Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   105280
Name   oriT_pRHB33-C04_2 in_silico
Organism   Escherichia fergusonii strain RHB33-C04
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP057216 (117147..117232 [-], 86 nt)
oriT length   86 nt
IRs (inverted repeats)      61..68, 73..80  (TTGGTGGT..ACCACCAA)
 27..34, 37..44  (GCAAAAAC..GTTTTTGC)
 8..13, 21..26  (TGATTT..AAATCA)
Location of nic site      53..54
Conserved sequence flanking the
  nic site    		  GGTGTGGTGC
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 86 nt

>oriT_pRHB33-C04_2
AATTACATGATTTAAAACGCAAATCAGCAAAAACTTGTTTTTGCGTGGGGTGTGGTGCTTTTGGTGGTGAGAACCACCAACCTGTT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Auxiliary protein

ID   1619 GenBank   WP_040100321
Name   WP_040100321_pRHB33-C04_2 insolico UniProt ID   _
Length   127 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 127 a.a.        Molecular weight: 14508.47 Da        Isoelectric Point: 4.7033

>WP_040100321.1 MULTISPECIES: conjugal transfer relaxosome DNA-binding protein TraM [Escherichia]
MARVILYISNDVYDKVNAIVEQRRQEGARDKDISLSGTASMLLELGLRVYDAQMERKESAFNQTEFNKLL
LECVVKTQSSVAKILGIESLSPHVSGNPKFEYANMVEDIREKVSSEMERFFPKNDEE

  Protein domains


Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-126)


  Protein structure



No available structure.



ID   1620 GenBank   WP_072039828
Name   WP_072039828_pRHB33-C04_2 insolico UniProt ID   _
Length   75 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 75 a.a.        Molecular weight: 8515.70 Da        Isoelectric Point: 10.3461

>WP_072039828.1 MULTISPECIES: conjugal transfer relaxosome protein TraY [Escherichia]
MSRNIIRPAPGNKVLLVLDDATNHKLLGARERSGRTKTNEVLVRLRDHLRRFPDFYNIDSIKEGAGETDS
TIKDI

  Protein domains


Predicted by InterproScan.

TraY domain (TraY)

(14-57)


  Protein structure



No available structure.




T4CP

ID   3576 GenBank   WP_105466876
Name   traC_HVZ08_RS23615_pRHB33-C04_2 insolico UniProt ID   _
Length   881 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 881 a.a.        Molecular weight: 99900.68 Da        Isoelectric Point: 6.1932

>WP_105466876.1 MULTISPECIES: type IV secretion system protein TraC [Escherichia]
MSNNPLEAVTQAVNSLVTALKLPDESAKANEVLGEMSFPQFSRLLPYRDYNQESGLFMNDTTMGFMLEAI
PINGANESIVEALDHMLRTKLPRGVPFCIHLMSSQLVGDRIEYGLREFSWSGEQAERFNAITRAYYMNAA
ATQFPLPEGMNLPLTLRHYRVFFSYCSPSKKKSRADILEMENLVKIIRASLQGASITTQAVDAQAFIDIV
GEMINHNPDSLYPKRRQLDPYSDLNYQCVEDSFDLKVRADYLTLGLRENGRNSTARILNFHLARNPEIAF
LWNMADNYSNLLNPELSISCPFILTLTLVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWG
ELRQRLGSGQSSVVSYFLNITAFCKDNNETALEVEQDILNSFRKNGFELISPRFNHMRNFLTCLPFMAGK
GLFKQLKEAGVVQRAESFNVANLMPLVADNPLTPAGLLAPTYRNQLAFIDIFFRGMNNTNYNMAVCGTSG
AGKTGLIQPLIRSVLDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLRFNPFANITDIDQSAERVRDQLS
VMASPNGNLDEVHEGLLLQAVRASWLAKKNRARIDDVVDFLKNARDNDQYVESPTIRSRLDEMIVLLDQY
TAGGTYGRYFNSDEPSLRDDAKMVVLELGGLEDRPSLLVAVMFSLIIYIENRMYRTPRNLKKLNVIDEGW
RLLDFKNHKVGEFIEKGYRTARRHTGAYITITQNIVDFDSDKASSAARAAWGNSSYKIILKQSAKEFAKY
NQLYPDQFLPLQRDMIGKFGAAKDQWFSSFLLQVENHSSWHRLFVDPLSRAMYSSDGPDFEFVQQKRKEG
LSIHEAVWQLAWKKSGPEMASLEAWLKEHEMSGERMTGNWS

  Protein domains


Predicted by InterproScan.

TraC protein (TraC_F_IV)

(39-277)

TraG P-loop domain (P-loop_TraG)

(468-772)

Family of unknown function (DUF5934) (DUF5934)

(290-447)

  Protein structure



No available structure.



ID   3577 GenBank   WP_181667511
Name   traD_HVZ08_RS23705_pRHB33-C04_2 insolico UniProt ID   _
Length   720 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 720 a.a.        Molecular weight: 81854.49 Da        Isoelectric Point: 5.1126

>WP_181667511.1 type IV conjugative transfer system coupling protein TraD [Escherichia fergusonii]
MSFSAKDMTQGGQIASMRIRMFSQIANIILYCLFIFFWILVGLVLWVKISWQTFVNGCIYWWCTTLEGMR
DLIRSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLASVVALVICLITFFVVSWILGRQGKQ
QSENEITGGRQLTDNPKEVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
QRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGEPFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVMNTRAFFRSPSHKIA
EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQTRPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFEPDVPEVVSGEDVTQAEQPQQPQQPVS
PAINDKKSDAGVNVPAGGIEQELKMKPEEEMEQQLPPGISESGEVVDMAVYEAWQREQNPDIQQKMQRRE
EVNINVHRERGEDVEPGDDF

  Protein domains


Predicted by InterproScan.

F sex factor protein N terminal (TraD_N)

(32-128)

