Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   106793
Name   oriT_pCFA1707-6 in_silico
Organism   Citrobacter freundii strain CFA1707
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP110909 (8964..10669 [-], 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_pCFA1707-6
GCCGTATGAATGACATTTATTTCCGTCCAATCCATCGAAATCAATATTTTGAGGAAATGAAAGCATGATAAAGAAACTTAAAGTAATCATGTTGGCGGCAATAGTTACCGGATGTTCATCGCCACCGCCTCCCGTCCCTGTAGAGTGGGATAAAGCCGCCGTCCCATTAAATACCAGTTTACCTCAATGGAGTGATAATAACATTATAGTCCCTTCCCCGACAGTTAACGGTAAATGGACATCATCAATCAGCGCACAAAGTTTCTACGATACAATATGGACTCCAGCAGTATTTTACGCAGTCGCCCATTCAACACGAATTGTCGTCACTGCACAATCCGGCACTGATTTCTTTAATGCCAAAAACTGGCTTCGCCAGAATGGCGCAAAAGGCGTTATTGAATACCAGCCTGTTTTTAATTGCCTGACGTGCAGAGAAACCACTATTTATTTCTCTCGCTAATCCATTTAAGCAACACAATCTAATAAGGATTTATCATGAAAAAAACCGTTATCGCGGCGGCTGTATTATGCCTGACCGCAGGAACGCCGATTTATTCCTTTGCCGCTGACCCGTGCGAAGTTGTTCTTTGCATGTACGGAAAAGCCACAGGTAATAGTGGTGGGGGTGAATGCAGTTCAGCAGAACGCGCATTTTTTAAAATCAACGCATTTAAAAAACACCATCGTTTTAATCCGGGTAAAACATTCGATATGCGAAAAGAATTTTTAGGGGAGTGCAAAGCCGCAGACCCTGAATCAATAAGCAAAATCCTTTCAAAATTTGGCAGAGTGAAAGGATAACTGACATATCCATTTTGATATGAGAGGTTCGAAATGATAAACGAAGATTTATTCATTAAGAATATACACTCAAAAAATCAGGACAGAATATCTGTAGCCCTGGTATATGACACGTTATCAAAAGAAGCCCACAGAGGTTGTGGGCTGTATTACGAAATATACGAAAGCTGTTTTATCGGTCTTTTGCGCGATCATCTTTCAGAACTTAATGAAGCTGACGCAAATAAATTACGACGCTATGCCGAAAGCAAAGGCACGAAAATTGATGATGCGTCCTACAGTGAAGCACTGGAAGCTGAAAGGGAGTGCAGGGCTGAAATATACCGCGAGCAAATGTAATCACACAAAACAAAAGTGTATTGTACACTACACAGACTAACAGGCGACGGGACTTTAAGGCTTCATTATTTTTGGCTTCAATTTCGAAGAAATTGTTAAGACGTAAAATCATGAAGTGGCACGCGGAAAGAAAATTCAATTTCGAAGAAATTGCTAATTTTCAGGAACCGCGCCCACCTGCGAACATTCGCCCACAGCGAATTGAGCAGGCCGGGGGGAGCCGCAAAAATTTTGCCGCCCCAGCGAGCAAAAAGGCACGCCCACGTGCCGTTTTTTGTGGGGGGCTTGCCCCGCACACCGTCGCAGCCAGGTAATATAACCCGCCCCAGCGGGGGATATTACCGATTAGGCGCGACCAACCCCTTTAAAGCAGCGTTCCGATTTTTTCGAGCTTGCGAGGAAAAATAGGCTAAACGCAGCGTCTTAAAGGGGTTGGTCGCGCGTAGCGCAAGACGGTGTGCCGCCTTTGACCTTGGGGGTTTTGGCTCGGCGTTCAGCCGGGACATTACCCCCATGTGTCATGCAGTGAGGGCGTCCAGCCCGAACGTAATGGCACAAGCCGT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


T4CP

ID   4525 GenBank   WP_117140887
Name   t4cp2_OQZ20_RS01050_pCFA1707-6 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: 65720.97 Da        Isoelectric Point: 7.4566

>WP_117140887.1 MULTISPECIES: type IV secretion system DNA-binding domain-containing protein [Enterobacteriaceae]
MGSHLMQRLNAFADAFSFFLLWLQNSPVILSLLAGLTLPFIFHLPREERKNAPFWLKSVACVSIFFFIFG
TISPLTIQGLSYFFKSLDNNILFRVPLWFMTIMFTASGLIFHIAARRLLAGEIDNLKHRMIKKSKLERNT
RTDVRKVKELLPDPIEYNPLDYIDLKKGVFIGLNKDDQPQYITIKEFKTQHAAIIGTTGSGKGVTATVLL
YQAILLGEAVFVEDPKDDEWAPHVLREACKKAGKKFTLINLNKLNFQLDLLADISHEQLEELFNAGFSLA
KKGEASDFYRISDRRAARNTSAIYEKGMTLRDLFNTDFVQSLREDVPAFCGELEEIALVNSINATKGFSL
KEVFDEGGCCYIIGSTRNQKIISAQRMILTRLIQIAETRDRINSTPRTVAIFLDELKYHLSRPALEGLGT
ARDKGVHIFMAFQAIDDLRDCPSDLNGDSVIGAIIENAKFKLIYKIQNPETAEWAAKMTGSILVDDEMRK
VRTDLSLTEKVDTDRMIRQAESYYVDSNMFLNLPEKVGFVFTSTELPRATKMFQVQVKKENIELLSFEYK
QATPEKNESQEHKPSINL

  Protein domains


Predicted by InterproScan.

Helicase HerA, central domain (DUF87)

(174-280)

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

(399-490)

  Protein structure



No available structure.



ID   4526 GenBank   WP_061586433
Name   t4cp2_OQZ20_RS01105_pCFA1707-6 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: 103112.03 Da        Isoelectric Point: 7.4626

>WP_061586433.1 MULTISPECIES: VirB3 family type IV secretion system protein [Enterobacteriaceae]
MAKLLKAMKRPAALWGVPMVPLLAVTGVTIIVAIWTSVALLFLLPVQFLVMKSLTRNEPMRFNLIAVWLR
AKGKPVANRLFGATTFMPVEHDDVDIKEFLDAMKLNQCATIKKYIPYSSHIHQHVVRSPKSDLYCTWELM
GTPFDCESDESLQFGTNQLHGLIRSFEGMPVTFYIHNDRNTFTDNLHKDSGNPYADEVSRLYYASVGLFR
RNRLFLTVCYRPFVSLEKAERKRMKDSQKLKELDGALLEMLEIKSTLDTALSRYGARPLGTFTEGNAVFS
SQLAFYEYLLTHQWRKVRVTRTPAYDVMGAAALFFSAESGQINHANGTQYFRGLEVKEFSEETATGMMDS
LLYAPCDYVITQSYTCMSREEAKKAIKRTRRLLMSADDDAVSQRLDLDVALDLLTSGKIAYGKHHFSIMV
YSPSLESLVADTNEISNALNNIGITPVPAEISLSAAYMAQLPGNYNLRPRKGELSSQNFVELAALHNFYP
GKRDKAPWGDAMALLRTPSGDGYYINLHNTLADKDEFNEKNPASTCILGTNGSGKTMLMTFFEIMQQKYG
REDSFSPDAKTKRLTTVYLDKDRGAEMNIRALGGRYYRVISGESTGWNPFSLPATKRNINFIKQLMKILC
TRNGSTISPRDERRLSDAVNAVMNDEPQYRVYGITRMLENLPEPATKEAQENGLSIRLSQWAQGGEFGWV
FDNESDTFDISNCDNFGIDGTEFLDDASVCAPISFYLLYRITSLLDGRRLVIFMDEFWKWLRDPVFKDFA
YNKLKTIRKLNGMLVVGTQSPAEIIKDDIAPAVIEQCGTQILAANPNADRAHYVDGMKFEPEVFDVVKGL
DPQARQYVVVKNQFRRGDTKRFAARVTLDLSGIGRYTKVMSGDAPNLEIFESIYREGMQPHEWLDTYLAK
AL

  Protein domains


Predicted by InterproScan.

TraG P-loop domain (P-loop_TraG)

(535-813)

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

(269-470)

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

(3-79)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 7011..20538

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
OQZ20_RS01010 (OQZ20_01005) 2444..2938 - 495 WP_223230020 DUF4326 domain-containing protein -
OQZ20_RS01015 (OQZ20_01010) 3007..3459 - 453 WP_151355700 DUF488 domain-containing protein -
OQZ20_RS01020 (OQZ20_01015) 3460..4107 - 648 WP_061586427 hypothetical protein -
OQZ20_RS01025 (OQZ20_01020) 4376..5023 + 648 WP_004178130 ParA family protein -
OQZ20_RS01030 (OQZ20_01025) 5064..5297 + 234 WP_004178129 hypothetical protein -
OQZ20_RS01035 (OQZ20_01030) 5335..5676 - 342 WP_011172022 hypothetical protein -
OQZ20_RS01040 (OQZ20_01035) 5737..6210 - 474 WP_061586426 thermonuclease family protein -
OQZ20_RS01045 (OQZ20_01040) 6247..7002 - 756 WP_023316386 MobC family replication-relaxation protein -
OQZ20_RS01050 (OQZ20_01045) 7011..8747 - 1737 WP_117140887 type IV secretion system DNA-binding domain-containing protein virb4
OQZ20_RS01055 (OQZ20_01050) 9527..9832 - 306 WP_032152569 hypothetical protein -
OQZ20_RS01060 (OQZ20_01055) 9866..10171 - 306 WP_061586437 conjugal transfer protein -
OQZ20_RS01065 (OQZ20_01060) 10207..10605 - 399 WP_073853226 cag pathogenicity island Cag12 family protein -
OQZ20_RS01070 (OQZ20_01065) 10602..11627 - 1026 WP_000125558 P-type DNA transfer ATPase VirB11 virB11
OQZ20_RS01075 (OQZ20_01070) 11617..12867 - 1251 WP_061586436 VirB10/TraB/TrbI family type IV secretion system protein virB10
OQZ20_RS01080 (OQZ20_01075) 12911..13819 - 909 WP_213858555 P-type conjugative transfer protein VirB9 virB9
OQZ20_RS01085 (OQZ20_01080) 13816..14499 - 684 WP_057517071 type IV secretion system protein virB8
OQZ20_RS01090 (OQZ20_01085) 14721..15794 - 1074 WP_061586435 type IV secretion system protein virB6
OQZ20_RS01095 (OQZ20_01090) 15805..16032 - 228 WP_073853223 EexN family lipoprotein -
OQZ20_RS01100 (OQZ20_01095) 16046..16756 - 711 WP_061586434 type IV secretion system protein -
OQZ20_RS01105 (OQZ20_01100) 16775..19513 - 2739 WP_061586433 VirB3 family type IV secretion system protein virb4
OQZ20_RS01110 (OQZ20_01105) 19526..19831 - 306 WP_012457109 TrbC/VirB2 family protein virB2
OQZ20_RS01115 (OQZ20_01110) 19828..20538 - 711 WP_061586432 lytic transglycosylase domain-containing protein virB1
OQZ20_RS01120 (OQZ20_01115) 20537..20659 + 123 WP_255093128 hypothetical protein -
OQZ20_RS01125 (OQZ20_01120) 20656..20874 - 219 WP_011172006 hypothetical protein -
OQZ20_RS01130 (OQZ20_01125) 20879..21094 - 216 WP_061586431 hypothetical protein -
OQZ20_RS01135 (OQZ20_01130) 21166..21621 - 456 WP_073853220 transcription termination/antitermination NusG family protein -
OQZ20_RS01140 (OQZ20_01135) 21872..22228 + 357 WP_032455359 helix-turn-helix transcriptional regulator -

Host bacterium

ID   7230 GenBank   NZ_CP110909
Plasmid name   pCFA1707-6 Incompatibility group   IncFII
Plasmid size   22675 bp Coordinate of oriT [Strand]   8964..10669 [-]
Host baterium   Citrobacter freundii strain CFA1707

Cargo genes

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