Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   114437
Name   oriT_AR_0157|unnamed6 in_silico
Organism   Citrobacter sp. CRE-46 strain AR_0157
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP029734 (4916..5001 [+], 86 nt)
oriT length   86 nt
IRs (inverted repeats)      61..68, 73..80  (TTGGTGGT..ACCACCAA)
 27..34, 37..44  (GCAAAAAC..GTTTTTGC)
 8..14, 20..26  (TGATTTA..TAAATCA)
Location of nic site      53..54
Conserved sequence flanking the
  nic site    		  TGTGTGGTGC
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 86 nt

>oriT_AR_0157|unnamed6
AATTACATGATTTAAAACGTAAATCAGCAAAAACTTGTTTTTGCGTAGTGTGTGGTGCTTTTGGTGGTGAGAACCACCAACCTGTT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Auxiliary protein

ID   5418 GenBank   WP_000089263
Name   WP_000089263_AR_0157|unnamed6 insolico UniProt ID   A0A3U3XJL9
Length   75 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 75 a.a.        Molecular weight: 8541.74 Da        Isoelectric Point: 8.6796

>WP_000089263.1 MULTISPECIES: conjugal transfer relaxosome protein TraY [Gammaproteobacteria]
MSRNIIRPAPGNKVLLVLDDATNHKLLGARERSGRTKTNEVLVRLRDHLNRFPDFYNLDAIKEGAEETDS
IIKDL

  Protein domains


Predicted by InterproScan.

TraY domain (TraY)

(14-60)


  Protein structure


Source ID Structure
AlphaFold DB A0A3U3XJL9

ID   5419 GenBank   WP_001354030
Name   WP_001354030_AR_0157|unnamed6 insolico UniProt ID   A0A734M5H3
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: 4.7116

>WP_001354030.1 MULTISPECIES: conjugal transfer relaxosome DNA-binding protein TraM [Gammaproteobacteria]
MARVILYISNDVYDKVNAIVEQRRQEGARDKDISVSGTASMLLELGLRVYEAQMERKESAFNQTEFNKLL
LECVVKTQSSVAKILGIESLSPHVSGNPKFEYANMVEDIREKVSSEMERFFPKNDEE

  Protein domains


Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-126)


  Protein structure


Source ID Structure
AlphaFold DB A0A734M5H3


T4CP

ID   10727 GenBank   WP_046072940
Name   traD_AN232_RS30805_AR_0157|unnamed6 insolico UniProt ID   _
Length   753 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 753 a.a.        Molecular weight: 85667.46 Da        Isoelectric Point: 5.1644

>WP_046072940.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILIGLVLWVKISWQTFINGCIYWWCTSLEGMR
DLIKSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLASVVALVICLITFFVVSWILGRQGKQ
QSENEVTGGRQLTDNPKDVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
QRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGDPFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVMNTRAFFRSPSHKIA
EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQARPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFEPEVASGEDVTQAEQPQQPQQPQQPQQ
PQQPQQPQQPQQPQQPQQPQQPQQPQQPQQPVSSVINDKKSDAGVSVPAGGIEQELKMKPEEEMEQQLPP
GISESGEVVDMAAYEAWQQENHPDIQQHMQRREEVNINVHRERGEDVEPGDDF

  Protein domains


Predicted by InterproScan.

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

(173-560)

F sex factor protein N terminal (TraD_N)

(32-128)

  Protein structure



No available structure.



ID   10728 GenBank   WP_000069777
Name   traC_AN232_RS30900_AR_0157|unnamed6 insolico UniProt ID   _
Length   876 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 876 a.a.        Molecular weight: 99195.86 Da        Isoelectric Point: 6.1126

>WP_000069777.1 MULTISPECIES: type IV secretion system protein TraC [Enterobacteriaceae]
MSNNPLEAVTQAVNSLVTALKLPDESAKANEVLGEMSFPQFSRLLPYRDYNQESGLFMNDTTMGFMLEAI
PINGANKSIVEALDHMLRTKLPRGIPLCIHLMSSQLVGDRIEYGLREFSWSGEQAERFNAITRAYYMKAA
ATQFPLPEGMNLPLTLRHYRVFISYCSPSKKKSRADILEMENLVKIIRASLQGASIATQTVDAQAFIDIV
GEMINHNPDSLYPKRRQLDPYSDLNYQCVEDSFDLNVRADYLTLGLRENGRNSTARILNFHLARNPEIAF
LWNMADNYSNLLNPELSISCPFILTLTLVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWG
ELRQRLGSGQSSVVSYFLNITAFCKDNNETALEVEQDILNSFRKNGFELISPRFNHMRNFLTCLPFMAGK
GLFKQLKEAGVVQRAESFNVANLMPLVADNPLTPAGLLAPTYRNQLAFIDIFFRGMNNTNYNMAVCGTSG
AGKTGLIQPLIRSVLDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLRFNPFANITDIDQSAERVRDQLS
VMASPNGNLDEVHEGLLLQAVRASWLAKENRARIDDVVDFLKNASDSEQYAGSPTIRSRLDEMIVLLDQY
TANGTYGQYFNSDEPSLRDDAKMVVLELGGLEDRPSLLVAVMFSLIIYIENRMYRTPRNLKKLNVIDEGW
RLLDFKNRKVGEFIEKGYRTARRHTGAYITITQNIVDFDSDKASSAARAAWGNSSYKIILKQSAKEFAKY
NQLYPDQFQPLQRDMIGKFGAAKDQWFSSFLLQVENHSSWHRLFVDPLSRAMYSSDGPDFEFVQQKRKEG
LSIHEAVWQLAWKKSGPEMASLEAWLEEHEKYRSVA

  Protein domains


Predicted by InterproScan.

Family of unknown function (DUF5934) (DUF5934)

(290-447)

TraG P-loop domain (P-loop_TraG)

(468-764)

TraC protein (TraC_F_IV)

(39-277)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 54379..75653

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
AN232_RS30805 (AN232_30805) 54379..56640 - 2262 WP_046072940 type IV conjugative transfer system coupling protein TraD virb4
AN232_RS30810 (AN232_30810) 56691..57428 - 738 WP_000199905 hypothetical protein -
AN232_RS30815 (AN232_30815) 57631..58362 - 732 WP_000782451 conjugal transfer complement resistance protein TraT -
AN232_RS30820 (AN232_30820) 58411..58896 - 486 WP_000605870 hypothetical protein -
AN232_RS30825 (AN232_30825) 58912..61734 - 2823 WP_001007039 conjugal transfer mating-pair stabilization protein TraG traG
AN232_RS30830 (AN232_30830) 61731..63104 - 1374 WP_000944331 conjugal transfer pilus assembly protein TraH traH
AN232_RS30835 (AN232_30835) 63091..63483 - 393 WP_000660699 F-type conjugal transfer protein TrbF -
AN232_RS30840 (AN232_30840) 63464..63811 - 348 WP_001309242 P-type conjugative transfer protein TrbJ -
AN232_RS30845 (AN232_30845) 63741..64286 - 546 WP_000059831 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
AN232_RS30850 (AN232_30850) 64273..64557 - 285 WP_000624194 type-F conjugative transfer system pilin chaperone TraQ -
AN232_RS30855 (AN232_30855) 64676..65020 - 345 WP_000556796 conjugal transfer protein TrbA -
AN232_RS30860 (AN232_30860) 65034..65777 - 744 WP_001030371 type-F conjugative transfer system pilin assembly protein TraF traF
AN232_RS30865 (AN232_30865) 65770..66027 - 258 WP_000864353 conjugal transfer protein TrbE -
AN232_RS30870 (AN232_30870) 66054..67904 - 1851 WP_000821856 type-F conjugative transfer system mating-pair stabilization protein TraN traN
AN232_RS30875 (AN232_30875) 67901..68539 - 639 WP_001080256 type-F conjugative transfer system pilin assembly protein TrbC trbC
AN232_RS30880 (AN232_30880) 68548..68853 - 306 WP_000224416 hypothetical protein -
AN232_RS30885 (AN232_30885) 68883..69875 - 993 WP_000830838 conjugal transfer pilus assembly protein TraU traU
AN232_RS30890 (AN232_30890) 69872..70504 - 633 WP_001203728 type-F conjugative transfer system protein TraW traW
AN232_RS30895 (AN232_30895) 70501..70887 - 387 WP_000214084 type-F conjugative transfer system protein TrbI -
AN232_RS30900 (AN232_30900) 70884..73514 - 2631 WP_000069777 type IV secretion system protein TraC virb4
AN232_RS30905 (AN232_30905) 73640..73987 - 348 WP_000836682 hypothetical protein -
AN232_RS30910 (AN232_30910) 74015..74233 - 219 WP_000556745 hypothetical protein -
AN232_RS30915 (AN232_30915) 74313..74789 - 477 WP_000549587 hypothetical protein -
AN232_RS30920 (AN232_30920) 74782..75003 - 222 WP_001278683 conjugal transfer protein TraR -
AN232_RS30925 (AN232_30925) 75138..75653 - 516 WP_000809881 type IV conjugative transfer system lipoprotein TraV traV
AN232_RS30930 (AN232_30930) 75650..75970 - 321 WP_001057307 conjugal transfer protein TrbD -
AN232_RS30935 (AN232_30935) 75957..76523 - 567 WP_000896599 conjugal transfer pilus-stabilizing protein TraP -

Host bacterium

ID   14872 GenBank   NZ_CP029734
Plasmid name   AR_0157|unnamed6 Incompatibility group   IncFII
Plasmid size   76953 bp Coordinate of oriT [Strand]   4916..5001 [+]
Host baterium   Citrobacter sp. CRE-46 strain AR_0157

Cargo genes

Drug resistance gene   blaTEM-1B, mph(A), erm(B)
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -