Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 100031 |
| Name | oriT_F  |
| Organism | Escherichia coli K-12 |
| Sequence Completeness | intact |
| NCBI accession of oriT (coordinates [strand]) | NC_002483 (66118..66407 [-], 290 nt) |
| oriT length | 290 nt |
| IRs (inverted repeats) | 225..232, 235..242 (GCAAAAAC..GTTTTTGC) |
| Location of nic site | 251..252 |
| Conserved sequence flanking the nic site |
GTGGGGTGT|GG |
| Note | (1) The auxiliary protein TraY_F has two binding sites on F plasmid:
① binding to oriT_F promote nicking activity of the relaxase TraI_F prior to conjugative transfer
② binding to Py promoter to up-regulate tra gene expression [PMID:10391902]. (2) During the F plasmid transfer process, the relaxase TraI_F can regulate its initiation and/or termination [PMID:11560509]. |
oriT sequence
Download Length: 290 nt
CGCACCGCTAGCAGCGCCCCTAGCGGTATCCTATAAAAAAACACACCGCGCCGCTAGCAGCACCCCTAATATAAAATAATGTTTTTTATAAAAATAGTCAGTACCACCCCTACAAAACGGTGTCGGCGCGTTGTTGTAGCCGCGCCGACACCGCTTTTTTAAATATCATAAAGAGAGTAAGAGAAACTAATTTTTCATAACACTCTATTTATAAAGAAAAATCAGCAAAAACTTGTTTTTGCGTGGGGTGTGGTGCTTTTGGTGGTGAGAACCACCAACCTGTTGAGCCT
Visualization of oriT structure (The oriT was characterized experimentally)
oriT secondary structure
Predicted by RNAfold.
Download structure file
Reference
[1] de la Cruz F et al. (2010) Conjugative DNA metabolism in Gram-negative bacteria. FEMS Microbiol Rev. 34(1):18-40. [PMID:19919603]
[2] Frost LS et al. (1994) Analysis of the sequence and gene products of the transfer region of the F sex factor. Microbiol Rev. 58(2):162-210. [PMID:7915817]
Relaxosome
This oriT is a component of a relaxosome.
| Relaxosome name | RelaxosomeF |
| oriT | oriT_F |
| Relaxase | TraI_F (MOBF) |
| Auxiliary protein | TraM_F , TraY_F , IHF_F |
Reference
[1] de la Cruz F et al. (2010) Conjugative DNA metabolism in Gram-negative bacteria. FEMS Microbiol Rev. 34(1):18-40. [PMID:19919603]
[2] Jun Lu et al. (2008) Structural basis of specific TraD-TraM recognition during F plasmid-mediated bacterial conjugation. Molecular microbiology. 70(1):89-99. [PMID:18717787]
[3] Heather Ragonese et al. (2007) The F plasmid-encoded TraM protein stimulates relaxosome-mediated cleavage at oriT through an interaction with TraI. Molecular microbiology. 63(4):1173-84. [PMID:17238924]
[4] R A Fekete et al. (2000) Mobilization of chimeric oriT plasmids by F and R100-1: role of relaxosome formation in defining plasmid specificity. Journal of bacteriology. 182(14):4022-7. [PMID:10869081]
[5] M T Howard et al. (1995) Stepwise assembly of a relaxosome at the F plasmid origin of transfer. The Journal of biological chemistry. 270(47):28381-6. [PMID:7499340]
[6] Frost LS et al. (1994) Analysis of the sequence and gene products of the transfer region of the F sex factor. Microbiol Rev. 58(2):162-210. [PMID:7915817]
Relaxase
| ID | 30 | GenBank | BAA97974 |
| Name | TraI_F |
UniProt ID | P14565 |
| Length | 1756 a.a. | PDB ID | |
| Note | (1) The auxiliary protein TraY_F has two binding sites on F plasmid:
binding to oriT_F promote nicking activity of the relaxase TraI_F prior to conjugative transfer
binding to Py promoter to up-regulate tra gene expression [PMID:10391902]. (2) During the F plasmid transfer process, the relaxase TraI_F can regulate its initiation and/or termination [PMID:11560509]. |
||
Relaxase protein sequence
Download Length: 1756 a.a. Molecular weight: 192015.91 Da Isoelectric Point: 5.8951
MMSIAQVRSAGSAGNYYTDKDNYYVLGSMGERWAGRGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQ
DGSNRHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQEPQLHTHAVVANVTQHNGEWKTLSSDKVGKTGFIENVYANQIAFGRLYREKLKEQVEA
LGYETEVVGKHGMWEMPGVPVEAFSGRSQTIREAVGEDASLKSRDVAALDTRKSKQHVDPEIKMAEWMQT
LKETGFDIRAYRDAADQRADLRTLTPGPASQDGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE
NGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS
DAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMAREQGREVQIIAADRRSQMNMKQDERLSGELITGR
RQLLEGMAFTPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKDAGVNTYRW
QGGEQRPATIISEPDRNVRYARLAGDFAASVKAGEESVAQVSGVREQAILTQAIRSELKTQGVLGLPEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDAQGETQVVRISSLDS
SWSLFRPEKMPVADGERLRVTGKIPGLRVSGGDRLQVASVSEDAMTVVVPGRAEPATLPVSDSPFTALKL
ENGWVETPGHSVSDSATVFASVTQMAMDNATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI
KTRAGETSLETAISHQKSALHTPAQQAIHLALPVVESKKLAFSMVDLLTEAKSFAAEGTGFTELGGEINA
QIKRGDLLYVDVAKGYGTGLLVSRASYEAEKSILRHILEGKEAVMPLMERVPGELMEKLTSGQRAATRMI
LETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPESERPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT
QLQQRSGETPDFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA
ADVAIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRQEGAWAPEHSVTEFSHSQEAKLAEA
QQKAMLKGEAFPDVPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDVREKAGELGKEQVM
VPVLNTANIRDGELRRLSTWETHRDALVLVDNVYHRIAGISKDDGLITLQDAEGNTRLISPREAVAEGVT
LYTPDTIRVGTGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGQQTREIRPGQEQAEQHIDLAYAI
TAHGAQGASETFAIALEGTEGNRKLMAGFESAYVALSRMKQHVQVYTDNRQGWTDAINNAVQKGTAHDVF
EPKPDREVMNAERLFSTARELRDVAAGRAVLRQAGLAGGDSPARFIAPGRKYPQPYVALPAFDRNGKSAG
IWLNPLTTDDGNGLRGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGVVVRIAGE
GRPWNPGAITGGRVWGDIPDNSVQPGAGNGEPVTAEVLAQRQAEEAIRRETERRADEIVRKMAENKPDLP
DGKTEQAVREIAGQERDRAAITEREAALPEGVLREPQRVREAVREIARENLLQERLQQMERDMVRDLQKE
KTLGGD
Protein domains
Predicted by InterproScan.
Protein structure
| Source | ID | Structure |
|---|---|---|
| PDB | 2Q7T | |
| PDB | 2Q7U | |
| PDB | 1P4D | |
| PDB | 2A0I | |
| PDB | 2L8B | |
| PDB | 3FLD | |
| AlphaFold DB | P14565 |
Reference
[1] de la Cruz F et al. (2010) Conjugative DNA metabolism in Gram-negative bacteria. FEMS Microbiol Rev. 34(1):18-40. [PMID:19919603]
[2] Frost LS et al. (1994) Analysis of the sequence and gene products of the transfer region of the F sex factor. Microbiol Rev. 58(2):162-210. [PMID:7915817]
Auxiliary protein
| ID | 46 | GenBank | NP_061450 |
| Name | TraM_F |
UniProt ID | P10026 |
| Length | 127 a.a. | PDB ID | 2G7O, 2G9E, 4QPO, 4QPQ |
| Note | _ | ||
Auxiliary protein sequence
Download Length: 127 a.a. Molecular weight: 14507.44 Da Isoelectric Point: 5.0516
MAKVNLYISNDAYEKINAIIEKRRQEGAREKDVSFSATASMLLELGLRVHEAQMERKESAFNQTEFNKLL
LECVVKTQSSVAKILGIESLSPHVSGNSKFEYANMVEDIREKVSSEMERFFPKNDDE
Protein domains
Predicted by InterproScan.
Protein structure
| Source | ID | Structure |
|---|---|---|
| PDB | 2G7O | |
| PDB | 2G9E | |
| PDB | 4QPO | |
| PDB | 4QPQ | |
| AlphaFold DB | P10026 |
Reference
[1] de la Cruz F et al. (2010) Conjugative DNA metabolism in Gram-negative bacteria. FEMS Microbiol Rev. 34(1):18-40. [PMID:19919603]
[2] Frost LS et al. (1994) Analysis of the sequence and gene products of the transfer region of the F sex factor. Microbiol Rev. 58(2):162-210. [PMID:7915817]
| ID | 47 | GenBank | NP_061452 |
| Name | TraY_F |
UniProt ID | P06627 |
| Length | 131 a.a. | PDB ID | _ |
| Note | The auxiliary protein TraY_F has two binding sites on F plasmid: binding to oriT_F promote nicking activity of the relaxase TraI_F prior to conjugative transfer binding to Py promoter to up-regulate tra gene expression [PMID:10391902]. | ||
Auxiliary protein sequence
Download Length: 131 a.a. Molecular weight: 15183.38 Da Isoelectric Point: 9.9240
MKRFGTRSATGKMVKLKLPVDVESLLIEASNRSGRSRSFEAVIRLKDHLHRYPKFNRAGNIYGKSLVKYL
TMRLDDETNQLLIAAKNRSGWCKTDEAADRVIDHLIKFPDFYNSEIFREADKEEDITFNTL
Protein domains
Predicted by InterproScan.
Protein structure
| Source | ID | Structure |
|---|---|---|
| AlphaFold DB | P06627 |
Reference
[1] de la Cruz F et al. (2010) Conjugative DNA metabolism in Gram-negative bacteria. FEMS Microbiol Rev. 34(1):18-40. [PMID:19919603]
[2] Frost LS et al. (1994) Analysis of the sequence and gene products of the transfer region of the F sex factor. Microbiol Rev. 58(2):162-210. [PMID:7915817]
T4CP
| ID | 30 | GenBank | BAA97972 |
| Name | TraD_F |
UniProt ID | P09130 |
| Length | 717 a.a. | PDB ID | 3D8A |
| Note | BAA97972 traD (plasmid) [Escherichia coli K-12]. | ||
T4CP protein sequence
Download Length: 717 a.a. Molecular weight: 81488.99 Da Isoelectric Point: 5.0504
MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILVGLVLWIKISWQTFVNGCIYWWCTTLEGMR
DLIKSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCSEQLWSAFVLAAVVALVICLITFFVVSWILGRQGKQ
QSENEVTGGRQLTDNPKDVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
QRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTYLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGEPFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAASLFDVMNTRAFFRSPSHKIA
EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQTRPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFEPDVPEVVSGEDVTQAEQPQQPVSPAI
NDKKSDSGVNVPAGGIEQELKMKPEEEMEQQLPPGISESGEVVDMAAYEAWQQENHPDIQQQMQRREEVN
INVHRERGEDVEPGDDF
Protein domains
Predicted by InterproScan.
Protein structure
| Source | ID | Structure |
|---|---|---|
| PDB | 3D8A | |
| AlphaFold DB | P09130 |
Reference
[1] de la Cruz F et al. (2010) Conjugative DNA metabolism in Gram-negative bacteria. FEMS Microbiol Rev. 34(1):18-40. [PMID:19919603]
[2] Frost LS et al. (1994) Analysis of the sequence and gene products of the transfer region of the F sex factor. Microbiol Rev. 58(2):162-210. [PMID:7915817]
[3] Cabezón E et al. (1994) Requirements for mobilization of plasmids RSF1010 and ColE1 by the IncW plasmid R388: trwB and RP4 traG are interchangeable. J Bacteriol. 176(14):4455-8. [PMID:8021231]
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 65556..91957
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| HXF02_RS00295 (D616_p97097) | 61551..61985 | + | 435 | WP_010892539 | conjugation system SOS inhibitor PsiB | - |
| HXF02_RS00300 (D616_p97098) | 61982..62744 | + | 763 | Protein_60 | plasmid SOS inhibition protein A | - |
| HXF02_RS00530 | 62918..63067 | + | 150 | Protein_61 | DUF5431 family protein | - |
| HXF02_RS00305 (D616_p97103) | 63009..63134 | + | 126 | WP_096937776 | type I toxin-antitoxin system Hok family toxin | - |
| HXF02_RS00310 (D616_p97004) | 63435..63732 | - | 298 | Protein_63 | hypothetical protein | - |
| HXF02_RS00320 (D616_p97003) | 64032..64319 | + | 288 | WP_000107542 | hypothetical protein | - |
| HXF02_RS00325 (D616_p97002) | 64438..65259 | + | 822 | WP_001234417 | DUF932 domain-containing protein | - |
| HXF02_RS00330 (D616_p97001) | 65556..66158 | - | 603 | WP_000243701 | transglycosylase SLT domain-containing protein | virB1 |
| HXF02_RS00335 (D616_p97066) | 66479..66862 | + | 384 | WP_001151527 | conjugal transfer relaxosome DNA-binding protein TraM | - |
| HXF02_RS00340 (D616_p97072) | 67049..67738 | + | 690 | WP_000283385 | conjugal transfer transcriptional regulator TraJ | - |
| HXF02_RS00345 (D616_p97057) | 67831..68232 | + | 402 | WP_001369361 | conjugal transfer relaxosome DNA-bindin protein TraY | - |
| HXF02_RS00350 (D616_p97080) | 68265..68630 | + | 366 | WP_000994779 | type IV conjugative transfer system pilin TraA | - |
| HXF02_RS00355 (D616_p97069) | 68645..68956 | + | 312 | WP_000012106 | type IV conjugative transfer system protein TraL | traL |
| HXF02_RS00360 (D616_p97074) | 68978..69544 | + | 567 | WP_000399792 | type IV conjugative transfer system protein TraE | traE |
| HXF02_RS00365 (D616_p97071) | 69531..70259 | + | 729 | WP_001230787 | type-F conjugative transfer system secretin TraK | traK |
| HXF02_RS00370 (D616_p97076) | 70259..71686 | + | 1428 | WP_000146685 | F-type conjugal transfer pilus assembly protein TraB | traB |
| HXF02_RS00375 (D616_p97064) | 71676..72266 | + | 591 | WP_000002792 | conjugal transfer pilus-stabilizing protein TraP | - |
| HXF02_RS00380 (D616_p97051) | 72259..72450 | + | 192 | WP_001345835 | conjugal transfer protein TrbD | - |
| HXF02_RS00385 (D616_p97049) | 72462..72713 | + | 252 | WP_001038342 | conjugal transfer protein TrbG | - |
| HXF02_RS00390 (D616_p97059) | 72710..73225 | + | 516 | WP_010892541 | type IV conjugative transfer system lipoprotein TraV | traV |
| HXF02_RS00395 (D616_p97062) | 73360..73581 | + | 222 | WP_001278689 | conjugal transfer protein TraR | - |
| HXF02_RS00400 (D616_p97075) | 73741..76368 | + | 2628 | WP_001064243 | type IV secretion system protein TraC | virb4 |
| HXF02_RS00405 (D616_p97048) | 76365..76751 | + | 387 | WP_000099690 | type-F conjugative transfer system protein TrbI | - |
| HXF02_RS00410 (D616_p97058) | 76748..77380 | + | 633 | WP_001203720 | type-F conjugative transfer system protein TraW | traW |
| HXF02_RS00415 (D616_p97061) | 77377..78369 | + | 993 | WP_000830185 | conjugal transfer pilus assembly protein TraU | traU |
| HXF02_RS00420 (D616_p97053) | 78378..79016 | + | 639 | WP_000777688 | type-F conjugative transfer system pilin assembly protein TrbC | trbC |
| HXF02_RS00425 (D616_p97065) | 79013..80821 | + | 1809 | WP_000821835 | type-F conjugative transfer system mating-pair stabilization protein TraN | traN |
| HXF02_RS00430 (D616_p97050) | 80848..81105 | + | 258 | WP_000864318 | conjugal transfer protein TrbE | - |
| HXF02_RS00435 (D616_p97073) | 81098..81841 | + | 744 | WP_001030367 | type-F conjugative transfer system pilin assembly protein TraF | traF |
| HXF02_RS00440 (D616_p97055) | 81857..82204 | + | 348 | WP_001287913 | conjugal transfer protein TrbA | - |
| HXF02_RS00445 (D616_p97107) | 82206..82520 | - | 315 | WP_000415566 | protein ArtA | - |
| HXF02_RS00450 (D616_p97070) | 82601..82885 | + | 285 | WP_000624109 | type-F conjugative transfer system pilin chaperone TraQ | - |
| HXF02_RS00455 (D616_p97060) | 82872..83417 | + | 546 | WP_000059850 | type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB | traF |
| HXF02_RS00460 (D616_p97052) | 83347..83688 | + | 342 | WP_001443031 | P-type conjugative transfer protein TrbJ | - |
| HXF02_RS00465 (D616_p97056) | 83675..84055 | + | 381 | WP_001366201 | F-type conjugal transfer protein TrbF | - |
| HXF02_RS00470 (D616_p97078) | 84055..85428 | + | 1374 | WP_021553026 | conjugal transfer pilus assembly protein TraH | traH |
| HXF02_RS00475 (D616_p97079) | 85425..88241 | + | 2817 | WP_001007055 | conjugal transfer mating-pair stabilization protein TraG | traG |
| HXF02_RS00480 (D616_p97068) | 88274..88795 | + | 522 | WP_000632670 | conjugal transfer entry exclusion protein TraS | - |
| HXF02_RS00485 (D616_p97067) | 88820..89551 | + | 732 | WP_000850422 | conjugal transfer complement resistance protein TraT | - |
| HXF02_RS00490 (D616_p97082) | 89804..91957 | + | 2154 | WP_000009350 | type IV conjugative transfer system coupling protein TraD | virb4 |
| HXF02_RS00495 | 91966..92364 | - | 399 | WP_000911324 | type II toxin-antitoxin system VapC family toxin | - |
| HXF02_RS00500 | 92364..92591 | - | 228 | WP_000450532 | toxin-antitoxin system antitoxin VapB | - |
Host bacterium
| ID | 30 | GenBank | NC_002483 |
| Plasmid name | F plasmid | Incompatibility group | IncFIC |
| Plasmid size | 99159 bp | Coordinate of oriT [Strand] | 66118..66407 [-] |
| Host baterium | Escherichia coli K-12 |
Cargo genes
| Drug resistance gene | - |
| Virulence gene | - |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |