Detailed information of oriT

oriT


The information of the oriT region


oriTDB ID   101001
Name   oriT_p838B-R experimental
Organism   Escherichia coli strain 838B
Sequence Completeness      intact
NCBI accession of oriT (coordinates [strand])   MH618673 (30133..30205 [-], 73 nt)
oriT length   73 nt
IRs (inverted repeats)      IR1: 1..8, 12..19  (GTCGGGGC..GCCCTGAC)
  IR2: 26..43, 46..63  (GGGAATGTCTGAGTGCGC..GCGCGGTCCGACATTCCC)
Location of nic site      71..72
Conserved sequence flanking the
  nic site  
 
 ATCCTG|T
Note   

  oriT sequence  


Download         Length: 73 nt

>oriT_p838B-R
GTCGGGGCAAAGCCCTGACCAGGTGGGGAATGTCTGAGTGCGCGTGCGCGGTCCGACATTCCCACATCCTGTC

Visualization of oriT structure (The oriT was characterized experimentally)

  oriT secondary structure

Predicted by RNAfold.

Download structure file

  Reference


[1] Robert A Moran et al. (2019) pBuzz: A cryptic rolling-circle plasmid from a commensal Escherichia coli has two inversely oriented oriTs and is mobilised by a B/O plasmid. Plasmid. 101:10-19. [PMID:30468749]


Relaxosome


This oriT is a component of a relaxosome.

Relaxosome name   Relaxosomep838B-R in_silico
oriT   oriT_p838B-R experimental
Relaxase   NikB_p838B-R experimental (_)
Auxiliary protein   NikA_p838B-R experimental

  Reference


[1] Robert A Moran et al. (2019) pBuzz: A cryptic rolling-circle plasmid from a commensal Escherichia coli has two inversely oriented oriTs and is mobilised by a B/O plasmid. Plasmid. 101:10-19. [PMID:30468749]


Relaxase


ID   1072 GenBank   AXQ86977
Name   NikB_p838B-R experimental UniProt ID   _
Length   903 a.a. PDB ID   
Note   

  Relaxase protein sequence


Download         Length: 903 a.a.        Molecular weight: 104567.95 Da        Isoelectric Point: 7.5259

>AXQ86977.1 NikB (plasmid) [Escherichia coli]
MNAIIPHKRRDGRSSFEDLIAYTSVRDDVQENELTEDSEIKSDVPHRNRFRRLVDYATRLRNEKFVSLID
VMKDGSQWVNFYGVTCFHNCNSLETAAEEMQYKADKAVFSRNDTDPVFHYILSWPAHESPRPEQLFDCVR
HTLKSLELSKHQYVAAVHTDTDNLHVHVAVNRVHPETGYINWLSWSQEKLSRACRELELKHGFAPDNGCF
VHAPGNRIVRKTALVRERRNAWRRGKKQTFREYIAQMSIAGLREEPAQDWLSLHKRLASDGLYITMQEGE
LVVKDGWDRAREGVALSSFGPSWTAEKLGRKLGEYQPVPTDIFSQVGTPGRYDPEAINVDIRPEKVAETE
SLKQYACRYFAERLPEMARNGELESCLDVHRTLAKAGLWMGIQHGHLVLHDGFDKQQTPVRADSVWPLMT
LDYMQDLDGGWQPVPKDIFTQVIPGERFRGRNLGTQAVSDYEWYRMRMGTGPQGAIKRELFSDKESLWGY
TTVQCESLIEDMIAGGNFSWQACHEMFARKGLMLQKQHHGLVIVDAFNHELTPVKASSIHPDLTLSRAEL
QAGPFEIAGADIFERVKPECRYNPELAASDEVEPGFRRDPVLRRERREARAAAREDLRARYLAWKEHWRK
PDLRYGERLREIHAACRRRKAYIRVQFRDPQLRKLHYHIAEVQRMQALIRLKESVKEERLSLIAEGKWYP
LSYRQWVEQQAVQGDRAALSQLRGWDYRDRRKDKRRTTNADRCVILCEPGGTPLYEDTGVLEARLQKDGS
VRFRDRRNGELVCVDYGDRVVFYHHQDRNELVDKLNLIAPVLFDREPGMGFEPEGSYQQFNDVFAEMVAW
HNAAGITGNGHFVISRPDVDLHRQRSEQYYHEYIRQQKSISGGHGASYAPVQDNEWTPPSPGM

  Protein domains


Predicted by InterproScan.

(62-315)


  Protein structure



No available structure.



  Reference


[1] Robert A Moran et al. (2019) pBuzz: A cryptic rolling-circle plasmid from a commensal Escherichia coli has two inversely oriented oriTs and is mobilised by a B/O plasmid. Plasmid. 101:10-19. [PMID:30468749]


Auxiliary protein


ID   382 GenBank   AXQ87038
Name   NikA_p838B-R experimental UniProt ID   _
Length   110 a.a. PDB ID   _
Note   

  Auxiliary protein sequence


Download         Length: 110 a.a.        Molecular weight: 12730.52 Da        Isoelectric Point: 9.9656

>AXQ87038.1 NikA (plasmid) [Escherichia coli]
MSEKKTRTGSENRKRIVKFTARFTEDEAEIVREKAESSGQTVSTFIRSSSLDKVVNCRTDDRMIDEIMRL
GRLQKHLFVEGKRTGDKEYAEVLVAITEYVNALRRDLMGR

  Protein domains



No domain identified.



  Protein structure



No available structure.



  Reference


[1] Robert A Moran et al. (2019) pBuzz: A cryptic rolling-circle plasmid from a commensal Escherichia coli has two inversely oriented oriTs and is mobilised by a B/O plasmid. Plasmid. 101:10-19. [PMID:30468749]


T4SS


T4SS were predicted by using oriTfinder2.

Region 1: 45259..84512

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
Locus_45 40432..41235 - 804 AXQ86982 StrA -
Locus_46 41296..42111 - 816 AXQ86983 Sul2 -
Locus_47 42975..45278 - 2304 AXQ86984 TrbC -
Locus_48 45259..46383 - 1125 AXQ86985 TrbB trbB
Locus_49 46380..47660 - 1281 AXQ86986 TrbA trbA
Locus_50 48073..48180 + 108 AXQ86987 hypothetical protein -
Locus_51 48716..49012 + 297 AXQ86988 hypothetical protein -
Locus_52 49133..49726 + 594 AXQ86989 hypothetical protein -
Locus_53 49971..50651 + 681 AXQ86990 hypothetical protein -
Locus_54 50849..51064 - 216 AXQ86991 hypothetical protein -
Locus_55 51068..51394 - 327 AXQ86992 hypothetical protein -
Locus_56 51727..52047 - 321 AXQ86993 hypothetical protein -
Locus_57 52241..52444 + 204 AXQ86994 PndC -
Locus_58 52299..52451 + 153 AXQ86995 PndA -
Locus_59 52589..53101 - 513 AXQ86996 hypothetical protein -
Locus_60 53280..54179 - 900 AXQ86997 hypothetical protein -
Locus_61 54453..55103 - 651 AXQ86998 ExcA -
Locus_62 55192..57357 - 2166 AXQ86999 TraY traY
Locus_63 57432..58001 - 570 AXQ87000 TraX -
Locus_64 57998..59203 - 1206 AXQ87001 TraW traW
Locus_65 59161..59781 - 621 AXQ87002 TraV traV
Locus_66 59781..62825 - 3045 AXQ87003 TraU traU
Locus_67 63120..63938 - 819 AXQ87004 TraT traT
Locus_68 63739..64104 - 366 AXQ87005 TraS -
Locus_69 64161..64559 - 399 AXQ87006 TraR traR
Locus_70 64606..65136 - 531 AXQ87007 TraQ traQ
Locus_71 65133..65846 - 714 AXQ87008 TraP traP
Locus_72 65843..67174 - 1332 AXQ87009 TraO traO
Locus_73 67178..68137 - 960 AXQ87010 TraN traN
Locus_74 68148..68843 - 696 AXQ87011 TraM traM
Locus_75 68855..69205 - 351 AXQ87012 TraL traL
Locus_76 69222..73283 - 4062 AXQ87013 SogL -
Locus_77 69222..73094 - 3873 AXQ87014 SogS -
Locus_78 73347..73637 - 291 AXQ87015 TraK traK
Locus_79 73634..74782 - 1149 AXQ87016 TraJ virB11
Locus_80 74766..75602 - 837 AXQ87017 TraI traI
Locus_81 75599..76057 - 459 AXQ87018 TraH -
Locus_82 76161..77363 - 1203 AXQ87019 TraF -
Locus_83 77465..78286 - 822 AXQ87020 TraE traE
Locus_84 78759..80120 - 1362 AXQ87021 PilV -
Locus_85 80138..80764 - 627 AXQ87022 PilU -
Locus_86 80780..81265 - 486 AXQ87023 PilT virB1
Locus_87 81310..81846 - 537 AXQ87024 PilS -
Locus_88 81908..83002 - 1095 AXQ87025 PilR -
Locus_89 83004..84512 - 1509 AXQ87026 PilQ virB11
Locus_90 84616..85074 - 459 AXQ87027 PilP -
Locus_91 85064..86359 - 1296 AXQ87028 PilO -
Locus_92 86380..87999 - 1620 AXQ87029 PilN -
Locus_93 88031..88468 - 438 AXQ87030 PilM -


Host bacterium


ID   1460 GenBank   MH618673
Plasmid name   p838B-R Incompatibility group   IncB/O/K/Z
Plasmid size   94803 bp Coordinate of oriT [Strand]   30133..30205 [-]
Host baterium   Escherichia coli strain 838B

Cargo genes


Drug resistance gene   resistance to streptomycin, amoxicillin, ampicillin, cephalothin, piperacillin, ticarcillin and sulfamethoxazole
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -