Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100689
Name   oriT_pAPEC-O78-2 in_silico
Organism   Escherichia coli strain 789
Sequence Completeness      intact
NCBI accession of oriT (coordinates [strand])   NZ_CP010317 (32945..33054 [+], 110 nt)
oriT length   110 nt
IRs (inverted repeats)      IR1: 24..31, 35..42  (GTCGGGGC..GCCCTGAC)
 IR2: 49..65, 72..88  (GTAATTGTAATAGCGTC..GACGGTATTACAATTAC)
Location of nic site      96..97
Conserved sequence flanking the
  nic site    		  CATCCTG|T
Note   predicted by the oriTfinder

  oriT sequence  


Download         Length: 110 nt

>oriT_pAPEC-O78-2
TCACTTCAGGCTCCTTACGGGGTGTCGGGGCGAAGCCCTGACCAGATGGTAATTGTAATAGCGTCGCGTGTGACGGTATTACAATTACACATCCTGTCCCGTTTTTCAGG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   761 GenBank   WP_001474686
Name   NikB_pAPEC-O78-2 insolico UniProt ID   E9LLX8
Length   899 a.a. PDB ID   
Note   putative relaxase

  Relaxase protein sequence


Download         Length: 899 a.a.        Molecular weight: 103834.33 Da        Isoelectric Point: 7.3473

>WP_001474686.1 MULTISPECIES: IncI1-type relaxase NikB [Enterobacteriaceae]
MNAVIPKKRRDGKSSFEDLVSYVSVRDDMTDEELNLSSSSQAEQPHRSRFSRLVDYATRLRNESFVALVD
VMKDGCEWVNFYGVTCFHNCTSLETAAADMEYIAQQAHYAKDNTDPVFHYILSWQAHESPRPEQIYDSVR
HTLKSLGLGEHQYVSAVHTDTDNLHVHVAVNRVHPVTGYLNCLSWSQEKLSRACRELELKHGFAPDNGCW
VHAPGNRIVRKTAVERDRQNAWTRGKKQTFREYVAQTAVAGLRSEPVHDWLSLHRRLAEDGLYLSQMDGK
FLVMDGWDRNREGVQLDSFGPSWCAEKLMKKMGDYTPVPKDIFSQVEAPGRYNPDFIAADVRPEKIAETE
SLQQYACRHLGERLPEMAREGRLENCQAIHRTLAEAGLWMRVQHGHLVICDGYDHNQTPVRADSVWSLLT
LDNVNQLDGGWQPVPTDIFLQVTPTERFRGRRMESCPATDKEWHRMRTGTGPQGAIKRELFSDKESLWGY
SISHCSPQIEEMITQGEFTWQRCHELFAQQGLMLQKQHHGLVVVDAFNHEQTPVKASSIHPDLTLGRAEP
QAGPFVSAPADLFDRVQPESRYNPELAVSDRYGVSSKRDPMLRRQRREARAEARADLRARYLAWREQWRK
PDLRYGERCREIHQACRLRKSHIRAQYDDPALRKLHYHIAEVQRMQALIRLKEDIRDERQKLIADGKWYP
PSYRQWVEIQAAQGDRAAVSQLRGWDYRDRRKDKSRTTTTDRCVVLCEPGGTPVYGNTGDLEARLQKNGS
VRFRDRRTGEFVCTDYGDRVVFRNHHDRNALADKLDLIAPVLFGRDPRMGFEPEGNDKQFNQVFAEMVAW
HNVTGRTGHEDYRITRPDVDHHREGSERYYRDYIAANSNDDASLPPPEQDKRWEPPSPG

  Protein domains


Predicted by InterproScan.

Relaxase/Mobilisation nuclease domain (Relaxase)

(62-314)


  Protein structure


Source ID Structure
AlphaFold DB E9LLX8


T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 1485..27585

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
AC789_RS25585 1..126 + 126 WP_005119525 IS1 family transposase -
AC789_RS25590 (AC789_106pl00010) 144..635 + 492 Protein_1 lipopolysaccharide core heptose(II)-phosphate phosphatase -
AC789_RS25595 (AC789_106pl00020) 1030..1488 + 459 WP_001079808 IncI1-type conjugal transfer lipoprotein TraH -
AC789_RS25600 (AC789_106pl00030) 1485..2303 + 819 WP_000646097 IncI1-type conjugal transfer lipoprotein TraI traI
AC789_RS25605 (AC789_106pl00040) 2300..3448 + 1149 WP_001024972 plasmid transfer ATPase TraJ virB11
AC789_RS28385 3445..3735 + 291 WP_001299214 hypothetical protein traK
AC789_RS25610 3750..4301 + 552 WP_000014584 phospholipase D family protein -
AC789_RS25615 (AC789_106pl00060) 4391..8158 + 3768 WP_001141534 LPD7 domain-containing protein -
AC789_RS25620 (AC789_106pl00070) 8176..8523 + 348 WP_001055900 conjugal transfer protein traL
AC789_RS25625 (AC789_106pl00080) 8520..9212 + 693 WP_000138552 DotI/IcmL family type IV secretion protein traM
AC789_RS25630 (AC789_106pl00090) 9223..10206 + 984 WP_001191878 IncI1-type conjugal transfer protein TraN traN
AC789_RS25635 (AC789_106pl00100) 10209..11498 + 1290 WP_001271997 conjugal transfer protein TraO traO
AC789_RS25640 (AC789_106pl00110) 11498..12202 + 705 WP_000801920 IncI1-type conjugal transfer protein TraP traP
AC789_RS25645 (AC789_106pl00120) 12202..12729 + 528 WP_001055569 conjugal transfer protein TraQ traQ
AC789_RS25650 (AC789_106pl00130) 12780..13184 + 405 WP_000086960 IncI1-type conjugal transfer protein TraR traR
AC789_RS25655 (AC789_106pl00140) 13248..13436 + 189 WP_001277255 putative conjugal transfer protein TraS -
AC789_RS25660 (AC789_106pl00150) 13420..14220 + 801 WP_001164788 IncI1-type conjugal transfer protein TraT traT
AC789_RS25665 (AC789_106pl00160) 14310..17354 + 3045 WP_044502553 IncI1-type conjugal transfer protein TraU traU
AC789_RS25670 (AC789_106pl00170) 17354..17968 + 615 WP_000337400 IncI1-type conjugal transfer protein TraV traV
AC789_RS25675 (AC789_106pl00180) 17935..19137 + 1203 WP_001189156 IncI1-type conjugal transfer protein TraW traW
AC789_RS25680 (AC789_106pl00190) 19166..19750 + 585 WP_001037985 IncI1-type conjugal transfer protein TraX -
AC789_RS25685 (AC789_106pl00200) 19847..22015 + 2169 WP_000698368 DotA/TraY family protein traY
AC789_RS25690 (AC789_106pl00210) 22086..22748 + 663 WP_000644794 plasmid IncI1-type surface exclusion protein ExcA -
AC789_RS25695 22820..23029 - 210 WP_000062603 HEAT repeat domain-containing protein -
AC789_RS30110 23421..23597 + 177 WP_001054900 hypothetical protein -
AC789_RS25710 24521..24772 + 252 WP_001291965 hypothetical protein -
AC789_RS25715 24844..24996 - 153 WP_001303307 Hok/Gef family protein -
AC789_RS25720 (AC789_106pl00280) 25288..26496 + 1209 WP_000121273 IncI1-type conjugal transfer protein TrbA trbA
AC789_RS25725 (AC789_106pl00290) 26515..27585 + 1071 WP_000151576 IncI1-type conjugal transfer protein TrbB trbB
AC789_RS25730 (AC789_106pl00300) 27578..29869 + 2292 WP_001289269 F-type conjugative transfer protein TrbC -

Host bacterium

ID   1149 GenBank   NZ_CP010317
Plasmid name   pAPEC-O78-2 Incompatibility group   IncI1
Plasmid size   106397 bp Coordinate of oriT [Strand]   32945..33054 [+]
Host baterium   Escherichia coli strain 789

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   arsH, arsA, arsC, arsB, arsD, arsR
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -