Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 100105 |
| Name | oriT_pCTXM360  |
| Organism | Klebsiella pneumoniae |
| Sequence Completeness | core |
| NCBI accession of oriT (coordinates [strand]) | NC_011641 (1896..2001 [+], 106 nt) |
| oriT length | 106 nt |
| IRs (inverted repeats) | 18..35, 41..58 (GTTTTTGGAGTACCGCCG..CGGCGGCCGTCCAAAAAC) |
| Location of nic site | _ |
| Conserved sequence flanking the nic site |
_ |
| Note | _ |
oriT sequence
Download Length: 106 nt
AGTACGGGACAAGATGTGTTTTTGGAGTACCGCCGACACGCGGCGGCCGTCCAAAAACGTCTTGGTCAGGGCAAGCCCCGACACCCCCTAACGAGGTTAGCTATCT
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 100 | GenBank | YP_002333288 |
| Name | MobA_pCTXM360 |
UniProt ID | B7T4S8 |
| Length | 658 a.a. | PDB ID | |
| Note | relaxase | ||
Relaxase protein sequence
Download Length: 658 a.a. Molecular weight: 75135.84 Da Isoelectric Point: 10.0285
MIPKIIEGRRDKKSSFGQLIKYMADKPSQELTDTVQPTPETALAVKSDMFEGLNNYLTRKQKVISTPVDV
EPGVQRVVVGDVTCQYNTFSLDGAAQEMNSVSQQSTRCKDPVMHYVLSWPDYEKPNDDQVFDSVKFTLAS
MGMSDHQYVAAIHRDTDNLHVHVAVNRINPQTYKAASSSFTKDTLHQACRLLELKNGWSHSNGAYVVNDR
QQIVRNPHSKKERGNWRSLDRINKMENKEGVETLYRYIVGDEQVGGSRQNLIHVSAGLREAKSWDDVHKT
FADIGLRVEKAQGKKGYVITHEHQNQKTAVKASLVFNKAQYTLKSMEERFGEYQPSHIEPAKVSVFKTAY
TPGAYRRDANKRLQRKIERAEERMLLKGRYRAYRNNLPVYSPDKDRIADEYRKIAQHTRLVKNNVRHSVS
DPHTRKLMYNLAEFKRLQAVANLRLSLREERNGFRAANPRLSYREWVEQEALKGDKAALSQMRGFAYSSR
KKEKYKQQLVEQIGFNRTFNAITSHDRDDVAVMASARHGVKPRLLKDGTVIFERDGKPVAADRGHIVLTE
SNGIDKEKTADLAIALTIAGKAKSVRVDGDGEFKELCCNRIVDAAVNHNHPVAQGITFTDAAQQAYAQNE
KHRLIREQNNSKNEMQFRSERDDKFNPK
Protein domains
Predicted by InterproScan.
Protein structure
| Source | ID | Structure |
|---|---|---|
| AlphaFold DB | B7T4S8 |
Reference
[1] Zhu WH et al. (2009) Complete nucleotide sequence of pCTX-M360, an intermediate plasmid between pEL60 and pCTX-M3, from a multidrug-resistant Klebsiella pneumoniae strain isolated in China. Antimicrob Agents Chemother. 53(12):5291-3. [PMID:19752275]
Auxiliary protein
| ID | 147 | GenBank | YP_002333287 |
| Name | MobB_pCTXM360 |
UniProt ID | B7T4S7 |
| Length | 105 a.a. | PDB ID | _ |
| Note | mobility protein B; conjugal transfer relaxosome component TraJ | ||
Auxiliary protein sequence
Download Length: 105 a.a. Molecular weight: 11646.32 Da Isoelectric Point: 9.9834
MSRSESRKTDDRIQVRCSTEVKAKLTEKAHEAGLSLSQYLIKSGLGKRIQSKGNYNALAALVKITALQKH
LFNEGAGVHSKEYSEILIEVKKAAQKLQQEMDGDT
Protein domains
No domain identified.
Protein structure
| Source | ID | Structure |
|---|---|---|
| AlphaFold DB | B7T4S7 |
Reference
[1] Zhu WH et al. (2009) Complete nucleotide sequence of pCTX-M360, an intermediate plasmid between pEL60 and pCTX-M3, from a multidrug-resistant Klebsiella pneumoniae strain isolated in China. Antimicrob Agents Chemother. 53(12):5291-3. [PMID:19752275]
| ID | 148 | GenBank | YP_002333286 |
| Name | MobC_pCTXM360 |
UniProt ID | B7T4S6 |
| Length | 121 a.a. | PDB ID | _ |
| Note | mobility protein C | ||
Auxiliary protein sequence
Download Length: 121 a.a. Molecular weight: 13567.20 Da Isoelectric Point: 9.6395
MPAKKKAFYSSEDIGKFKSILDDLPDVTSERLEKKHVLDELKSDIKKLKDSKGYEDKEILKFLNDAGFSD
VTLRDIKDITAGRVGKKRTSNSRKKTTGVDEEQRTQNGSTGQNPDASGPQY
Protein domains
No domain identified.
Protein structure
| Source | ID | Structure |
|---|---|---|
| AlphaFold DB | B7T4S6 |
Reference
[1] Zhu WH et al. (2009) Complete nucleotide sequence of pCTX-M360, an intermediate plasmid between pEL60 and pCTX-M3, from a multidrug-resistant Klebsiella pneumoniae strain isolated in China. Antimicrob Agents Chemother. 53(12):5291-3. [PMID:19752275]
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 4797..23900
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| HS563_RS00010 (pCTXM360_p01) | 324..716 | + | 393 | WP_227648760 | hypothetical protein | - |
| HS563_RS00430 | 706..861 | + | 156 | WP_227520852 | hypothetical protein | - |
| HS563_RS00015 (pCTXM360_p02) | 1362..1727 | - | 366 | WP_011091067 | hypothetical protein | - |
| HS563_RS00435 | 1742..2320 | + | 579 | WP_223811519 | plasmid mobilization protein MobA | - |
| HS563_RS00025 (pCTXM360_p04) | 2307..4286 | + | 1980 | WP_050868819 | TraI/MobA(P) family conjugative relaxase | - |
| HS563_RS00030 (pCTXM360_p05) | 4300..4800 | + | 501 | WP_004187320 | DotD/TraH family lipoprotein | - |
| HS563_RS00035 (pCTXM360_p06) | 4797..5576 | + | 780 | WP_004187315 | type IV secretory system conjugative DNA transfer family protein | traI |
| HS563_RS00040 (pCTXM360_p07) | 5587..6750 | + | 1164 | WP_004187313 | plasmid transfer ATPase TraJ | virB11 |
| HS563_RS00045 (pCTXM360_p08) | 6740..7000 | + | 261 | WP_004187310 | IcmT/TraK family protein | traK |
| HS563_RS00440 | 7025..10120 | + | 3096 | WP_227648761 | LPD7 domain-containing protein | - |
| HS563_RS00055 (pCTXM360_p10) | 10160..10714 | + | 555 | WP_011154467 | hypothetical protein | traL |
| HS563_RS00060 | 10715..10912 | - | 198 | WP_004187464 | Hha/YmoA family nucleoid-associated regulatory protein | - |
| HS563_RS00065 | 10899..11309 | - | 411 | WP_004187465 | H-NS family nucleoid-associated regulatory protein | - |
| HS563_RS00070 (pCTXM360_p12) | 11308..12090 | + | 783 | WP_011091073 | DotI/IcmL family type IV secretion protein | traM |
| HS563_RS00075 (pCTXM360_p13) | 12099..13250 | + | 1152 | WP_011091074 | DotH/IcmK family type IV secretion protein | traN |
| HS563_RS00080 (pCTXM360_p14) | 13262..14611 | + | 1350 | WP_011091075 | conjugal transfer protein TraO | traO |
| HS563_RS00445 | 14623..15039 | + | 417 | WP_227648762 | hypothetical protein | traP |
| HS563_RS00450 | 15008..15328 | + | 321 | WP_227648763 | hypothetical protein | traP |
| HS563_RS00090 (pCTXM360_p16) | 15352..15882 | + | 531 | WP_011091077 | conjugal transfer protein TraQ | traQ |
| HS563_RS00095 (pCTXM360_p17) | 15899..16288 | + | 390 | WP_011091078 | DUF6750 family protein | traR |
| HS563_RS00100 (pCTXM360_p19) | 16334..16828 | + | 495 | WP_011091080 | hypothetical protein | - |
| HS563_RS00105 (pCTXM360_p20) | 16825..19875 | + | 3051 | WP_011091081 | hypothetical protein | traU |
| HS563_RS00110 (pCTXM360_p21) | 19872..21080 | + | 1209 | WP_011091082 | conjugal transfer protein TraW | traW |
| HS563_RS00115 (pCTXM360_p22) | 21077..21727 | + | 651 | WP_011091083 | hypothetical protein | - |
| HS563_RS00120 (pCTXM360_p23) | 21720..23900 | + | 2181 | WP_004187492 | DotA/TraY family protein | traY |
| HS563_RS00125 (pCTXM360_p24) | 23903..24556 | + | 654 | WP_011091084 | hypothetical protein | - |
| HS563_RS00130 (pCTXM360_p25) | 24613..24861 | + | 249 | WP_015062836 | IncL/M type plasmid replication protein RepC | - |
| HS563_RS00135 (pCTXM360_p27) | 25147..26214 | + | 1068 | WP_050868820 | plasmid replication initiator RepA | - |
| HS563_RS00140 (pCTXM360_p28) | 27218..28078 | - | 861 | WP_000027057 | broad-spectrum class A beta-lactamase TEM-1 | - |
| HS563_RS00145 (pCTXM360_p29) | 28261..28818 | - | 558 | WP_001235713 | recombinase family protein | - |
Host bacterium
| ID | 100 | GenBank | NC_011641 |
| Plasmid name | pCTXM360 | Incompatibility group | IncL/M |
| Plasmid size | 68018 bp | Coordinate of oriT [Strand] | 1896..2001 [+] |
| Host baterium | Klebsiella pneumoniae |
Cargo genes
| Drug resistance gene | blaTEM-1B, blaCTX-M-3 |
| Virulence gene | - |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |