 family protein -
LO739_RS24415 (LO739_24410) 6360..7385 - 1026 WP_045895968 P-type DNA transfer ATPase VirB11 virB11
LO739_RS24420 (LO739_24415) 7375..8625 - 1251 WP_045895967 VirB10/TraB/TrbI family type IV secretion system protein virB10
LO739_RS24425 (LO739_24420) 8672..9580 - 909 WP_077874239 P-type conjugative transfer protein VirB9 virB9
LO739_RS24430 (LO739_24425) 9577..10260 - 684 WP_045895965 type IV secretion system protein virB8
LO739_RS24435 (LO739_24430) 10482..11555 - 1074 WP_045895964 type IV secretion system protein virB6
LO739_RS24440 (LO739_24435) 11566..11793 - 228 WP_059321746 EexN family lipoprotein -
LO739_RS24445 (LO739_24440) 11807..12511 - 705 WP_045895962 type IV secretion system protein -
LO739_RS24450 (LO739_24445) 12529..15267 - 2739 WP_012457110 VirB3 family type IV secretion system protein virb4
LO739_RS24455 (LO739_24450) 15280..15585 - 306 WP_012457109 TrbC/VirB2 family protein virB2
LO739_RS24460 (LO739_24455) 15582..16292 - 711 WP_004178175 lytic transglycosylase domain-containing protein virB1
LO739_RS24465 (LO739_24460) 16410..16628 - 219 WP_004178172 hypothetical protein -
LO739_RS24470 (LO739_24465) 16633..16848 - 216 WP_004178170 hypothetical protein -
LO739_RS24475 (LO739_24470) 16920..17375 - 456 WP_009309974 transcription termination/antitermination NusG family protein -
LO739_RS24480 (LO739_24475) 17626..17985 + 360 WP_034950652 helix-turn-helix transcriptional regulator -
LO739_RS24485 (LO739_24480) 18445..19146 + 702 WP_255212247 RepA family replication protein -
LO739_RS24490 (LO739_24485) 20211..21233 + 1023 WP_000156884 IS110-like element IS5708 family transposase -

Host bacterium

ID   21586 GenBank   NZ_CP087284
Plasmid name   pYUSHP29-4 Incompatibility group   IncFII
Plasmid size   30678 bp Coordinate of oriT [Strand]   4722..6427 [-]
Host baterium   Leclercia adecarboxylata strain SH19PE29

Cargo genes

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