Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 117992 |
| Name | oriT_p2HDMI12  |
| Organism | Candidatus Hamiltonella defensa strain MI12 isolate MI12 |
| Sequence Completeness | - |
| NCBI accession of oriT (coordinates [strand]) | NZ_CP023990 (41129..41174 [+], 46 nt) |
| oriT length | 46 nt |
| IRs (inverted repeats) | _ |
| Location of nic site | _ |
| Conserved sequence flanking the nic site |
_ |
| Note | Predicted by oriTfinder 2.0 |
oriT sequence
Download Length: 46 nt
>oriT_p2HDMI12
TTTAAAGCAAAAAACGGATGCTCCATACTCGCCATTTCATCCCTGA
TTTAAAGCAAAAAACGGATGCTCCATACTCGCCATTTCATCCCTGA
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 11413 | GenBank | WP_235661299 |
| Name | mobP1_CJJ19_RS11285_p2HDMI12 |
UniProt ID | _ |
| Length | 387 a.a. | PDB ID | |
| Note | Predicted by oriTfinder 2.0 | ||
Relaxase protein sequence
Download Length: 387 a.a. Molecular weight: 45210.74 Da Isoelectric Point: 10.6861
>WP_235661299.1 MobP1 family relaxase [Candidatus Hamiltonella defensa]
MMGVKVKKEERIRRVAEQRREKIRRFPEAHKARHGGKNYSRGVRDRAFKNGNSREVLVRITGSGRTPRGV
KNEINYIAREGELTLRDSEGKEYCIQEREERHQSYAFMTDQEDKQGHRDESAPKLVHNMVFSSPNVASVS
EADAFKAVETTLKEKYPDNRFIMAYHKDTDSHHVHVLLRIPDNYGKRINIRKQDLRDLREKFAGQLQKMG
YNVTCTHQYQFGLKSELKREHDRQRGLYEVVKFGRASYRFNPKNGDQNYITLRTLKNKTEVTYWGVNLAE
EIEREQIKTGSVISFKKEGATAVKVPKLNRQGKQVGWTQTHRNHWRIENQAQMGIKPKPFPKEIKLDSPE
QLMKHKRSMSVFKQSKAAMLVLKEQLKKGIKMGGIKF
MMGVKVKKEERIRRVAEQRREKIRRFPEAHKARHGGKNYSRGVRDRAFKNGNSREVLVRITGSGRTPRGV
KNEINYIAREGELTLRDSEGKEYCIQEREERHQSYAFMTDQEDKQGHRDESAPKLVHNMVFSSPNVASVS
EADAFKAVETTLKEKYPDNRFIMAYHKDTDSHHVHVLLRIPDNYGKRINIRKQDLRDLREKFAGQLQKMG
YNVTCTHQYQFGLKSELKREHDRQRGLYEVVKFGRASYRFNPKNGDQNYITLRTLKNKTEVTYWGVNLAE
EIEREQIKTGSVISFKKEGATAVKVPKLNRQGKQVGWTQTHRNHWRIENQAQMGIKPKPFPKEIKLDSPE
QLMKHKRSMSVFKQSKAAMLVLKEQLKKGIKMGGIKF
Protein domains
No domain identified.
Protein structure
No available structure.
T4CP
| ID | 13338 | GenBank | WP_171967947 |
| Name | t4cp2_CJJ19_RS11210_p2HDMI12 |
UniProt ID | _ |
| Length | 309 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
T4CP protein sequence
Download Length: 309 a.a. Molecular weight: 35377.55 Da Isoelectric Point: 5.2281
>WP_171967947.1 hypothetical protein [Candidatus Hamiltonella defensa]
MTGFAPFMLDATQRNVIFVKQLMKIICTLNGNTLTTREELRLNTGVARVMALPHDVRRFGVTALINHISE
PDNREARENGVKIRLSRWAQGGDLAWVFDNDNDTFDLSQYDNFGIDGTEFLDNPEVCPAIAFYLLYRVTR
LLDGRRLVIFMDEFWQWIGNPAFADFVYNRLKTMRKLNGIIIPATQSPEEILKSSVSGAMREQCTTHIYL
ANPKADYDQYVNQLKVPERYFNIIKNLDPLSRQFLIVKSPLYKGNLNDFAALVTLDLSGLGVTTKLLSTD
KDDLEVFDSLFKDGLRPDEWIDTYLKLVS
MTGFAPFMLDATQRNVIFVKQLMKIICTLNGNTLTTREELRLNTGVARVMALPHDVRRFGVTALINHISE
PDNREARENGVKIRLSRWAQGGDLAWVFDNDNDTFDLSQYDNFGIDGTEFLDNPEVCPAIAFYLLYRVTR
LLDGRRLVIFMDEFWQWIGNPAFADFVYNRLKTMRKLNGIIIPATQSPEEILKSSVSGAMREQCTTHIYL
ANPKADYDQYVNQLKVPERYFNIIKNLDPLSRQFLIVKSPLYKGNLNDFAALVTLDLSGLGVTTKLLSTD
KDDLEVFDSLFKDGLRPDEWIDTYLKLVS
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 3075..25046
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| CJJ19_RS11085 (CJJ19_11160) | 15..731 | + | 717 | WP_171967940 | StbB family protein | - |
| CJJ19_RS11090 (CJJ19_11165) | 733..1041 | + | 309 | WP_015873781 | plasmid stabilization protein StbC | - |
| CJJ19_RS11095 (CJJ19_11170) | 1283..2401 | - | 1119 | WP_235661303 | shufflon system plasmid conjugative transfer pilus tip adhesin PilV | - |
| CJJ19_RS11100 (CJJ19_11175) | 2413..3078 | - | 666 | WP_171967941 | A24 family peptidase | - |
| CJJ19_RS11105 (CJJ19_11180) | 3075..3536 | - | 462 | WP_171967960 | lytic transglycosylase domain-containing protein | virB1 |
| CJJ19_RS11110 (CJJ19_11185) | 3631..4257 | - | 627 | WP_235661304 | type 4 pilus major pilin | - |
| CJJ19_RS11115 (CJJ19_11190) | 4261..5361 | - | 1101 | WP_171967942 | type II secretion system F family protein | - |
| CJJ19_RS11120 (CJJ19_11195) | 5470..5949 | + | 480 | WP_100097226 | Hsp20 family protein | - |
| CJJ19_RS11125 (CJJ19_11200) | 5988..7496 | - | 1509 | WP_171967962 | GspE/PulE family protein | virB11 |
| CJJ19_RS11130 (CJJ19_11205) | 7514..7978 | - | 465 | WP_100097227 | type IV pilus biogenesis protein PilP | - |
| CJJ19_RS12420 (CJJ19_11215) | 8003..8767 | - | 765 | WP_235661311 | type 4b pilus protein PilO2 | - |
| CJJ19_RS11140 (CJJ19_11220) | 8689..9255 | - | 567 | WP_171967943 | type 4b pilus protein PilO2 | - |
| CJJ19_RS12425 | 9255..9749 | - | 495 | WP_235661305 | hypothetical protein | - |
| CJJ19_RS12430 | 9752..10099 | - | 348 | WP_235661306 | hypothetical protein | - |
| CJJ19_RS12435 | 10105..10893 | - | 789 | WP_235661307 | secretin N-terminal domain-containing protein | - |
| CJJ19_RS11150 (CJJ19_11230) | 10992..11441 | - | 450 | WP_235661308 | type IV pilus biogenesis protein PilM | - |
| CJJ19_RS11155 (CJJ19_11235) | 11438..12355 | - | 918 | WP_171967944 | cag pathogenicity island Cag12 family protein | - |
| CJJ19_RS11160 (CJJ19_11240) | 12398..14250 | - | 1853 | Protein_18 | type IV secretory system conjugative DNA transfer family protein | - |
| CJJ19_RS11165 (CJJ19_11245) | 14237..15268 | - | 1032 | WP_171967945 | P-type DNA transfer ATPase VirB11 | virB11 |
| CJJ19_RS11170 (CJJ19_11250) | 15265..16656 | - | 1392 | WP_320410335 | VirB10/TraB/TrbI family type IV secretion system protein | virB10 |
| CJJ19_RS11175 (CJJ19_11255) | 16653..17582 | - | 930 | WP_015873769 | P-type conjugative transfer protein VirB9 | virB9 |
| CJJ19_RS11180 (CJJ19_11260) | 17585..18463 | - | 879 | WP_235661310 | virB8 family protein | virB8 |
| CJJ19_RS11185 (CJJ19_11265) | 18654..19241 | + | 588 | WP_171967946 | recombinase family protein | - |
| CJJ19_RS11190 (CJJ19_11270) | 19299..20288 | - | 990 | WP_171967965 | type IV secretion system protein | virB6 |
| CJJ19_RS11195 (CJJ19_11275) | 20198..20488 | - | 291 | WP_050879624 | type IV secretion system protein | virB6 |
| CJJ19_RS11200 (CJJ19_11280) | 20546..20833 | - | 288 | WP_015873764 | EexN family lipoprotein | - |
| CJJ19_RS11205 (CJJ19_11285) | 20830..21575 | - | 746 | Protein_27 | type IV secretion system protein | - |
| CJJ19_RS11210 (CJJ19_11290) | 21586..22515 | - | 930 | WP_171967947 | hypothetical protein | virb4 |
| CJJ19_RS11215 (CJJ19_11295) | 22512..22904 | - | 393 | WP_171967948 | hypothetical protein | virb4 |
| CJJ19_RS11220 (CJJ19_11300) | 22904..24334 | - | 1431 | WP_171967949 | VirB3 family type IV secretion system protein | virb4 |
| CJJ19_RS11225 (CJJ19_11305) | 24349..24624 | - | 276 | WP_015873762 | TrbC/VirB2 family protein | virB2 |
| CJJ19_RS11230 (CJJ19_11310) | 24645..25046 | - | 402 | WP_171967950 | transglycosylase SLT domain-containing protein | virB1 |
| CJJ19_RS11235 (CJJ19_11315) | 25130..25357 | - | 228 | WP_171967951 | hypothetical protein | - |
| CJJ19_RS11240 (CJJ19_11320) | 25382..25699 | - | 318 | WP_015873760 | hypothetical protein | - |
| CJJ19_RS11250 (CJJ19_11330) | 26543..27163 | - | 621 | WP_171967952 | helix-turn-helix domain-containing protein | - |
| CJJ19_RS11255 (CJJ19_11335) | 27160..27375 | - | 216 | WP_234817550 | hypothetical protein | - |
| CJJ19_RS11260 | 27416..27553 | - | 138 | WP_158531027 | hypothetical protein | - |
| CJJ19_RS11265 (CJJ19_11340) | 27647..28159 | - | 513 | WP_100097242 | DNA-3-methyladenine glycosylase | - |
| CJJ19_RS11270 (CJJ19_11345) | 28163..28384 | - | 222 | WP_100097243 | hypothetical protein | - |
| CJJ19_RS11275 (CJJ19_11350) | 28374..29381 | - | 1008 | WP_171967953 | Rpn family recombination-promoting nuclease/putative transposase | - |
Host bacterium
| ID | 18425 | GenBank | NZ_CP023990 |
| Plasmid name | p2HDMI12 | Incompatibility group | - |
| Plasmid size | 42977 bp | Coordinate of oriT [Strand] | 41129..41174 [+] |
| Host baterium | Candidatus Hamiltonella defensa strain MI12 isolate MI12 |
Cargo genes
| Drug resistance gene | - |
| Virulence gene | - |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | AcrIIA7 |