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

(173-560)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 116579..148435

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HVZ08_RS23495 (HVZ08_23490) 112570..113004 + 435 WP_032235533 conjugation system SOS inhibitor PsiB -
HVZ08_RS23500 (HVZ08_23495) 113001..113763 + 763 Protein_114 plasmid SOS inhibition protein A -
HVZ08_RS24660 113936..114088 + 153 Protein_115 DUF5431 family protein -
HVZ08_RS23505 (HVZ08_23500) 114033..114155 + 123 WP_223170659 type I toxin-antitoxin system Hok family toxin -
HVZ08_RS24470 (HVZ08_23505) 114456..114753 - 298 Protein_117 hypothetical protein -
HVZ08_RS23510 (HVZ08_23510) 114824..115030 + 207 WP_181667506 single-stranded DNA-binding protein -
HVZ08_RS23515 (HVZ08_23515) 115055..115342 + 288 WP_021569031 hypothetical protein -
HVZ08_RS23520 (HVZ08_23520) 115461..116282 + 822 WP_042973148 DUF932 domain-containing protein -
HVZ08_RS23525 (HVZ08_23525) 116579..117181 - 603 WP_072156291 transglycosylase SLT domain-containing protein virB1
HVZ08_RS23530 (HVZ08_23530) 117505..117888 + 384 WP_040100321 conjugal transfer relaxosome DNA-binding protein TraM -
HVZ08_RS23535 (HVZ08_23535) 118083..118754 + 672 WP_040100314 conjugal transfer transcriptional regulator TraJ -
HVZ08_RS23540 (HVZ08_23540) 118892..119119 + 228 WP_072039828 conjugal transfer relaxosome protein TraY -
HVZ08_RS23545 (HVZ08_23545) 119153..119518 + 366 WP_040100313 type IV conjugative transfer system pilin TraA -
HVZ08_RS23550 (HVZ08_23550) 119533..119844 + 312 WP_000012106 type IV conjugative transfer system protein TraL traL
HVZ08_RS23555 (HVZ08_23555) 119866..120432 + 567 WP_000399792 type IV conjugative transfer system protein TraE traE
HVZ08_RS23560 (HVZ08_23560) 120419..121147 + 729 WP_202117066 type-F conjugative transfer system secretin TraK traK
HVZ08_RS23565 (HVZ08_23565) 121147..122574 + 1428 WP_000146635 F-type conjugal transfer pilus assembly protein TraB traB
HVZ08_RS23570 (HVZ08_23570) 122564..123154 + 591 WP_000002784 conjugal transfer pilus-stabilizing protein TraP -
HVZ08_RS23575 (HVZ08_23575) 123141..123461 + 321 WP_249418243 conjugal transfer protein TrbD -
HVZ08_RS23580 (HVZ08_23580) 123458..123973 + 516 WP_105466871 type IV conjugative transfer system lipoprotein TraV traV
HVZ08_RS23585 (HVZ08_23585) 124107..124328 + 222 WP_105466872 conjugal transfer protein TraR -
HVZ08_RS23590 (HVZ08_23590) 124473..125219 - 747 WP_001016257 IS21-like element ISEc12 family helper ATPase IstB -
HVZ08_RS23595 (HVZ08_23595) 125234..126775 - 1542 WP_001298859 IS21-like element ISEc12 family transposase -
HVZ08_RS23600 (HVZ08_23600) 126956..127381 + 426 WP_181667507 hypothetical protein -
HVZ08_RS24665 127461..127678 + 218 Protein_137 hypothetical protein -
HVZ08_RS23605 (HVZ08_23605) 127675..128079 + 405 WP_105466874 hypothetical protein -
HVZ08_RS23610 (HVZ08_23610) 128076..128423 + 348 WP_105466875 hypothetical protein -
HVZ08_RS23615 (HVZ08_23615) 128549..131194 + 2646 WP_105466876 type IV secretion system protein TraC virb4
HVZ08_RS23620 (HVZ08_23620) 131576..132682 - 1107 WP_181667508 hypothetical protein -
HVZ08_RS23625 (HVZ08_23625) 132766..133146 + 381 WP_040100306 type-F conjugative transfer system protein TrbI -
HVZ08_RS23630 (HVZ08_23630) 133143..133775 + 633 WP_181667509 type-F conjugative transfer system protein TraW traW
HVZ08_RS23635 (HVZ08_23635) 133772..134764 + 993 WP_040100302 conjugal transfer pilus assembly protein TraU traU
HVZ08_RS23640 (HVZ08_23640) 134773..135411 + 639 WP_000777692 type-F conjugative transfer system pilin assembly protein TrbC trbC
HVZ08_RS23645 (HVZ08_23645) 135408..137216 + 1809 WP_040100300 type-F conjugative transfer system mating-pair stabilization protein TraN traN
HVZ08_RS23650 (HVZ08_23650) 137243..137503 + 261 WP_000864348 conjugal transfer protein TrbE -
HVZ08_RS23655 (HVZ08_23655) 137496..138239 + 744 WP_181667534 type-F conjugative transfer system pilin assembly protein TraF traF
HVZ08_RS23660 (HVZ08_23660) 138400..138636 + 237 WP_000270010 type-F conjugative transfer system pilin chaperone TraQ -
HVZ08_RS23665 (HVZ08_23665) 138623..139168 + 546 WP_000059821 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
HVZ08_RS23670 (HVZ08_23670) 139158..139438 + 281 Protein_151 P-type conjugative transfer protein TrbJ -
HVZ08_RS23675 (HVZ08_23675) 139425..139805 + 381 WP_249540839 F-type conjugal transfer protein TrbF -
HVZ08_RS23680 (HVZ08_23680) 139805..141178 + 1374 WP_181667510 conjugal transfer pilus assembly protein TraH traH
HVZ08_RS23685 (HVZ08_23685) 141175..143994 + 2820 WP_151674034 conjugal transfer mating-pair stabilization protein TraG traG
HVZ08_RS23690 (HVZ08_23690) 144019..144516 + 498 WP_137546094 surface exclusion protein -
HVZ08_RS23695 (HVZ08_23695) 144548..145279 + 732 WP_000850424 conjugal transfer complement resistance protein TraT -
HVZ08_RS23700 (HVZ08_23700) 145482..146222 + 741 WP_151674032 hypothetical protein -
HVZ08_RS23705 (HVZ08_23705) 146273..148435 + 2163 WP_181667511 type IV conjugative transfer system coupling protein TraD virb4
HVZ08_RS23710 (HVZ08_23710) 148444..148842 - 399 WP_000911313 type II toxin-antitoxin system VapC family toxin -
HVZ08_RS23715 (HVZ08_23715) 148842..149069 - 228 WP_000450520 toxin-antitoxin system antitoxin VapB -

Host bacterium

ID   5718 GenBank   NZ_CP057216
Plasmid name   pRHB33-C04_2 Incompatibility group   IncFIB
Plasmid size   160081 bp Coordinate of oriT [Strand]   117147..117232 [-]
Host baterium   Escherichia fergusonii strain RHB33-C04

Cargo genes

Drug resistance gene   -
Virulence gene   pefA, pefC, pefD
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -