Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 100507 |
| Name | oriT_pNDM-OM  |
| Organism | Klebsiella pneumoniae |
| Sequence Completeness | core |
| NCBI accession of oriT (coordinates [strand]) | NC_019889 (14418..14523 [+], 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 | predicted by the oriTfinder |
oriT sequence
Download Length: 106 nt
>oriT_pNDM-OM
AGTACGGGACAAGATGTGTTTTTGGAGTACCGCCGACACGCGGCGGCCGTCCAAAAACGTCTTGGTCAGGGCAAGCCCCGACACCCCCTAACGAGGTTAGCTATCT
AGTACGGGACAAGATGTGTTTTTGGAGTACCGCCGACACGCGGCGGCCGTCCAAAAACGTCTTGGTCAGGGCAAGCCCCGACACCCCCTAACGAGGTTAGCTATCT
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 578 | GenBank | YP_007195471 |
| Name | PutativerelaxaseofpNDM-OM |
UniProt ID | B7T4S7 |
| Length | 105 a.a. | PDB ID | |
| Note | putative relaxase | ||
Relaxase protein sequence
Download Length: 105 a.a. Molecular weight: 11646.32 Da Isoelectric Point: 9.9834
>YP_007195471.1 MobB (plasmid) [Klebsiella pneumoniae]
MSRSESRKTDDRIQVRCSTEVKAKLTEKAHEAGLSLSQYLIKSGLGKRIQSKGNYNALAALVKITALQKH
LFNEGAGVHSKEYSEILIEVKKAAQKLQQEMDGDT
MSRSESRKTDDRIQVRCSTEVKAKLTEKAHEAGLSLSQYLIKSGLGKRIQSKGNYNALAALVKITALQKH
LFNEGAGVHSKEYSEILIEVKKAAQKLQQEMDGDT
Protein domains
No domain identified.
Protein structure
| Source | ID | Structure |
|---|---|---|
| AlphaFold DB | B7T4S7 |
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 17319..36737
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| HTA49_RS00120 (D647_p14070) | 12404..12715 | + | 312 | WP_015058934 | hypothetical protein | - |
| HTA49_RS00125 (D647_p14071) | 12848..13384 | + | 537 | WP_015058935 | hypothetical protein | - |
| HTA49_RS00130 (D647_p14065) | 13885..14280 | - | 396 | WP_015058936 | hypothetical protein | - |
| HTA49_RS00545 | 14279..14842 | + | 564 | WP_227537722 | plasmid mobilization protein MobA | - |
| HTA49_RS00140 (D647_p14063) | 14829..16808 | + | 1980 | WP_015058937 | TraI/MobA(P) family conjugative relaxase | - |
| HTA49_RS00145 (D647_p14062) | 16822..17322 | + | 501 | WP_004187320 | DotD/TraH family lipoprotein | - |
| HTA49_RS00150 (D647_p14061) | 17319..18098 | + | 780 | WP_015058938 | type IV secretory system conjugative DNA transfer family protein | traI |
| HTA49_RS00155 (D647_p14060) | 18109..19272 | + | 1164 | WP_004187313 | plasmid transfer ATPase TraJ | virB11 |
| HTA49_RS00160 (D647_p14018) | 19262..19522 | + | 261 | WP_004187310 | IcmT/TraK family protein | traK |
| HTA49_RS00550 | 19547..23074 | + | 3528 | WP_015058939 | LPD7 domain-containing protein | - |
| HTA49_RS00170 (D647_p14019) | 22998..23552 | + | 555 | WP_015243643 | hypothetical protein | traL |
| HTA49_RS00175 | 23553..23750 | - | 198 | WP_004187464 | Hha/YmoA family nucleoid-associated regulatory protein | - |
| HTA49_RS00180 | 23737..24147 | - | 411 | WP_004187465 | H-NS family nucleoid-associated regulatory protein | - |
| HTA49_RS00185 (D647_p14059) | 24146..24928 | + | 783 | WP_015058941 | DotI/IcmL family type IV secretion protein | traM |
| HTA49_RS00190 (D647_p14058) | 24937..26088 | + | 1152 | WP_011091074 | DotH/IcmK family type IV secretion protein | traN |
| HTA49_RS00195 (D647_p14057) | 26100..27449 | + | 1350 | WP_015058942 | conjugal transfer protein TraO | traO |
| HTA49_RS00200 (D647_p14056) | 27461..28165 | + | 705 | WP_015243644 | conjugal transfer protein TraP | traP |
| HTA49_RS00205 (D647_p14055) | 28189..28719 | + | 531 | WP_011091077 | conjugal transfer protein TraQ | traQ |
| HTA49_RS00210 (D647_p14020) | 28736..29125 | + | 390 | WP_011091078 | DUF6750 family protein | traR |
| HTA49_RS00215 (D647_p14074) | 29171..29665 | + | 495 | WP_015243645 | hypothetical protein | - |
| HTA49_RS00220 (D647_p14054) | 29662..32712 | + | 3051 | WP_011091081 | hypothetical protein | traU |
| HTA49_RS00225 (D647_p14053) | 32709..33917 | + | 1209 | WP_011091082 | conjugal transfer protein TraW | traW |
| HTA49_RS00230 (D647_p14052) | 33914..34564 | + | 651 | WP_011091083 | hypothetical protein | - |
| HTA49_RS00235 (D647_p14051) | 34557..36737 | + | 2181 | WP_004187492 | DotA/TraY family protein | traY |
| HTA49_RS00240 (D647_p14050) | 36740..37393 | + | 654 | WP_011091084 | hypothetical protein | - |
| HTA49_RS00245 (D647_p14049) | 37450..37698 | + | 249 | WP_015062836 | IncL/M type plasmid replication protein RepC | - |
| HTA49_RS00250 (D647_p14023) | 37984..39051 | + | 1068 | WP_050868820 | plasmid replication initiator RepA | - |
| HTA49_RS00255 (D647_p14022) | 40055..40915 | - | 861 | WP_000027057 | broad-spectrum class A beta-lactamase TEM-1 | - |
Host bacterium
| ID | 968 | GenBank | NC_019889 |
| Plasmid name | pNDM-OM | Incompatibility group | IncL/M |
| Plasmid size | 87185 bp | Coordinate of oriT [Strand] | 14418..14523 [+] |
| Host baterium | Klebsiella pneumoniae |
Cargo genes
| Drug resistance gene | blaTEM-1B, aac(3)-IId, blaNDM-1, sul1, armA, msr(E), mph(E) |
| Virulence gene | - |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |