Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   101498
Name   oriT_p4219 in_silico
Organism   Escherichia coli strain GN04219
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_JALJQL010000002 (116207..116330 [+], 124 nt)
oriT length   124 nt
IRs (inverted repeats)      92..99, 113..120  (ATAATGTA..TACATTAT)
 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_p4219
GGTTGGTGGTTCTCACCACCAAAAGCACCACACACTACGCAAAAACAAGTTTTTGCTGATTTGCTATTTGAATCATTAACTTATGTTTTAAATAATGTATTTTAATTTATTTTACATTATAAAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Auxiliary protein

ID   474 GenBank   WP_001151562
Name   WP_001151562_p4219 insolico UniProt ID   A0A7I0KNG1
Length   127 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 127 a.a.        Molecular weight: 14420.36 Da        Isoelectric Point: 4.8624

>WP_001151562.1 MULTISPECIES: conjugal transfer relaxosome DNA-binding protein TraM [Enterobacteriaceae]
MAKVQAYVSDEIVYKINKIVERRRAEGAKSTDVSFSSISTMLLELGLRVHEAQMERKESAFNQAEFNKVL
LECAVKTQSTVAKILGIESLSPHVSGNPKFEYANMVEDIRDKVSSEMERFFPENDEE

  Protein domains


Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-126)


  Protein structure


Source ID Structure
AlphaFold DB A0A7I0KNG1

ID   475 GenBank   WP_001254388
Name   WP_001254388_p4219 insolico UniProt ID   W9A0Z2
Length   75 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 75 a.a.        Molecular weight: 9072.20 Da        Isoelectric Point: 10.2071

>WP_001254388.1 MULTISPECIES: conjugal transfer relaxosome protein TraY [Enterobacterales]
MRRRNARGGISRTVSVYLDEDTNNRLIRAKDRSGRSKTIEVQIRLRDHLKRFPDFYNEEIFREVIEENES
TFKEL

  Protein domains


Predicted by InterproScan.

TraY domain (TraY)

(14-61)


  Protein structure


Source ID Structure
AlphaFold DB W9A0Z2


T4CP

ID   960 GenBank   WP_021526623
Name   traD_MWG55_RS16380_p4219 insolico UniProt ID   _
Length   750 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 750 a.a.        Molecular weight: 85328.11 Da        Isoelectric Point: 5.1644

>WP_021526623.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILVGLILWVKISWQTFVNGCIYWWCTTLEGMR
DLIKSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLATVVALVICLITFFVVSWILGRQGKQ
QSENEVTGGRQLTDNPKDVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
QRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGDPFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVMNTRAFFRSPSHKIA
EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQARPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFEPEVASGEDVTQAEQPQQPQQPQQPQQ
PQQPQQPQQPQQPQQPQQPQQPQQPQQPVSSVINDKKSDAGVSVPAGGIEQELKMKPEEEMEQQLPPGIS
ESGEVVDMAAYEAWQQENHPDIQQHMQRREEVNINVHRERGEDVEPGDDF

  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.



ID   961 GenBank   WP_000069778
Name   traC_MWG55_RS17130_p4219 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: 99300.06 Da        Isoelectric Point: 6.3461

>WP_000069778.1 MULTISPECIES: type IV secretion system protein TraC [Enterobacteriaceae]
MSNNPLEAVTQAVNSLVTALKLPDESAKANEVLGEMSFPQFSRLLPYRDYNQESGLFMNDTTMGFMLEAI
PINGANKSIVEALDHMLRTKLPRGIPLCIHLMSSQLVGDRIEYGLREFSWSGEQAERFNAITRAYYMKAA
ATQFPLPEGMNLPLTLRHYRVFISYCSPSKKKSRADILEMENLVKIIRASLQGASIATQTVDAQAFIDIV
GEMINHNPDSLYPKRRQLDPYSDLNYQCVEDSFDLNVRADYLTLGLRENGRNSTARILNFHLARNPEIAF
LWNMADNYSNLLNPELSISCPFILTLTLVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWG
ELRQRLGSGQSSVVSYFLNITAFCKDNNETALEVEQDILNSFRKNGFELISPRFNHMRNFLTCLPFMAGK
GLFKQLKEAGVVQRAESFNVANLMPLVADNPLTPAGLLAPTYRNQLAFIDIFFRGMNNTNYNMAVCGTSG
AGKTGLIQPLIRSVLDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLRFNPFANITDIDQSAERVRDQLS
VMASPNGNLDEVHEGLLLQAVRASWLAKENRARIDDVVDFLKNASDSEQYAGSPTIRSRLDEMIVLLDQY
TANGTYGRYFNSDEPSLRDDARMVVLELGGLEDRPSLLVAVMFSLIIYIENRMYRTPRTLKKLNVIDEGW
RLLDFKNRKVGEFIQKGYRTCRRHTGAYITITQNIVDFDSDKASSAARAAWGNSSYKIILKQSAKEFAKY
NQLFPDQFQPLQRDMIGKFGAAKDQWFSSFLLQVENHSSWHRLFVDPLSRAMYSSDGPDFEFVQQKRREG
MSIHEAVWQLAWKKSGPEMASLEAWLEEHEKYRSVA

  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.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 115635..138885

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
MWG55_RS17015 (MWG55_17005) 111612..112046 + 435 WP_000845910 conjugation system SOS inhibitor PsiB -
MWG55_RS17020 (MWG55_17010) 112043..112806 + 764 Protein_134 plasmid SOS inhibition protein A -
MWG55_RS17025 (MWG55_17015) 112980..113129 + 150 Protein_135 DUF5431 family protein -
MWG55_RS17030 (MWG55_17020) 113071..113196 + 126 WP_096937776 type I toxin-antitoxin system Hok family toxin -
MWG55_RS17035 (MWG55_17025) 113514..113811 - 298 Protein_137 hypothetical protein -
MWG55_RS17040 (MWG55_17030) 114112..114399 + 288 WP_000107526 hypothetical protein -
MWG55_RS17045 (MWG55_17035) 114518..115339 + 822 WP_001234489 DUF932 domain-containing protein -
MWG55_RS17050 (MWG55_17040) 115635..116237 - 603 WP_001323326 transglycosylase SLT domain-containing protein virB1
MWG55_RS17055 (MWG55_17045) 116568..116951 + 384 WP_001151562 conjugal transfer relaxosome DNA-binding protein TraM -
MWG55_RS17060 (MWG55_17050) 117145..117831 + 687 WP_000332487 PAS domain-containing protein -
MWG55_RS17065 (MWG55_17055) 117925..118152 + 228 WP_001254388 conjugal transfer relaxosome protein TraY -
MWG55_RS17070 (MWG55_17060) 118186..118545 + 360 WP_001098988 type IV conjugative transfer system pilin TraA -
MWG55_RS17075 (MWG55_17065) 118560..118871 + 312 WP_000012100 type IV conjugative transfer system protein TraL traL
MWG55_RS17080 (MWG55_17070) 118893..119459 + 567 WP_000399776 type IV conjugative transfer system protein TraE traE
MWG55_RS17085 (MWG55_17075) 119446..120174 + 729 WP_001230787 type-F conjugative transfer system secretin TraK traK
MWG55_RS17090 (MWG55_17080) 120174..121601 + 1428 WP_000146665 F-type conjugal transfer pilus assembly protein TraB traB
MWG55_RS17095 (MWG55_17085) 121591..122181 + 591 WP_000002787 conjugal transfer pilus-stabilizing protein TraP -
MWG55_RS17100 (MWG55_17090) 122168..122488 + 321 WP_001057275 conjugal transfer protein TrbD virb4
MWG55_RS17105 (MWG55_17095) 122481..122733 + 253 Protein_151 conjugal transfer protein TrbG -
MWG55_RS17110 (MWG55_17100) 122730..123245 + 516 WP_000809888 type IV conjugative transfer system lipoprotein TraV traV
MWG55_RS17115 (MWG55_17105) 123380..123601 + 222 WP_001278694 conjugal transfer protein TraR -
MWG55_RS17120 (MWG55_17110) 123594..124067 + 474 WP_000549566 hypothetical protein -
MWG55_RS17125 (MWG55_17115) 124147..124365 + 219 WP_000556746 hypothetical protein -
MWG55_RS26810 124393..124606 + 214 Protein_156 hypothetical protein -
MWG55_RS17130 (MWG55_17120) 124732..127362 + 2631 WP_000069778 type IV secretion system protein TraC virb4
MWG55_RS17135 (MWG55_17125) 127359..127745 + 387 WP_000214082 type-F conjugative transfer system protein TrbI -
MWG55_RS17140 (MWG55_17130) 127742..128374 + 633 WP_001203736 type-F conjugative transfer system protein TraW traW
MWG55_RS17145 (MWG55_17135) 128371..129363 + 993 WP_000830838 conjugal transfer pilus assembly protein TraU traU
MWG55_RS17150 (MWG55_17140) 129393..129698 + 306 WP_000224418 hypothetical protein -
MWG55_RS17155 (MWG55_17145) 129707..130345 + 639 WP_001080251 type-F conjugative transfer system pilin assembly protein TrbC trbC
MWG55_RS17160 (MWG55_17150) 130342..132192 + 1851 WP_000821859 type-F conjugative transfer system mating-pair stabilization protein TraN traN
MWG55_RS17165 (MWG55_17155) 132219..132476 + 258 WP_000864314 conjugal transfer protein TrbE -
MWG55_RS17170 (MWG55_17160) 132469..133212 + 744 WP_001030385 type-F conjugative transfer system pilin assembly protein TraF traF
MWG55_RS17175 (MWG55_17165) 133226..133567 + 342 WP_001298557 conjugal transfer protein TrbA -
MWG55_RS17180 (MWG55_17170) 133548..133883 - 336 WP_000736414 hypothetical protein -
MWG55_RS17185 (MWG55_17175) 133964..134248 + 285 WP_000624107 type-F conjugative transfer system pilin chaperone TraQ -
MWG55_RS17190 (MWG55_17180) 134235..134780 + 546 WP_000059830 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
MWG55_RS17195 (MWG55_17185) 134710..135057 + 348 WP_001309242 P-type conjugative transfer protein TrbJ -
MWG55_RS17200 (MWG55_17190) 135038..135430 + 393 WP_000660700 F-type conjugal transfer protein TrbF -
MWG55_RS17205 (MWG55_17195) 135417..136790 + 1374 WP_000944331 conjugal transfer pilus assembly protein TraH traH
MWG55_RS17210 (MWG55_17200) 136787..138885 + 2099 WP_268651453 conjugal transfer mating-pair stabilization protein TraG traG

Host bacterium

ID   1942 GenBank   NZ_JALJQL010000002
Plasmid name   p4219 Incompatibility group   IncFII
Plasmid size   138885 bp Coordinate of oriT [Strand]   116207..116330 [+]
Host baterium   Escherichia coli strain GN04219

Cargo genes

Drug resistance gene   tet(B), blaTEM-1B, aph(6)-Id, aph(3'')-Ib, sul2
Virulence gene   senB
Metal resistance gene   merR, merT, merP, merA, merD, merE
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -