Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 101001 |
| Name | oriT_p838B-R  |
| 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
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  |
| oriT | oriT_p838B-R |
| Relaxase | NikB_p838B-R (_) |
| Auxiliary protein | NikA_p838B-R |
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 |
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
MNAIIPHKRRDGRSSFEDLIAYTSVRDDVQENELTEDSEIKSDVPHRNRFRRLVDYATRLRNEKFVSLID
VMKDGSQWVNFYGVTCFHNCNSLETAAEEMQYKADKAVFSRNDTDPVFHYILSWPAHESPRPEQLFDCVR
HTLKSLELSKHQYVAAVHTDTDNLHVHVAVNRVHPETGYINWLSWSQEKLSRACRELELKHGFAPDNGCF
VHAPGNRIVRKTALVRERRNAWRRGKKQTFREYIAQMSIAGLREEPAQDWLSLHKRLASDGLYITMQEGE
LVVKDGWDRAREGVALSSFGPSWTAEKLGRKLGEYQPVPTDIFSQVGTPGRYDPEAINVDIRPEKVAETE
SLKQYACRYFAERLPEMARNGELESCLDVHRTLAKAGLWMGIQHGHLVLHDGFDKQQTPVRADSVWPLMT
LDYMQDLDGGWQPVPKDIFTQVIPGERFRGRNLGTQAVSDYEWYRMRMGTGPQGAIKRELFSDKESLWGY
TTVQCESLIEDMIAGGNFSWQACHEMFARKGLMLQKQHHGLVIVDAFNHELTPVKASSIHPDLTLSRAEL
QAGPFEIAGADIFERVKPECRYNPELAASDEVEPGFRRDPVLRRERREARAAAREDLRARYLAWKEHWRK
PDLRYGERLREIHAACRRRKAYIRVQFRDPQLRKLHYHIAEVQRMQALIRLKESVKEERLSLIAEGKWYP
LSYRQWVEQQAVQGDRAALSQLRGWDYRDRRKDKRRTTNADRCVILCEPGGTPLYEDTGVLEARLQKDGS
VRFRDRRNGELVCVDYGDRVVFYHHQDRNELVDKLNLIAPVLFDREPGMGFEPEGSYQQFNDVFAEMVAW
HNAAGITGNGHFVISRPDVDLHRQRSEQYYHEYIRQQKSISGGHGASYAPVQDNEWTPPSPGM
Protein domains
Predicted by InterproScan.
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 |
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
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 | - |