Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   104936
Name   oriT_CD3406|unnamed3 in_silico
Organism   Serratia proteamaculans strain CD3406
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP117171 (1726..3431 [+], 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_CD3406|unnamed3
GCCGTATGAATGACATCTATTTCCGTCCAATTCATCGAAACCAGTATTTTGAGGAAATGAAAGCATGATAAAGCAAATTAAAGTAATCATGTTGGCAGCAATAGTTACCGGATGTTCATCGCCACCTCCTCCCGTTCCTGTGGAGTGGGATAAAGCCGCTGCCCCATTAAATACCAGTTTACCGCAATGGAGTGACAATAACGTTATAGTCCCTTCCCCGACAGTTAACGGTAAATGGACATCATCAATCAGTGCACAAAGTTTCTACGATACAACATGGACTCCAGCAGTATTTTACGCAGTCGCCCATTCAACACGAATTGTCGTCACTGCACAATCAGGCACTGATTTCTTTAATGCCAAAAACTGGCTTCGCCAGAATGGCGCAAAAGGCGTTATTGAATACCAGCCTGTCTTTAATTGCCTGACGTGCAGAGAAACCACTATTTATTTCTCTCGCTAATCCATTTAAGCAACACAATCTAATAAGGATTTATCATGAAAAAAACCGTTATCGCGGCGGCTGTATTATGCCTGACCGCAGGAACGCCGATTTATTCCTTTGCCGCTGACCCGTGCGAAGTTGTTCTTTGCATGTACGGAAAAGCTACAGGTAATAGTGGTGGGAGTGAATGCAGTTCAGCAGAACGCGCATTTTTTAAAATAAACGCATTTAAAAAACACCATCGTTTTAATCCGGGTAAAACATTCGATATGCGAAAAGAATTTTTAGGGGAGTGCAAAGCCGCAGACCCTGAATCAATAAGCAAAATCCTTTCAAAATTTGGCAGAGTGAAAGGATAACTGACATATCCATTTTAATATGAGAGGTTCGAAATGATAAACGAAGATTTATTCATTAAGAATATACACTCAAAAAATCAGGACAGAATATCTGTAGCCCTGGTATATTACACGTTATCAAAAGAAGCCCACCGAGGTTGTGGGCTGTATTACGAAATATATGAAAGTTGTTTTATCGGTCTTTTGCGCGATCATCTTTCAGAACTTAATGAAGCTGACGCAAATAAATTAAGACGCTATGCCGAGAGTAAAGGTACGAAAATTGATGATGCGTCCTACAGTGAAGCACTGGAAGCTGAAAGGGAGTGCAGGGCTGAAATATACCGCGAGCAAATGTAATCACACAAAACAAAAGTGTATTGTACAATACACAGACTAACAGGCGACGGGGTTTTAAGGCTTCATTATTTTTGGCTTCAATTTCGAAGAAATTGTTAAGACGAAAAATAATGAAGTGGTACGCGGAAAGAAAATTCAATTTCGGAGAAATTGCTAATTTTCAGGAACCGCGCCCACCTGCGAACATTCGCCCACAGCGAATTGAGCAGGCCGGGGGGAGCCGCAAAAATTTTGCCGCCCCAGCGAGCAAAAAGGCACGCCCACGTGCCGTTTTTTGTGGGGGGCTTGCCCCGCACACCGTCGCAGCCAGGTAATATAACCCGCCCCAGCGGGGGATATTACCGATTAGGCGCGACCAACCCCTTTAAAGCAGCGTTCCGATTTTTTCGAGCTTGCGAGGAAAAATAGGCTAAACGCAGCGTCTTAAAGGGGTTGGTCGCGCGTAGCGCAAGACGGTGTGCCGCCTTTGACCTTGGGGGTTTTGGCTCGGCGTCCAGCCGGGACATTACCCCCATGTGTCATGCAGTGAGGGCGTCCAGCCCGAACGTAATGGCACACGCCGT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


T4CP

ID   3420 GenBank   WP_023316385
Name   t4cp2_JET59_RS27585_CD3406|unnamed3 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: 65637.82 Da        Isoelectric Point: 7.2144

>WP_023316385.1 MULTISPECIES: type IV secretion system DNA-binding domain-containing protein [Enterobacterales]
MGSHLMQRLNAFADAFSFFLLWLQNSPVILSLLAGLTLPFIFHLPREERNNAPFWLKSVACVSIFFFIFG
TISPLTIQGLSYFFKSLDNNILFRVPLWIMTIVFTAAGLIFHIAARRLLAGEIDNLKHRMIKKSKLERNT
RTDVRKVKELLPDPIEYNPLDYIDLKKGVFIGLNKDDQPQYITIKEFKTQHAAIIGTTGSGKGVTATVLL
YQAILLGEAVFVEDPKDDEWAPHVLREACKKAGKKFTLINLNKLNFQLDLLADISHEQLEELFNAGFSLA
KKGEASDFYRISDRRAARNTSAIYEKGMTLRDLFNTDFVQSLREDVPAFCGELEEIALVNSINAKNGFSL
KEVFDEGGCCYIIGSTRNQKIISAQRMILTRLIQIAETRDRINSTPRTVAIFLDELKYHLSRPALEGLGT
ARDKGVHIFMAFQAIDDLRDCPSDLNGDSVIGAIIENAKFKLIYKIQNPETAEWAAKMTGSILVDDEMRK
VRTDLSLTEKVDTDRMIRQAESYYVDSNMFLNLPEKVGFVFTSTELPRATKMFQVQVKKENIELLSFEYK
QATPEKNESQEHKPSINL

  Protein domains


Predicted by InterproScan.

Helicase HerA, central domain (DUF87)

(174-314)

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

(336-537)

  Protein structure



No available structure.



ID   3421 GenBank   WP_032152565
Name   t4cp2_JET59_RS27675_CD3406|unnamed3 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: 103042.92 Da        Isoelectric Point: 7.2988

>WP_032152565.1 MULTISPECIES: VirB3 family type IV secretion system protein [Enterobacterales]
MAKLLKAMKRPAALWGVPMVPLLAVTGVTIIVAIWTSVALLFLLPVQFLVMKSLTRNEPMRFNLIAVWLR
AKGNPVANRLFGATTFMPVEHDDVDIKEFLDAMKLNQCATIKKYIPYSSHIHQHVVRSPKSDLYCTWELM
GTPFDCESDESLQFGTNQLHGLIRSFEGMPVTFYIHNDRNTFTDNLHKDSGNPYADEVSRLYYASVGLFR
RNRLFLTVCYRPFVSLEKAERKRMKDSQKLKELDGALLEMLEIKSTLDTALSRYGARPLGTFTEGSAVFS
SQLAFYEYLLTHQWRKVRVTRTPAYDVMGAAALFFSAESGQINHANGTQYFRGLEVKEFSEETATGMMDS
LLYAPCDYVITQSYTCMSREEAKKAIKRTRRLLMSADDDAVSQRLDLDVALDLLTSGKIAYGKHHFSIMV
YSPSLESLVADTNEISNALNNIGITPVPAEISLSAAYMAQLPGNYNLRPRKGELSSQNFVELAALHNFYP
GKRDKAPWGDAMALLRTPSGDGYYINLHNTLADKDEFNEKNPASTCILGTNGSGKTMLMTFFEIMQQKYG
REDSFSPDAKTKRLTTVYLDKDRGAEMNIRALGGRYYRVISGESTGWNPFSLPATKRNINFIKQLMKILC
TRNGSTISPRDERRLSDAVNAVMNDEPQYRVYGITRMLENLPEPATKEAQENGLSIRLSQWAQGGEFGWV
FDNESDTFDISNCDNFGIDGTEFLDDASVCAPISFYLLYRITSLLDGRRLVIFMDEFWKWLRDPVFKDFA
YNKLKTIRKLNGMLVVGTQSPAEIIKDDIAPAVIEQCGTQILAANPNADRAHYVDGMKFEPEVFDVVKGL
DPQARQYVVVKNQFKRGDTKRFAARVTLDLSGIGRYTKVMSGDAPNLEIFESIYREGMQPHEWLDTYLAK
AL

  Protein domains


Predicted by InterproScan.

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

(269-470)

TraG P-loop domain (P-loop_TraG)

(535-813)

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

(3-79)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 15857..23468

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
JET59_RS27630 (JET59_027630) 11526..11807 - 282 WP_000780222 helix-turn-helix transcriptional regulator -
JET59_RS27635 (JET59_027635) 11788..12117 - 330 WP_000493286 type II toxin-antitoxin system RelE/ParE family toxin -
JET59_RS27640 (JET59_027640) 13001..13660 - 660 WP_023316392 RepA family replication protein -
JET59_RS27645 (JET59_027645) 14162..14521 - 360 WP_032152563 helix-turn-helix transcriptional regulator -
JET59_RS27650 (JET59_027650) 14774..15229 + 456 WP_009309974 transcription termination/antitermination NusG family protein -
JET59_RS27655 (JET59_027655) 15301..15516 + 216 WP_004178170 hypothetical protein -
JET59_RS27660 (JET59_027660) 15521..15739 + 219 WP_004178172 hypothetical protein -
JET59_RS27665 (JET59_027665) 15857..16567 + 711 WP_004178175 lytic transglycosylase domain-containing protein virB1
JET59_RS27670 (JET59_027670) 16564..16869 + 306 WP_012457109 TrbC/VirB2 family protein virB2
JET59_RS27675 (JET59_027675) 16882..19620 + 2739 WP_032152565 VirB3 family type IV secretion system protein virb4
JET59_RS27680 (JET59_027680) 19638..20339 + 702 WP_023316379 type IV secretion system protein -
JET59_RS27685 (JET59_027685) 20351..20575 + 225 WP_032152566 EexN family lipoprotein -
JET59_RS27690 (JET59_027690) 20588..21658 + 1071 WP_023316380 type IV secretion system protein virB6
JET59_RS27695 (JET59_027695) 21880..22563 + 684 WP_023316381 type IV secretion system protein virB8
JET59_RS27700 (JET59_027700) 22560..23468 + 909 WP_077763931 P-type conjugative transfer protein VirB9 virB9

Host bacterium

ID   5374 GenBank   NZ_CP117171
Plasmid name   CD3406|unnamed3 Incompatibility group   IncFII
Plasmid size   23984 bp Coordinate of oriT [Strand]   1726..3431 [+]
Host baterium   Serratia proteamaculans strain CD3406

Cargo genes

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