Detailed information of oriT
oriT
The information of the oriT region
oriTDB ID | 104974 |
Name | oriT_pSalMiami |
Organism | Salmonella enterica subsp. enterica strain BAA-1586 |
Sequence Completeness | - |
NCBI accession of oriT (coordinates [strand]) | NZ_CP023469 (61541..61810 [+], 270 nt) |
oriT length | 270 nt |
IRs (inverted repeats) | 245..253, 262..270 (CACCCCTGG..CCAGGGGTG) 92..98, 111..117 (ATTTAAT..ATTAAAT) 103..108, 111..116 (TTTAAT..ATTAAA) 31..38, 41..48 (GCAAAATT..AATTTTGC) |
Location of nic site | _ |
Conserved sequence flanking the nic site |
_ |
Note | Predicted by oriTfinder 2.0 |
oriT sequence
Download Length: 270 nt
GTCCTCACCACCAAAAGCACCACACCCCACGCAAAATTAAAATTTTGCTGATTTGTTTTTAGTAACAGTGAGTTATGTTCATAATAATGTAATTTAATTTATTTTAATGTATTAAATAGCGGTGCAGGCACGTCGCCGGCACCGCTATGACGACGCTATACAGGGGTAGTACTGACTATTTTTATAAAAAACATTGCATTATATCAGGGGCGCTGCTAGCGTCGCTGTGCCTGTTTTTAAGTAACACCCCTGGGGGCGCTGCCAGGGGTG
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure fileRelaxase
ID | 3494 | GenBank | WP_117338900 |
Name | traI_COO54_RS24070_pSalMiami | UniProt ID | _ |
Length | 1752 a.a. | PDB ID | |
Note | Predicted by oriTfinder 2.0 |
Relaxase protein sequence
Download Length: 1752 a.a. Molecular weight: 191392.56 Da Isoelectric Point: 5.8093
MMSIAQVRSAGSAAGYYSDRDNYYVLGSLEERWAGKGAEQLGLQGAVDKEVFTRELEGRLPDGADLSRQQ
DGGNKHRPGYDLTFSAPKSVSLMAMLAGDKRLTEAHNQAVDIAVRQVEAMASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQEPQLHTHAVVANVTLHDGEWKTLSSDKVGKTGFIENVYANQIAFGKIYRAVLKEKVEA
LGYETEVVGKHGMWEMPGVPVEAFSSRSQAIREAVGEDASLKSRDVAALDTRKSKQHVDPEVKMAEWMQT
LKDTGFDISAYREAADRRAEIQAAQPVPSQEQPDIQQAVTQAIAGLSDRKVQFTYTDVLARTVGMLPPEA
GVIEKARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSSDIMKQNRVTVHPEKSVPRTGSYSD
AVSVLAQDRPSLAIISGQGGAAGQRERVAELTMMAREQGREVQIIAADRRSQMNLKQDERLSGELITGRR
QLQEGMTFSPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKEAGVNSYRWQ
GRQQTPATVISEPDRNVRYARLAGDFVAAVKAGEESVAQVSGVREQAILAGMIRSELKTQGILGQQDTMM
TALSPVWLDSRNRYLRDMYREGMVMEQWNPEKRSHDRYVIDRVAAQSHSLTLRDAQRGTQMVRISALDSS
WSLFRPEKIPVADGERLMVTGKIPGLLVSGGDRLQVSAVNDGMMTVIVPGRAELASLPVGDSPFTALKLE
NGWVETPGHSVSDSAKVFASVTQMAMDNATLNGLARSGRDVRLYSSLDETRTAEKISRHPSFTVVSEQIK
ARAGEVSLETAISLQKAGLHTPAQQAIHLALPVVESKNLAFSQVELLTEAKSFAAEGTGFADLGREIDAQ
IKRGDLLHVDVAKGYGTDLLVSRASYEAEKSILRHILEGKEAVTPLMERVPGELMETLTSGQRATTRMIL
ETKDRFTVVQGYAGGGKTTQFRAVMSAVNLLPENERPHVVGLGPTHRAVGEMRSAGVEAQTLASFLHDTQ
LQQRSGETPDFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSAA
DVAIMKEIVRQTPELRDAVYSLINRDVNKALSGLENVKPVQIPRLKGVWAPENSVTEFSRLQERELAEAA
QEAEKKGEAFPDVPVTLYEAIVRDYTGRTPDAREQTLIVTHLNADRRVLNSMIQDALAKPGEQQVTVPVL
TTANIRDGELRRLSTWEAHPGALALVDNVYHRIAGISKEDGLITLEDKAGNTRLISPREAAAEGVTLYNP
ETIRVGAGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGKQTRVVRPGQDRAEQHIDLAYAITAHG
AQGASETFAIALEGTEGGRKQMAGFESAYVALSRMKQHVQVYTDDRQGWVKAINSAEQKGTAHDVLEPKS
EREMMNAERLFRIARELRDVAAGRAVLRNAGLAQGDSRARFIAPGRKYPQPYVALPAFDRNGKSAGIWLN
PLTTDDGAGLRGFSGEGRVKGSEEAQFVVLQGSRNGESLLADNMQEGVRIARDNPDSGVVVRIAGDGRPW
NPGAITGGRVWGDIPDSSVQPGAGNGEPVTAEILAQRQAEEAVCRETEQRAAEIVRKMAEDKPDLPEEKT
AQAVREIAGQEQDRMTPPERETPLPESVLREPVRERETIREVARENRVRERLQQMEQEMVRDLQKEKTPG
GD
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
Auxiliary protein
ID | 1554 | GenBank | WP_001151546 |
Name | WP_001151546_pSalMiami | UniProt ID | Q93GP1 |
Length | 126 a.a. | PDB ID | _ |
Note | Predicted by oriTfinder 2.0 |
Auxiliary protein sequence
Download Length: 126 a.a. Molecular weight: 14366.30 Da Isoelectric Point: 5.7236
MAKVNVYISNEVHNKITAIVEKRRQEGARDKDISFSGTSSMLLELGLRVYEAQMERKESPFNQTEFNKVL
LENVLKTQSSVAKILGIGSLSPHVAGNPKFEYANMVEDIKEKVSSEMERFFHENEE
Protein domains
Predicted by InterproScan.
Protein structure
Source | ID | Structure |
---|---|---|
AlphaFold DB | Q93GP1 |
ID | 1555 | GenBank | WP_001676655 |
Name | WP_001676655_pSalMiami | UniProt ID | H3JT82 |
Length | 75 a.a. | PDB ID | _ |
Note | Predicted by oriTfinder 2.0 |
Auxiliary protein sequence
Download Length: 75 a.a. Molecular weight: 9147.26 Da Isoelectric Point: 9.6183
MRRRNAREGISRTVSVYLDEDTNNRLIRAKDRSGRSKTIEVQIRLRDHLKRYPDFYNEEIFREVIEETES
TFKEI
Protein domains
Predicted by InterproScan.
Protein structure
Source | ID | Structure |
---|---|---|
AlphaFold DB | H3JT82 |
T4CP
ID | 3441 | GenBank | WP_117338895 |
Name | traC_COO54_RS23985_pSalMiami | UniProt ID | _ |
Length | 882 a.a. | PDB ID | _ |
Note | Predicted by oriTfinder 2.0 |
T4CP protein sequence
Download Length: 882 a.a. Molecular weight: 100386.16 Da Isoelectric Point: 6.6137
MKNLLDTVTQAANSLLTALKLPDESAQANQILGEMSFPQFSRLLPYRDYNQESGLFMNDATMGFMLEATP
VNGANETIALSLDHLLRTKLPRGIPLCVHLMSSQLVGERIEYGLREFSWSGEQAERFNAITRAYYMKAAE
THFPLPEGMNLPLTLRHYRVFISYCAPSRKKSRTDILEMENLVKIIRASLQGAYISTQTVDAKAFINIVG
EMINHNPESLHPTRRRLDPYSDLNYQCVDDSFDLKVRQDYLTLGLRDNGKNSTARIMSFHLARNPEIAFL
WNSADNYSNLLNPELSISCPFILTLTLVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWGD
LRQRLASNQSSVVSYFFNITAFCRDNKETALETEQDILNSFRKNGFELISPRFNHMRNFLACLPFMAGKG
LFKQLKEAGVVQRAESFNVANLMPLVADNPLTPAGLLAPTYRNQLAFIDIFFRGMNNTNYNMAVCGTSGA
GKTGLIQPLIRSVLDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLRFNPFANITNIDQSAERIRDQLSV
MASPNGNLDEVHEGLLLQAVRAAWLTKKNRARIDDVVDFLENARTSEQYAESPGIRSRLDEMIVLLNQYT
AAGTYGRYFNSDEPSLRDDARMVVLELGGLEDRPSLLVAVMFSLIIYIENRMYRTPRNLKKLNVIDEGWR
LLDFKNRKVGDFIEKGYRTARRHTGAYITITQNIVDFDSDKASSAARAAWGNSSYKIILKQSAKEFAKYN
QLYPDQFPQLHREMIEKFGAAKDQWFSSFLLQVENHSSWHRLFVDPLSRAMYSSDGPDFEFVQQMRKEGL
SIHEAVWQLAWKKSGPEMASLEAWLQEHETFRGTYEYKAETD
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
ID | 3442 | GenBank | WP_117338899 |
Name | traD_COO54_RS24065_pSalMiami | UniProt ID | _ |
Length | 730 a.a. | PDB ID | _ |
Note | Predicted by oriTfinder 2.0 |
T4CP protein sequence
Download Length: 730 a.a. Molecular weight: 82666.30 Da Isoelectric Point: 5.2394
MSFNAKDMTQGGQIASMRIRMFSQIANIIFYCLFIFFWILVGLVLWVKLSWQTFVNGCIYWWCTTLEGMR
DLIKSQPVYEIRYYGQTFRMNAAQVLQDKYTVWCGEQLWSAFVLAACVALVICLITFFMTTWILGRQGKQ
QSEDDVTGGRQLTDNPKDVARMLKKDGKASDILIGDLPIIKDSEIQNFLLHGTVSTGKSEIIRRLANYAR
QRGDMVVMYDRSCEFVKSYYDPSIDKILNPCDARCAAWDLWRECLTLPDFDNAANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDSDRSYSKLVDTLLSIKIEKLRTYLRDSPAANLVEEKIEKTAISIRAVLTNYVKA
VRYLQGIERNGEPFTIRDWMRGVREDQKNGWLFISSNADTHSSLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEIVPEARKFGGCYVFGIQSSTQMEDIYGEKAAATLLDVMNTRAFFRSPSYKIA
DYVAHEIGEKEILKASEQYSYGADPVRDGVSTGKEMERVTLVSYSDIQSLPDLTCYVTLPGPYPAVKLAL
KYQERPKVAPEFIPREMNPEAEARLSAVLAAREAEGRQMSSLFEPDTEAVAPAAAEAQAEQPQQPQQPQQ
PQQPQQPTVVSDKKSAAAGTAANTSAGGVGQELKMKQEDEEQPLPPGINASGEVVDMAVYERWRQEQELN
TQQQMQRREEVNINVHRGHGKDEPEPGDHF
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 61000..87387
Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
---|---|---|---|---|---|---|
COO54_RS23885 (COO54_23775) | 56156..58153 | + | 1998 | WP_117338888 | ParB/RepB/Spo0J family partition protein | - |
COO54_RS23890 (COO54_23780) | 58193..58627 | + | 435 | WP_010999943 | conjugation system SOS inhibitor PsiB | - |
COO54_RS23895 (COO54_23785) | 58624..59361 | + | 738 | WP_117338889 | plasmid SOS inhibition protein A | - |
COO54_RS24255 | 59610..59768 | + | 159 | WP_001704449 | hypothetical protein | - |
COO54_RS23900 (COO54_23790) | 59871..60689 | + | 819 | Protein_71 | DUF932 domain-containing protein | - |
COO54_RS23905 (COO54_23795) | 61000..61470 | - | 471 | WP_042828200 | transglycosylase SLT domain-containing protein | virB1 |
COO54_RS23915 (COO54_23805) | 61886..62266 | + | 381 | WP_001151546 | conjugal transfer relaxosome DNA-binding protein TraM | - |
COO54_RS23920 (COO54_23810) | 62459..63145 | + | 687 | WP_085376305 | PAS domain-containing protein | - |
COO54_RS23925 (COO54_23815) | 63239..63466 | + | 228 | WP_001676655 | conjugal transfer relaxosome protein TraY | - |
COO54_RS23930 (COO54_23820) | 63508..63870 | + | 363 | WP_001274202 | type IV conjugative transfer system pilin TraA | - |
COO54_RS23935 (COO54_23825) | 63885..64196 | + | 312 | WP_000012129 | type IV conjugative transfer system protein TraL | traL |
COO54_RS23940 (COO54_23830) | 64218..64784 | + | 567 | WP_058215155 | type IV conjugative transfer system protein TraE | traE |
COO54_RS23945 (COO54_23835) | 64771..65511 | + | 741 | WP_117338891 | type-F conjugative transfer system secretin TraK | traK |
COO54_RS23950 (COO54_23840) | 65511..66932 | + | 1422 | WP_117338892 | F-type conjugal transfer pilus assembly protein TraB | traB |
COO54_RS23955 (COO54_23845) | 66922..67518 | + | 597 | WP_047593686 | conjugal transfer pilus-stabilizing protein TraP | - |
COO54_RS23960 (COO54_23850) | 67496..67741 | + | 246 | WP_117338893 | DUF2689 domain-containing protein | virb4 |
COO54_RS23965 (COO54_23855) | 67738..68253 | + | 516 | WP_085376303 | type IV conjugative transfer system lipoprotein TraV | traV |
