Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   108362
Name   oriT_pCF5125-4 in_silico
Organism   Citrobacter freundii strain CF5125
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP125314 (2313..2436 [-], 124 nt)
oriT length   124 nt
IRs (inverted repeats)      101..106, 119..124  (TTTAAT..ATTAAA)
 91..99, 113..121  (AATAATGTA..TACATTATT)
 90..95, 107..112  (AAATAA..TTATTT)
 39..46, 49..56  (GCAAAAAC..GTTTTTGC)
 3..10, 15..22  (TTGGTGGT..ACCACCAA)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 124 nt

>oriT_pCF5125-4
GGTTGGTGGTTCTCACCACCAAAAGCACCACACCCCACGCAAAAACAAGTTTTTGCTGATTTGCTTTTTGAATCATTAGCTTATGTTTTAAATAATGTATTTTAATTTATTTTACATTATTAAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Auxiliary protein

ID   2684 GenBank   WP_001254386
Name   WP_001254386_pCF5125-4 insolico UniProt ID   A0A3Z6KJB5
Length   75 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 75 a.a.        Molecular weight: 9005.11 Da        Isoelectric Point: 10.1422

>WP_001254386.1 MULTISPECIES: conjugal transfer relaxosome protein TraY [Gammaproteobacteria]
MRRRNARGGISRTVSVYLDEDTNNRLIKAKDRSGRSKTIEVQIRLRDHLKRFPDFYNEEIFREVTEESES
TFKEL

  Protein domains


Predicted by InterproScan.

TraY domain (TraY)

(14-61)


  Protein structure


Source ID Structure
AlphaFold DB A0A3Z6KJB5

ID   2685 GenBank   WP_000124981
Name   WP_000124981_pCF5125-4 insolico UniProt ID   A0A630FTW9
Length   127 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 127 a.a.        Molecular weight: 14542.59 Da        Isoelectric Point: 5.0278

>WP_000124981.1 MULTISPECIES: conjugal transfer relaxosome DNA-binding protein TraM [Gammaproteobacteria]
MARVNLYISNEVHEKINMIVEKRRQEGARDKDISLSGTASMLLELGLRVYDAQMERKESAFNQTEFNKLL
LECVVKTQSTVAKILGIESLSPHVSGNPKFEYASMVDDIREKVSVEMDRFFPKNDDE

  Protein domains


Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-126)


  Protein structure


Source ID Structure
AlphaFold DB A0A630FTW9


T4CP

ID   5973 GenBank   WP_032316743
Name   traD_QKW62_RS28015_pCF5125-4 insolico UniProt ID   _
Length   744 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 744 a.a.        Molecular weight: 84613.33 Da        Isoelectric Point: 5.0504

>WP_032316743.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILVGLVLWVKISWQTFVNGCIYWWCTTLEGMR
DLIKSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLATVVALVICLITFFVVSWILGRQGKQ
QSENEVTGGRQLTDNPKDVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
QRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGESFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVMNTRAFFRSPSHKIA
EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQARPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFEPDVPEVVSGEDVTQAEQPQQPQQPQQ
PQQPQQPQQPQQPQQPQQPQQPVSPAINDKKSDSGVNVPAGGIEQELKMKPEEEMEQQLPPGISESGEVV
DMAAYEAWQQENHPDIQQQMQRREEVNINVHRERGEDVEPGDDF

  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   5974 GenBank   WP_015059012
Name   traC_QKW62_RS28120_pCF5125-4 insolico UniProt ID   _
Length   875 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 875 a.a.        Molecular weight: 99393.22 Da        Isoelectric Point: 6.3465

>WP_015059012.1 MULTISPECIES: type IV secretion system protein TraC [Gammaproteobacteria]
MNNPLEAVTQAVNSLVTALKLPDESAKANEVLGEMSFPQFSRLLPYRDYNQESGLFMNDTTMGFMLEAIP
INGANESIVEALDHMLRTKLPRGVPFCIHLMSSQLVGDRIEYGLREFSWSGEQAERFNAITRAYYMNAAA
TQFPLPEGMNLPLTLRHYRVFFSYCSPSKKKSRADILEMENLVKIIRASLQGASITTQAVDAQAFIDIVG
EMINHNPDSLYPKRRQLDPYSDLNYQCVEDSFDLKVRADYLTLGLRENGRNSTARILNFHLARNPEIAFL
WNMADNYSNLLNPEMSISCPFILTLTLVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWGE
LRQRLGSGQSSVVSYFLNITAFCKDNNETALEVEQDILNSFRKNGFELISPRFNHMRNFLTCLPFMAGKG
LFKQLKEAGVVQRAESFNVANLMPLVADNPLTPAGLLAPTYRNQLAFIDIFFKGMNNTNYNMAVCGTSGA
GKTGLIQPLIRSVLDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLRFNPFANITDIDQSAERVRDQLSV
MASPNGNLDEVHEGLLLQAVRASWLAKKKQARIDDVVDFLKNARDNDQYVESPTIRSRLDEMIVLLDQYT
ANGTYGRYFNSDEPSLRDDARMVVLELGGLEDRPSLLVAVMFSLIIYIENRMYRTPRNLKKLNVIDEGWR
LLDFKNRKVGEFIQKGYRTCRRHTGAYITITQNIVDFDSDKASSAARAAWGNSSYKIILKQSAKEFAKYN
QLYPDQFLPLQRDMIGKFGAAKDQWFSSFLLQVENHSSWHRLFVDPLSRAMYSSDGPDFEFVQQKRKEGL
SIHEAVWQLAWKKSGPEMASLEAWLEEHEKYRSVA

  Protein domains


Predicted by InterproScan.

Family of unknown function (DUF5934) (DUF5934)

(290-446)

TraG P-loop domain (P-loop_TraG)

(467-771)

TraC protein (TraC_F_IV)

(38-276)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 46562..71507

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
QKW62_RS28015 (QKW62_28010) 46562..48796 - 2235 WP_032316743 type IV conjugative transfer system coupling protein TraD virb4
QKW62_RS28020 (QKW62_28015) 48847..49584 - 738 WP_015059020 hypothetical protein -
QKW62_RS28025 (QKW62_28020) 49787..50518 - 732 WP_021559024 conjugal transfer complement resistance protein TraT -
QKW62_RS28030 (QKW62_28025) 50543..51064 - 522 WP_000632668 conjugal transfer entry exclusion protein TraS -
QKW62_RS28035 (QKW62_28030) 51097..53913 - 2817 WP_015059018 conjugal transfer mating-pair stabilization protein TraG traG
QKW62_RS28040 (QKW62_28035) 53910..55283 - 1374 WP_000944325 conjugal transfer pilus assembly protein TraH traH
QKW62_RS28045 (QKW62_28040) 55270..55662 - 393 WP_000126338 F-type conjugal transfer protein TrbF -
QKW62_RS28050 (QKW62_28045) 55616..55930 - 315 WP_001384255 P-type conjugative transfer protein TrbJ -
QKW62_RS28055 (QKW62_28050) 55920..56465 - 546 WP_000059817 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
QKW62_RS28060 (QKW62_28055) 56452..56688 - 237 WP_000270010 type-F conjugative transfer system pilin chaperone TraQ -
QKW62_RS28065 (QKW62_28060) 56849..57592 - 744 WP_015059017 type-F conjugative transfer system pilin assembly protein TraF traF
QKW62_RS28070 (QKW62_28065) 57585..57842 - 258 WP_053913405 conjugal transfer protein TrbE -
QKW62_RS28075 (QKW62_28070) 57869..59719 - 1851 WP_015059015 type-F conjugative transfer system mating-pair stabilization protein TraN traN
QKW62_RS28080 (QKW62_28075) 59716..60138 - 423 WP_001229309 HNH endonuclease signature motif containing protein -
QKW62_RS28085 (QKW62_28080) 60164..60535 - 372 WP_000056336 hypothetical protein -
QKW62_RS28090 (QKW62_28085) 60532..61170 - 639 WP_000087532 type-F conjugative transfer system pilin assembly protein TrbC trbC
QKW62_RS28095 (QKW62_28090) 61197..61718 - 522 WP_015059014 hypothetical protein -
QKW62_RS28100 (QKW62_28095) 61781..62089 - 309 WP_000412447 hypothetical protein -
QKW62_RS28105 (QKW62_28100) 62116..63108 - 993 WP_000830838 conjugal transfer pilus assembly protein TraU traU
QKW62_RS28110 (QKW62_28105) 63105..63737 - 633 WP_001203735 type-F conjugative transfer system protein TraW traW
QKW62_RS28115 (QKW62_28110) 63734..64120 - 387 WP_015059013 type-F conjugative transfer system protein TrbI -
QKW62_RS28120 (QKW62_28115) 64117..66744 - 2628 WP_015059012 type IV secretion system protein TraC virb4
QKW62_RS28125 (QKW62_28120) 66904..67125 - 222 WP_001278692 conjugal transfer protein TraR -
QKW62_RS28130 (QKW62_28125) 67260..67775 - 516 WP_000809902 type IV conjugative transfer system lipoprotein TraV traV
QKW62_RS28135 (QKW62_28130) 67772..68023 - 252 WP_001038341 conjugal transfer protein TrbG -
QKW62_RS28140 (QKW62_28135) 68035..68232 - 198 WP_001324648 conjugal transfer protein TrbD -
QKW62_RS28145 (QKW62_28140) 68219..68809 - 591 WP_000002778 conjugal transfer pilus-stabilizing protein TraP -
QKW62_RS28150 (QKW62_28145) 68799..70226 - 1428 WP_032297072 F-type conjugal transfer pilus assembly protein TraB traB
QKW62_RS28155 (QKW62_28150) 70226..70954 - 729 WP_001230787 type-F conjugative transfer system secretin TraK traK
QKW62_RS28160 (QKW62_28155) 70941..71507 - 567 WP_000399794 type IV conjugative transfer system protein TraE traE

Host bacterium

ID   8797 GenBank   NZ_CP125314
Plasmid name   pCF5125-4 Incompatibility group   IncFII
Plasmid size   71751 bp Coordinate of oriT [Strand]   2313..2436 [-]
Host baterium   Citrobacter freundii strain CF5125

Cargo genes

Drug resistance gene   rmtB, blaTEM-1B, fosA3
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -