Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 103317 |
| Name | oriT_pIBACIncN  |
| Organism | Citrobacter freundii strain AA535 |
| Sequence Completeness | - |
| NCBI accession of oriT (coordinates [strand]) | NZ_MH536949 (30848..30947 [+], 100 nt) |
| oriT length | 100 nt |
| IRs (inverted repeats) | 77..82, 90..95 (AAAAAA..TTTTTT) 78..83, 90..95 (AAAAAA..TTTTTT) 79..84, 90..95 (AAAAAA..TTTTTT) 20..26, 38..44 (TAAATCA..TGATTTA) |
| Location of nic site | 62..63 |
| Conserved sequence flanking the nic site |
GGTGTATAGC |
| Note | Predicted by oriTfinder 2.0 |
oriT sequence
Download Length: 100 nt
>oriT_pIBACIncN
TATTTATTTTTTTATCTTTTAAATCAGTACGATAGCGTGATTTATCGCGCTGCGTTAGGTGTATAGCAGGTTAAGGAAAAAAAATCATCTTTTTTGGTAG
TATTTATTTTTTTATCTTTTAAATCAGTACGATAGCGTGATTTATCGCGCTGCGTTAGGTGTATAGCAGGTTAAGGAAAAAAAATCATCTTTTTTGGTAG
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 2477 | GenBank | WP_012561142 |
| Name | TrwC_HTT39_RS00165_pIBACIncN |
UniProt ID | A0A1S6KKJ9 |
| Length | 1078 a.a. | PDB ID | |
| Note | Predicted by oriTfinder 2.0 | ||
Relaxase protein sequence
Download Length: 1078 a.a. Molecular weight: 120195.37 Da Isoelectric Point: 6.5230
>WP_012561142.1 MULTISPECIES: MobF family relaxase [Enterobacterales]
MLDITTITRQNVTSVVGYYSDAKDDYYSKDSSFTSWQGTGAEALGLSGDVESARFKELLVGEIDTFTHMQ
RHVGDAKKERLGYDLTFSAPKGVSMQALIHGDKTIIEAHEKAVAAAVREAEKLAQARTTRQGKSVTQNTN
NLVVATFRHETSRALDPDLHTHAFVMNMTQREDGQWRALKNDELMRNKMHLGDVYKQELALELTKAGYEL
RYNSKNNTFDMAHFSDEQIRAFSRRSEQIEKGLAAMGLTRETADAQTKSRVSMATREKKTEHSREEIHQE
WASRAKTLGIDFDNREWQGHGKPLEADIARNMAPDFTSPEVKADRAIQFAVKSLSERDASFERQKLIQIA
NKQVLGHATIADVEKAYLKAVQKGAIIEGEARYQSTLKVGASVMAETLTRKEWIDSLTNSGMRADKARFA
VDDGIKNGRLKKTSHRVTTVEGIRLERSILTIESRGRGQMPRQLTAEIAGQLLAGKTLKKEQMRAVTEIV
TSKDRFVAAHGYAGTGKSYMTMAAKELLESQGLKVTALAPYGTQKKALEDDGLPARTVAAFLKAKDKKLD
EKSVVFIDEAGVIPARQMKQLMEVIEKHNARAVFLGDTSQTKAVEAGKPFEQLIKADMQTSYMKDIQRQK
NEVLLEAVKYAAEGNAARALKNITGVNELKEEAPRLAQLADRYLSLSSEQQDATLIISGTNASRKTLNDY
IRGNLGLAGTGETFTLLDRVDSTQAERRDSRYFSKGQIIIPEQDYKNGMKRGESYQVLDTGPGNKLTVES
SSGEQIAFSPRTHTKLSVYQAVSAELAPGDKVMVTRNDKTLDVANGDRFTVKTVEGEKLTLEDKKGRTVE
LDKKQASYLSYAYATTVHKSQGLTCDRVLFNIDTKSLTTSKDVFYVGISRARHEVEIFTDDKKSLASSVS
RDSPKTTAAEIDRFFGLEARFKDIGRDTSLETRSAEKGLPEATGESMAFNQKPDEHNMTTGTDYQPVSNA
EDAFHLKQNPMDDSVGLRRHEAQQNDAELAHDYAAADDQQWSAQEYADYEHYAEASDYDFDSSIYDDYAM
PQTSQAEQSHTGKEHTHEHEHEEGGHEI
MLDITTITRQNVTSVVGYYSDAKDDYYSKDSSFTSWQGTGAEALGLSGDVESARFKELLVGEIDTFTHMQ
RHVGDAKKERLGYDLTFSAPKGVSMQALIHGDKTIIEAHEKAVAAAVREAEKLAQARTTRQGKSVTQNTN
NLVVATFRHETSRALDPDLHTHAFVMNMTQREDGQWRALKNDELMRNKMHLGDVYKQELALELTKAGYEL
RYNSKNNTFDMAHFSDEQIRAFSRRSEQIEKGLAAMGLTRETADAQTKSRVSMATREKKTEHSREEIHQE
WASRAKTLGIDFDNREWQGHGKPLEADIARNMAPDFTSPEVKADRAIQFAVKSLSERDASFERQKLIQIA
NKQVLGHATIADVEKAYLKAVQKGAIIEGEARYQSTLKVGASVMAETLTRKEWIDSLTNSGMRADKARFA
VDDGIKNGRLKKTSHRVTTVEGIRLERSILTIESRGRGQMPRQLTAEIAGQLLAGKTLKKEQMRAVTEIV
TSKDRFVAAHGYAGTGKSYMTMAAKELLESQGLKVTALAPYGTQKKALEDDGLPARTVAAFLKAKDKKLD
EKSVVFIDEAGVIPARQMKQLMEVIEKHNARAVFLGDTSQTKAVEAGKPFEQLIKADMQTSYMKDIQRQK
NEVLLEAVKYAAEGNAARALKNITGVNELKEEAPRLAQLADRYLSLSSEQQDATLIISGTNASRKTLNDY
IRGNLGLAGTGETFTLLDRVDSTQAERRDSRYFSKGQIIIPEQDYKNGMKRGESYQVLDTGPGNKLTVES
SSGEQIAFSPRTHTKLSVYQAVSAELAPGDKVMVTRNDKTLDVANGDRFTVKTVEGEKLTLEDKKGRTVE
LDKKQASYLSYAYATTVHKSQGLTCDRVLFNIDTKSLTTSKDVFYVGISRARHEVEIFTDDKKSLASSVS
RDSPKTTAAEIDRFFGLEARFKDIGRDTSLETRSAEKGLPEATGESMAFNQKPDEHNMTTGTDYQPVSNA
EDAFHLKQNPMDDSVGLRRHEAQQNDAELAHDYAAADDQQWSAQEYADYEHYAEASDYDFDSSIYDDYAM
PQTSQAEQSHTGKEHTHEHEHEEGGHEI
Protein domains
Predicted by InterproScan.
Protein structure
| Source | ID | Structure |
|---|---|---|
| AlphaFold DB | A0A1S6KKJ9 |
Auxiliary protein
| ID | 1065 | GenBank | WP_001749975 |
| Name | WP_001749975_pIBACIncN |
UniProt ID | A0A5C2CVS6 |
| Length | 138 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
Auxiliary protein sequence
Download Length: 138 a.a. Molecular weight: 15332.60 Da Isoelectric Point: 5.9670
>WP_001749975.1 MULTISPECIES: hypothetical protein [Gammaproteobacteria]
MPIITAKVSDELLAYIDLVSGGNRSDYLRRCIEAGPGDRESGLKIVADRLSDVNRKLDYLFDRASDADFG
PLRDELKAITETLSGVKFPPAGQMMLHESLAIETLILLRSIAEPGKTKAAKAEVERNGYKVWEPKKER
MPIITAKVSDELLAYIDLVSGGNRSDYLRRCIEAGPGDRESGLKIVADRLSDVNRKLDYLFDRASDADFG
PLRDELKAITETLSGVKFPPAGQMMLHESLAIETLILLRSIAEPGKTKAAKAEVERNGYKVWEPKKER
Protein domains
No domain identified.
Protein structure
| Source | ID | Structure |
|---|---|---|
| AlphaFold DB | A0A5C2CVS6 |
T4CP
| ID | 2261 | GenBank | WP_000342688 |
| Name | t4cp2_HTT39_RS00170_pIBACIncN |
UniProt ID | _ |
| Length | 509 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
T4CP protein sequence
Download Length: 509 a.a. Molecular weight: 57762.87 Da Isoelectric Point: 9.6551
>WP_000342688.1 MULTISPECIES: type IV secretion system DNA-binding domain-containing protein [Enterobacterales]
MDDRERGLAFLFAITLPPVMVWFLVAKFTYGIDPSTAKYLIPYLVKNTFSLWPLWSALIAGWFIGVGGLI
AFIIYDKSRVFKGERFKKIYRGTELVRARTLADKTRERGVNQLTVANIPIPTYAENLHFSIAGTTGTGKT
TIFNELLFKSIIRGGKNIALDPNGGFLKNFYRPGDVILNAYDKRTEGWVFFNEIRRSYDYERLVNSIVQE
SPDMATEEWFGYGRLIFSEVSKKLHSLYSTVTMEEVIHWACNVDQKKLKEFLMGTPAEAIFSGSEKAVGS
ARFVLSKNLAPHLKMPEGNFSLRDWLDDGKPGTLFITWQEEMKRSLNPLISCWLDSIFSIVLGMGEKESR
INVFIDELESLQFLPNLNDALTKGRKSGLCVYAGYQTYSQLVKVYGRDMAQTILANMRSNIVLGGSRLGD
ETLDQMSRSLGEIEGEVERKESDPQKPWIVRKRRDVKVVRAVTPTEISMLPNLTGYLALPGDMPVAKFKA
KHVKYHRKNPVPGIELREI
MDDRERGLAFLFAITLPPVMVWFLVAKFTYGIDPSTAKYLIPYLVKNTFSLWPLWSALIAGWFIGVGGLI
AFIIYDKSRVFKGERFKKIYRGTELVRARTLADKTRERGVNQLTVANIPIPTYAENLHFSIAGTTGTGKT
TIFNELLFKSIIRGGKNIALDPNGGFLKNFYRPGDVILNAYDKRTEGWVFFNEIRRSYDYERLVNSIVQE
SPDMATEEWFGYGRLIFSEVSKKLHSLYSTVTMEEVIHWACNVDQKKLKEFLMGTPAEAIFSGSEKAVGS
ARFVLSKNLAPHLKMPEGNFSLRDWLDDGKPGTLFITWQEEMKRSLNPLISCWLDSIFSIVLGMGEKESR
INVFIDELESLQFLPNLNDALTKGRKSGLCVYAGYQTYSQLVKVYGRDMAQTILANMRSNIVLGGSRLGD
ETLDQMSRSLGEIEGEVERKESDPQKPWIVRKRRDVKVVRAVTPTEISMLPNLTGYLALPGDMPVAKFKA