COO54_RS23970 (COO54_23860) | 68388..68609 | + | 222 | WP_001278699 | conjugal transfer protein TraR | - |
COO54_RS23975 (COO54_23865) | 68602..69069 | + | 468 | WP_000549562 | hypothetical protein | - |
COO54_RS23980 (COO54_23870) | 69066..69449 | + | 384 | WP_117338894 | hypothetical protein | - |
COO54_RS23985 (COO54_23875) | 69465..72113 | + | 2649 | WP_117338895 | type IV secretion system protein TraC | virb4 |
COO54_RS23990 (COO54_23880) | 72088..72474 | + | 387 | WP_000105164 | type-F conjugative transfer system protein TrbI | - |
COO54_RS23995 (COO54_23885) | 72471..73103 | + | 633 | WP_079967495 | type-F conjugative transfer system protein TraW | traW |
COO54_RS24000 (COO54_23890) | 73100..74092 | + | 993 | WP_000833319 | conjugal transfer pilus assembly protein TraU | traU |
COO54_RS24005 (COO54_23895) | 74111..74419 | + | 309 | WP_080235917 | hypothetical protein | - |
COO54_RS24010 (COO54_23900) | 74404..75042 | + | 639 | WP_000554823 | type-F conjugative transfer system pilin assembly protein TrbC | trbC |
COO54_RS24015 (COO54_23905) | 75079..75498 | + | 420 | WP_001229397 | HNH endonuclease signature motif containing protein | - |
COO54_RS24020 (COO54_23910) | 75495..77321 | + | 1827 | WP_117338896 | type-F conjugative transfer system mating-pair stabilization protein TraN | traN |
COO54_RS24025 (COO54_23915) | 77332..77547 | + | 216 | WP_000700023 | conjugal transfer protein TrbE | - |
COO54_RS24030 (COO54_23920) | 77559..78308 | + | 750 | WP_117338897 | type-F conjugative transfer system pilin assembly protein TraF | traF |
COO54_RS24035 (COO54_23925) | 78522..78815 | + | 294 | WP_001233881 | type-F conjugative transfer system pilin chaperone TraQ | - |
COO54_RS24040 (COO54_23930) | 78802..79350 | + | 549 | WP_000055840 | type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB | traF |
COO54_RS24045 (COO54_23935) | 79340..80722 | + | 1383 | WP_117338898 | conjugal transfer pilus assembly protein TraH | traH |
COO54_RS24050 (COO54_23940) | 80719..83541 | + | 2823 | WP_001007086 | conjugal transfer mating-pair stabilization protein TraG | traG |
COO54_RS24055 (COO54_23945) | 83557..84051 | + | 495 | WP_077916534 | entry exclusion protein | - |
COO54_RS24060 (COO54_23950) | 84087..84818 | + | 732 | WP_031608647 | conjugal transfer complement resistance protein TraT | - |
COO54_RS24065 (COO54_23955) | 85195..87387 | + | 2193 | WP_117338899 | type IV conjugative transfer system coupling protein TraD | virb4 |
Host bacterium
ID | 5412 | GenBank | NZ_CP023469 |
Plasmid name | pSalMiami | Incompatibility group | IncFII |
Plasmid size | 94044 bp | Coordinate of oriT [Strand] | 61541..61810 [+] |
Host baterium | Salmonella enterica subsp. enterica strain BAA-1586 |
Cargo genes
Drug resistance gene | - |
Virulence gene | paa, faeC, faeD, faeE, faeF, faeH, faeI |
Metal resistance gene | - |
Degradation gene | - |
Symbiosis gene | - |
Anti-CRISPR | - |