Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 114672 |
| Name | oriT_pShin-09  |
| Organism | Shinella sp. HZN7 |
| Sequence Completeness | - |
| NCBI accession of oriT (coordinates [strand]) | NZ_CP015745 (43362..43403 [+], 42 nt) |
| oriT length | 42 nt |
| IRs (inverted repeats) | _ |
| Location of nic site | _ |
| Conserved sequence flanking the nic site |
_ |
| Note | Predicted by oriTfinder 2.0 |
oriT sequence
Download Length: 42 nt
>oriT_pShin-09
GGATCCGAAGGGCGCAATTATACGTCACTGGCGCGACGCCCT
GGATCCGAAGGGCGCAATTATACGTCACTGGCGCGACGCCCT
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 9410 | GenBank | WP_064334681 |
| Name | traA_shn_RS33055_pShin-09 |
UniProt ID | A0A1A9GCZ2 |
| Length | 1103 a.a. | PDB ID | |
| Note | Predicted by oriTfinder 2.0 | ||
Relaxase protein sequence
Download Length: 1103 a.a. Molecular weight: 122644.80 Da Isoelectric Point: 9.9811
>WP_064334681.1 Ti-type conjugative transfer relaxase TraA [Shinella sp. HZN7]
MAVPHFSVSVVARGSGRSAVLSAAYRHCAKMAFEREARTIDYTRKQGLLHEEFVIPADAPEWLRSMIADR
SVAGASEAFWNKVEAFEKRSDAQLAKDVTIALPLELTAQQNIALMRDFVDRHIRSKGMVADWVYHDAPGN
PHVHLMTTLRPLTEDGFGAKKVAVVGPDGNAVRNDAGKIVYELWAGSTDDFNSFRDGWFACQNRHLALAG
LDIRVDGRSFEKQGIDLEPTIHLGVGTKAIERKADRASKPLELERVELQDARRAENARRIDRNPKLVLDL
ITREKSVFDERDVAKILHRYIDDPALFQSLMVRIILHPDTFRLERERIEFATGVRLPAKYTTRDMIRLEA
EMANRAIWLSQRSSHSVRDAALAATFKRHDRLSDEQRTAIEHVAGAERIAAVVGRAGAGKTTMMRAAREA
WEAAGYRVVGGALAGKAAEGLEKEAGIVSRTLSSWEIRWNQGRDQLDSKTMFVLDEAGMVSSRQMALFVE
AVTKAGAKLVLIGDPEQLQPIEAGAAFRAIADRIGYAELETIYRQREQWMRDASLDLARGKVGKAVDAYR
ANGKVIGWDLKADAVDNLIAAWDRDYDPTKTSLILAHLRRDVHMLNQMARIKLIERGVLDKGTMFKTADG
DRNFAVGDQIVFLKNEGSLGVKNGMLAKVVETGAGRITAQVGDGEHVRQVLVEQRFYNNLDYGYATTIHK
SQGATVDRVKVLASLSLDRHLTYVAMTRHSEDLAVYYGRRSFAKNGGLIQILSRRNAKDTTLDYEKGAFY
RQALRFAEARGLNIVSVARTLLHDRLEWTVRQKDKLANLGARLAAIAGKLGLVRGASHSPTQKTTKEAKP
MVSGVTTFAKSFEQAVEDKVAADPGLKKQWEEVSTRFHLVYAKPESAFKAIDVEAMLKDETVAKSTLATI
GSNPEHFGGLKGKTGMFASRTDSREREKAETNAPALARNLERYLRQRADAERKYEVEERAVRLKVSIDIP
ALSVNAKQTLERVRDAIDRNDLPAGLEYALADKMVKVELDGFARAVAERFGERTFLPLAAKDANGQTFST
VTAGMTAAQKAEVQSAWNAMRTVQQLAAHERTTEALKQAETLRQTKRQGLSLK
MAVPHFSVSVVARGSGRSAVLSAAYRHCAKMAFEREARTIDYTRKQGLLHEEFVIPADAPEWLRSMIADR
SVAGASEAFWNKVEAFEKRSDAQLAKDVTIALPLELTAQQNIALMRDFVDRHIRSKGMVADWVYHDAPGN
PHVHLMTTLRPLTEDGFGAKKVAVVGPDGNAVRNDAGKIVYELWAGSTDDFNSFRDGWFACQNRHLALAG
LDIRVDGRSFEKQGIDLEPTIHLGVGTKAIERKADRASKPLELERVELQDARRAENARRIDRNPKLVLDL
ITREKSVFDERDVAKILHRYIDDPALFQSLMVRIILHPDTFRLERERIEFATGVRLPAKYTTRDMIRLEA
EMANRAIWLSQRSSHSVRDAALAATFKRHDRLSDEQRTAIEHVAGAERIAAVVGRAGAGKTTMMRAAREA
WEAAGYRVVGGALAGKAAEGLEKEAGIVSRTLSSWEIRWNQGRDQLDSKTMFVLDEAGMVSSRQMALFVE
AVTKAGAKLVLIGDPEQLQPIEAGAAFRAIADRIGYAELETIYRQREQWMRDASLDLARGKVGKAVDAYR
ANGKVIGWDLKADAVDNLIAAWDRDYDPTKTSLILAHLRRDVHMLNQMARIKLIERGVLDKGTMFKTADG
DRNFAVGDQIVFLKNEGSLGVKNGMLAKVVETGAGRITAQVGDGEHVRQVLVEQRFYNNLDYGYATTIHK
SQGATVDRVKVLASLSLDRHLTYVAMTRHSEDLAVYYGRRSFAKNGGLIQILSRRNAKDTTLDYEKGAFY
RQALRFAEARGLNIVSVARTLLHDRLEWTVRQKDKLANLGARLAAIAGKLGLVRGASHSPTQKTTKEAKP
MVSGVTTFAKSFEQAVEDKVAADPGLKKQWEEVSTRFHLVYAKPESAFKAIDVEAMLKDETVAKSTLATI
GSNPEHFGGLKGKTGMFASRTDSREREKAETNAPALARNLERYLRQRADAERKYEVEERAVRLKVSIDIP
ALSVNAKQTLERVRDAIDRNDLPAGLEYALADKMVKVELDGFARAVAERFGERTFLPLAAKDANGQTFST
VTAGMTAAQKAEVQSAWNAMRTVQQLAAHERTTEALKQAETLRQTKRQGLSLK
Protein domains
Predicted by InterproScan.
Protein structure
| Source | ID | Structure |
|---|---|---|
| AlphaFold DB | A0A1A9GCZ2 |
T4CP
| ID | 10930 | GenBank | WP_064334678 |
| Name | traG_shn_RS33040_pShin-09 |
UniProt ID | _ |
| Length | 658 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
T4CP protein sequence
Download Length: 658 a.a. Molecular weight: 70816.95 Da Isoelectric Point: 8.4449
>WP_064334678.1 Ti-type conjugative transfer system protein TraG [Shinella sp. HZN7]
MNRIMLFIAPVALMILAAVAITGVEHWLSAFGKTEAARQALDRTGIAVPYLTAAFIGIVFLFASAGAIRV
KTAGWGVVAGGVATILIAAFRETIRLSALTDQVPVGKSIIAYVDPATLIGAGAAAMAACFALRVALVGNA
AFASAEPRRIRGKRALHGEADWMKLADAAKLLSDAGGIVIGEQYRVDRDSVAERSFRADSPETWGAGGTS
PLLCFDGSFGSSHGIVFAGSGGFKTTSVTIPTALKWGGSLIVLDPSNEVAPMVTAHRAGADRDVFVVDPK
KPEIGFNALDWIGQFGGTKEEDIASVASWIMSDSGGTRGVRDDFFRASALQLLTAMIADVCLSGHTEKES
QTLRQVRANLSEPEPQLRQRLQEIYDNSGSDFVKENVAAFVNMTPETFSGVYANAIKETHWLSYPNYAAL
VSGKTFSTSDLAAGNTDAFINIDLKTLETHAGLARVIIGSFLNAIYNRDGSMKGRALFLLDEVARLGYMR
ILETARDAGRKYGITLLMIYQSIGQMRETYGGRDAASKWFESASWISFAAINDTETADYISRRCGMTTVE
IDQVSRSSQMKGSSRTRSKQLAARPLILPHEVLRMRADEQIVFTAGNAPLRCGRAIWFRRDDMKACVGTN
RFHKLGSPPEASLVEPARSAASKVDPEK
MNRIMLFIAPVALMILAAVAITGVEHWLSAFGKTEAARQALDRTGIAVPYLTAAFIGIVFLFASAGAIRV
KTAGWGVVAGGVATILIAAFRETIRLSALTDQVPVGKSIIAYVDPATLIGAGAAAMAACFALRVALVGNA
AFASAEPRRIRGKRALHGEADWMKLADAAKLLSDAGGIVIGEQYRVDRDSVAERSFRADSPETWGAGGTS
PLLCFDGSFGSSHGIVFAGSGGFKTTSVTIPTALKWGGSLIVLDPSNEVAPMVTAHRAGADRDVFVVDPK
KPEIGFNALDWIGQFGGTKEEDIASVASWIMSDSGGTRGVRDDFFRASALQLLTAMIADVCLSGHTEKES
QTLRQVRANLSEPEPQLRQRLQEIYDNSGSDFVKENVAAFVNMTPETFSGVYANAIKETHWLSYPNYAAL
VSGKTFSTSDLAAGNTDAFINIDLKTLETHAGLARVIIGSFLNAIYNRDGSMKGRALFLLDEVARLGYMR
ILETARDAGRKYGITLLMIYQSIGQMRETYGGRDAASKWFESASWISFAAINDTETADYISRRCGMTTVE
IDQVSRSSQMKGSSRTRSKQLAARPLILPHEVLRMRADEQIVFTAGNAPLRCGRAIWFRRDDMKACVGTN
RFHKLGSPPEASLVEPARSAASKVDPEK
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
| ID | 10931 | GenBank | WP_064334708 |
| Name | t4cp2_shn_RS33240_pShin-09 |
UniProt ID | _ |
| Length | 818 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
T4CP protein sequence
Download Length: 818 a.a. Molecular weight: 91874.67 Da Isoelectric Point: 6.0699
>WP_064334708.1 conjugal transfer protein TrbE [Shinella sp. HZN7]
MVALKRFRATGPSFADLVPYAGLVDNGVLLLKDGSLMAGWYFAGPDSESATDLERNELSRQINTILSRLG
SGWMIQVEAVRIPTFDYPSDDRCHFPDAVTRAIDAERRAHFAREQGHFESKHALVLTYRPLESKKTALSK
YIYSDEDSRKKTYADTVLFIFKNAIREIEQYFANTLSIRRMETREVGERGGERLARYDELLQFVRFCVTG
ENHPIRLPDAPMYLDWIATAELEHGLTPKVENRFLAVVAIDGLPAESWPGILNSLDLMPLTYRWSSRFIF
LDAEEARQKLERTRKKWQQKVRPFFDQLFQTQSRSVDQDAMTMVAETEDAIAQASSQLVAYGYYTPVIVL
FDHDREALQEKAEAIRRLIQAEGFGARIETLNATDAFLGSLPGNWYCNIREPLINTSNLADLMPLNSVWS
GRPAAPCPFYPPNSPPLMQVASGSTPFRLNLHVDDVGHTLIFGPTGSGKSTLLALIAAQFRRYERAQIFA
FDKGNSLLPLTLAGGGDHYEIGGDAQDEARVLAFCPLSDLTSDADRAWATEWIEMLVALQGVAITPDHRN
AISRQIGLMASAAGRSLSDFVSGVQMREIKDALHHYTVDGPMGQLLDAEQDGLSLGALQTFEIEHLMNMG
ERNLVPVLTYLFRRIEKRLDGSPSLIVLDEAWLMLGHPVFRSKIREWLKVLRKANCAVVLATQSISDAER
SGIIDVLKESCPTKICLPNGAAREPGTREFYERIGFNERQIEIVSNAIPKREYYAVTPEGRRLFDMALGP
VALSFVGASGKEDLKRIRTLSSEHGRDWPIHWLRTRGVHDAASLLNFE
MVALKRFRATGPSFADLVPYAGLVDNGVLLLKDGSLMAGWYFAGPDSESATDLERNELSRQINTILSRLG
SGWMIQVEAVRIPTFDYPSDDRCHFPDAVTRAIDAERRAHFAREQGHFESKHALVLTYRPLESKKTALSK
YIYSDEDSRKKTYADTVLFIFKNAIREIEQYFANTLSIRRMETREVGERGGERLARYDELLQFVRFCVTG
ENHPIRLPDAPMYLDWIATAELEHGLTPKVENRFLAVVAIDGLPAESWPGILNSLDLMPLTYRWSSRFIF
LDAEEARQKLERTRKKWQQKVRPFFDQLFQTQSRSVDQDAMTMVAETEDAIAQASSQLVAYGYYTPVIVL
FDHDREALQEKAEAIRRLIQAEGFGARIETLNATDAFLGSLPGNWYCNIREPLINTSNLADLMPLNSVWS
GRPAAPCPFYPPNSPPLMQVASGSTPFRLNLHVDDVGHTLIFGPTGSGKSTLLALIAAQFRRYERAQIFA
FDKGNSLLPLTLAGGGDHYEIGGDAQDEARVLAFCPLSDLTSDADRAWATEWIEMLVALQGVAITPDHRN
AISRQIGLMASAAGRSLSDFVSGVQMREIKDALHHYTVDGPMGQLLDAEQDGLSLGALQTFEIEHLMNMG
ERNLVPVLTYLFRRIEKRLDGSPSLIVLDEAWLMLGHPVFRSKIREWLKVLRKANCAVVLATQSISDAER
SGIIDVLKESCPTKICLPNGAAREPGTREFYERIGFNERQIEIVSNAIPKREYYAVTPEGRRLFDMALGP
VALSFVGASGKEDLKRIRTLSSEHGRDWPIHWLRTRGVHDAASLLNFE
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 80765..88518
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| shn_RS33205 (shn_33205) | 76137..77351 | - | 1215 | WP_064334702 | plasmid replication protein RepC | - |
| shn_RS33210 (shn_33210) | 77507..78529 | - | 1023 | WP_064334703 | plasmid partitioning protein RepB | - |
| shn_RS33215 (shn_33215) | 78526..79740 | - | 1215 | WP_064334742 | plasmid partitioning protein RepA | - |
| shn_RS33220 (shn_33220) | 80129..80752 | + | 624 | WP_064334704 | acyl-homoserine-lactone synthase | - |
| shn_RS33225 (shn_33225) | 80765..81742 | + | 978 | WP_064334705 | P-type conjugative transfer ATPase TrbB | virB11 |
| shn_RS33230 (shn_33230) | 81732..82115 | + | 384 | WP_064334706 | TrbC/VirB2 family protein | virB2 |
| shn_RS33235 (shn_33235) | 82108..82407 | + | 300 | WP_064334707 | conjugal transfer protein TrbD | virB3 |
| shn_RS33240 (shn_33240) | 82417..84873 | + | 2457 | WP_064334708 | conjugal transfer protein TrbE | virb4 |
| shn_RS33245 (shn_33245) | 84845..85648 | + | 804 | WP_064334709 | P-type conjugative transfer protein TrbJ | virB5 |
| shn_RS33250 (shn_33250) | 85642..85818 | + | 177 | WP_064334710 | entry exclusion protein TrbK | - |
| shn_RS33255 (shn_33255) | 85823..87001 | + | 1179 | WP_064334711 | P-type conjugative transfer protein TrbL | virB6 |
| shn_RS33260 (shn_33260) | 87026..87688 | + | 663 | WP_064334712 | conjugal transfer protein TrbF | virB8 |
| shn_RS33265 (shn_33265) | 87706..88518 | + | 813 | WP_064334713 | P-type conjugative transfer protein TrbG | virB9 |
| shn_RS33270 (shn_33270) | 88522..88959 | + | 438 | WP_064334714 | conjugal transfer protein TrbH | - |
| shn_RS35565 | 89026..89706 | + | 681 | Protein_89 | conjugal transfer protein TrbI | - |
| shn_RS33280 (shn_33280) | 89890..90648 | - | 759 | WP_064328977 | IS21-like element helper ATPase IstB | - |
| shn_RS33285 (shn_33285) | 90645..92099 | - | 1455 | WP_084437716 | IS21 family transposase | - |
| shn_RS35570 | 92568..92771 | + | 204 | Protein_92 | transposase | - |
| shn_RS33290 (shn_33290) | 92761..93408 | - | 648 | WP_245337556 | helix-turn-helix domain-containing protein | - |
Host bacterium
| ID | 15107 | GenBank | NZ_CP015745 |
| Plasmid name | pShin-09 | Incompatibility group | - |
| Plasmid size | 127666 bp | Coordinate of oriT [Strand] | 43362..43403 [+] |
| Host baterium | Shinella sp. HZN7 |
Cargo genes
| Drug resistance gene | - |
| Virulence gene | - |
| Metal resistance gene | - |
| Degradation gene | nahM, nahO |
| Symbiosis gene | fixA, fixB, mLTONO_5487 |
| Anti-CRISPR | - |