KHVKYHRKNPVPGIELREI
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 2665..12994
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| HTT39_RS00285 | 917..1177 | - | 261 | WP_016359294 | hypothetical protein | - |
| HTT39_RS00015 | 1233..1544 | - | 312 | WP_013279382 | hypothetical protein | - |
| HTT39_RS00020 | 1580..1894 | - | 315 | WP_016338363 | TrbM/KikA/MpfK family conjugal transfer protein | - |
| HTT39_RS00025 | 1891..2235 | - | 345 | WP_012561155 | hypothetical protein | - |
| HTT39_RS00030 | 2251..2628 | - | 378 | WP_193567606 | H-NS family nucleoid-associated regulatory protein | - |
| HTT39_RS00035 | 2665..3402 | + | 738 | WP_013279384 | lytic transglycosylase domain-containing protein | virB1 |
| HTT39_RS00040 | 3411..3692 | + | 282 | WP_016338364 | transcriptional repressor KorA | - |
| HTT39_RS00045 | 3702..3995 | + | 294 | WP_001749962 | hypothetical protein | virB2 |
| HTT39_RS00050 | 4046..4363 | + | 318 | WP_000496058 | VirB3 family type IV secretion system protein | virB3 |
| HTT39_RS00055 | 4363..6963 | + | 2601 | WP_012561149 | VirB4 family type IV secretion/conjugal transfer ATPase | virb4 |
| HTT39_RS00060 | 6981..7694 | + | 714 | WP_001749960 | type IV secretion system protein | virB5 |
| HTT39_RS00065 | 7702..7929 | + | 228 | WP_001749959 | IncN-type entry exclusion lipoprotein EexN | - |
| HTT39_RS00070 | 7945..8985 | + | 1041 | WP_001749958 | type IV secretion system protein | virB6 |
| HTT39_RS00075 | 9056..9214 | + | 159 | WP_012561180 | hypothetical protein | - |
| HTT39_RS00080 | 9204..9902 | + | 699 | WP_000646594 | type IV secretion system protein | virB8 |
| HTT39_RS00085 | 9913..10797 | + | 885 | WP_000735066 | TrbG/VirB9 family P-type conjugative transfer protein | virB9 |
| HTT39_RS00090 | 10797..11957 | + | 1161 | WP_000101710 | type IV secretion system protein VirB10 | virB10 |
| HTT39_RS00095 | 11999..12994 | + | 996 | WP_012561144 | ATPase, T2SS/T4P/T4SS family | virB11 |
| HTT39_RS00100 | 12994..13098 | + | 105 | Protein_19 | phospholipase D family protein | - |
| HTT39_RS00105 | 13450..14769 | + | 1320 | WP_004152397 | IS1182-like element ISKpn6 family transposase | - |
| HTT39_RS00110 | 15019..15900 | - | 882 | WP_004199234 | carbapenem-hydrolyzing class A beta-lactamase KPC-2 | - |
| HTT39_RS00115 | 16027..16806 | - | 780 | WP_004152394 | IS21-like element ISKpn7 family helper ATPase IstB | - |
| HTT39_RS00120 | 16803..17828 | - | 1026 | WP_004199214 | IS21 family transposase | - |
Host bacterium
| ID | 3760 | GenBank | NZ_MH536949 |
| Plasmid name | pIBACIncN | Incompatibility group | IncN |
| Plasmid size | 49804 bp | Coordinate of oriT [Strand] | 30848..30947 [+] |
| Host baterium | Citrobacter freundii strain AA535 |
Cargo genes
| Drug resistance gene | blaKPC-2 |
| Virulence gene | - |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |