Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   103934
Name   oriT_pRM13672 in_silico
Organism   Salmonella enterica subsp. enterica serovar Typhimurium strain RM13672
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP047324 (60644..60913 [+], 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)
 33..38, 41..46  (AAAATT..AATTTT)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 270 nt

>oriT_pRM13672
GTCCTCACCACCAAAAGCACCACACCCCACGCAAAATTAAAATTTTTCTGATTTGTTTTTAGTAACAGTGAGTTATGTTCATAATAATGTAATTTAATTTATTTTAATGTATTAAATAGCGGTGCAGGCACGTCGCCGGCACCGCTATGACGACGCTATACAGGGGTAGTACTGACTATTTTTATAAAAAACATTGCATTATATCAGGGGCGCTGCTAGCGTCGCTGTGCCTGTTTTTAAGTAACACCCCTGGGGGCGCTGCCAGGGGTG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2926 GenBank   WP_000986921
Name   traI_GTH51_RS24115_pRM13672 insolico UniProt ID   Q93GL4
Length   1752 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1752 a.a.        Molecular weight: 191683.72 Da        Isoelectric Point: 5.9311

>WP_000986921.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Salmonella]
MMSIAQVRSAGSAAGYYSDRDNYYVLGSMEERWAGKGAEQLGLQGTVDKEVFTRVLEGRLPDGADLSRQQ
DGGNKHRPGYDLTFSAPKSVSLMAMLAGDKRLTEAHNQAVDIAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQEPQLHTHAVVVNVTQHDGEWKTLSSDKVGKTGFIENVYANQIAFGKIYRAVLKEKVEA
LGYETEVVGKHGMWEMPGVPVEAFSSRSQAIREAVGEDASLKSRDVAALDTRKSKQHVDPEVKMAEWMQT
LKDTGFDISAYRESADRRAEIQAAQPVPSQEQPDIQQAVTQAIAGLSDRKVQFTYTDVLARTVGMLPPEA
GVIEKARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSSDIMKQNRVTVHPEKSVPRTGSYSD
AVSVLAQDRPSLAIISGQGGAAGQRERVAELTMMAREQGREVQIIVADRRSQTNLKQDERLSGELITGRR
QLQEGMLFSPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKEAGVNSYRWQ
GRQQTPATVISEPDRNVRYARLAGDFVAAVKAGEESVAQVSGMREQAILAGMIRSELKTQGILGQQDTMM
TALSPVWLDSRNRYLRDMYREGMVMEQWNPEKRSHDRYVIDRVTAQSHSLTLRDAQGETQMVRISALDSS
WSLFRPEKMPVADGERLMVTGKIPGLRVSVGDRLQVSAVNDGVMTVTVPGRAEPASLPVGDSPFTALKLE
NGWVETPGHSVSDSAKVFASVTQMAMDNATLNSLARSGRDVRLYSSLDETRTAEKLSRHPSFTVVSEQIK
ARAGEVSLETAISRQKAGLHTPAQQAIHLALPVVESKNLAFSQVDLLTEAKSFAAEGTGFADLGREIDAQ
IKRGDLLYVDVAKGYGTDLLISRASYDAEKSILHHILEGKEAVTPLMERVPGELMETLTSGQRAATRMIL
ETKDRFTVVQGYAGVGKTTQFRAVMSAVNLLPESERPRVVGLGPTHRAVGEMRSAGVEAQTLASFLHDTQ
LQQRSGETPDFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSAA
DVAIMKEIVRQTPELRDAVYSLINRDVNKALSGLENVKPVQVPRLKGAWAPENSVTEFSRLQERELAKAA
QEAEKKGEAFPDVPVTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIQDALAKPGEQQVTVPVL
TTANIRDGELRRLSTWEAHPGALALVDNVYHRIAGISKEDGLITLEDKAGNTRLISPREAAAEGVTLYNP
ETIRVGAGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGKQTRVVRPGQDRAEQHIDLAYAITAHS
AQGASETFAIALEGTEGGRKQMAGFESAYVALSRMKQHVQVYTDDRQGWVKAINSAEQKGTAHDVLEPKS
EREMMNAERLFSTARELRDVAAGRAVLRNAGLAQGDSRARFIAPGRKYPQPYVALPAFDRNGKSAGIWLN
PLTTDDGAGLRGFTGEGRVKGSEEAQFVALQGSRNGESLLAGSMQDGVRIARENPDSGVVVRIVGDGRPW
NPVAITGGRVWGDIPDSNVQPGAGNGEPVTAEILAQRQAEEAVRRETERRADEIVRKMAEDKSDLPEEKT
AQAVREIAGQEQDRMTPPEREPPLPESVLREPQRERETIREVARENRGRERLQQMEQEMVRDLQKEKTPG
GD

  Protein domains


Predicted by InterproScan.

AAA domain (AAA_30)

(967-1158)

TrwC relaxase (TrwC)

(11-282)

DNA relaxase TraI 2B/2B-like domain (TraI_2B)

(632-711)

single-stranded DNA binding TraI N-terminal subdomain (ssDNA_TraI_N)

(574-626)

DNA helicase TraI (TraI_C)

(1430-1553)


  Protein structure


Source ID Structure
AlphaFold DB Q93GL4


Auxiliary protein

ID   1203 GenBank   WP_001151546
Name   WP_001151546_pRM13672 insolico 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

>WP_001151546.1 MULTISPECIES: conjugal transfer relaxosome DNA-binding protein TraM [Salmonella]
MAKVNVYISNEVHNKITAIVEKRRQEGARDKDISFSGTSSMLLELGLRVYEAQMERKESPFNQTEFNKVL
LENVLKTQSSVAKILGIGSLSPHVAGNPKFEYANMVEDIKEKVSSEMERFFHENEE

  Protein domains


Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-126)


  Protein structure


Source ID Structure
AlphaFold DB Q93GP1

ID   1204 GenBank   WP_001676655
Name   WP_001676655_pRM13672 insolico 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

>WP_001676655.1 MULTISPECIES: conjugal transfer relaxosome protein TraY [Salmonella]
MRRRNAREGISRTVSVYLDEDTNNRLIRAKDRSGRSKTIEVQIRLRDHLKRYPDFYNEEIFREVIEETES
TFKEI

  Protein domains


Predicted by InterproScan.

TraY domain (TraY)

(14-61)


  Protein structure


Source ID Structure
AlphaFold DB H3JT82


T4CP

ID   2777 GenBank   WP_000793310
Name   traC_GTH51_RS24020_pRM13672 insolico UniProt ID   _
Length   882 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 882 a.a.        Molecular weight: 100382.20 Da        Isoelectric Point: 6.9316

>WP_000793310.1 MULTISPECIES: type IV secretion system protein TraC [Salmonella]
MKNLLDTVTQAANSLLTALKLPDESAQANQILGEMSFPQFSRLLPYRDYNQESGLFMNDATMGFMLEATP
VNGANETIALSLDHLLRTKLPRGIPLCVHLMSSQLVGERIEYGLRKFSWSGEQAERFNAITRAYYMKAAE
THFPLPEGMNLPLTLRHYRVFISYCAPSRKKSRADILEMENLVKIIRASLQGAYISTQTVDAKAFINIVG
EMINHNPESIHPTRRRLDPYSDLNYQCVDDSFDLKVRQDYLTLGLRDNGKNSTARIMSFHLARNPEIAFL
WNSADNYSNLLNPELSISCPFILTLTLVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWGD
LRQRLASNQSSVVSYFFNITAFCRDNKETALETEQDILNSFRKNGFELISPRFNHMRNFLACLPFMAGKG
LFKQLKEAGVVQRAESFNVTNLMPLVADNPLTPAGLLAPTYRNQLAFIDIFFRGMNNTNYNMAVCGTSGA
GKTGLIQPLIRSVLDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLRFNPFANITNIDQSAERIRDQLSV
MASPNGNLDEVHEGLLLQAVRAAWLTKKNRARIDDVVDFLENARTSEQYAESPGIRSRLDEMIVLLNQYT
AAGTYGRYFNSDEPSLRDDARMVVLELGGLEDRPSLLVAVMFSLIIYIENRMYRTPRNLKKLNVIDEGWR
LLDFKNRKVGDFIEKGYRTARRHTGAYITITQNIVDFDSDKASSAARAAWGNSSYKIILKQSAKEFAKYN
QLYPDQFPQLHREMIEKFGAAKDQWFSSFLLQVENHSSWHRLFVDPLSRAMYSSDGPDFEFVQQKRKEGL
SIHEAVWQLAWKKSGPEMASLEAWLQEHETFRGTYEYKAETD

  Protein domains


Predicted by InterproScan.

Family of unknown function (DUF5934) (DUF5934)

(289-446)

TraG P-loop domain (P-loop_TraG)

(468-763)

TraC protein (TraC_F_IV)

(38-276)

  Protein structure



No available structure.



ID   2778 GenBank   WP_000009318
Name   traD_GTH51_RS24100_pRM13672 insolico UniProt ID   _
Length   720 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 720 a.a.        Molecular weight: 81447.01 Da        Isoelectric Point: 5.1045

>WP_000009318.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Salmonella]
MSFNAKDMTQGGQIASMRIRMFSQIANIIFYCLFIFFWILVGLVLWVKLSWQTFVNGGIYWWCTTLEGMR
DLIKSQPVYEIRYYGQTFRMNAAQVLQDKYTVWCGEQLWSAFVLAACVALVICLITFFMTTWILGRQGKQ
QSEDDVTGGRQLTDNPKDVARMLKKDGKASDILIGDLPIIKDSEIQNFLLHGTVSTGKSEIIRRLANYAR
QRGDMVVMYDRSCEFVKSYYDPSIDKILNPCDARCAAWDLWRECLTLPDFDNAANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDSDRSYSKLVDTLLSIKIEKLRTYLRDSPAANLVEEKIEKTAISIRAVLTNYVKA
VRYLQGIERNGEPFTIRDWMRGVREDQKNGWLFISSNADTHSSLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEIVPEARKFGGCYVFGIQSSTQMEDIYGEKAAATLLDVMNTRAFFRSPSYKIA
DYVAHEIGEKEILKASEQYSYGADPVRDGVSTGKEMERVTLVSYSDIQSLPDLTCYVTLPGPYPAVKLAL
KYQERPKVAPEFIPREMNPEAEARLSAVLAAREAEVRQMSSLFEPDTEAVAPTAAEAQAEQPQQPQPTVV
SDKKSAAAGTAVNTPAGGVGQELKMKPEDEEQPLPPGINASGEVVDMAAYERWRQEQEVNTQQQMQRREE
VNINVHRGHGKDEPEPGDDF

  Protein domains


Predicted by InterproScan.

F sex factor protein N terminal (TraD_N)

(32-128)

Type IV secretion-system coupling protein DNA-binding domain (TrwB_AAD_bind)

(173-560)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 60103..86459

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
GTH51_RS23920 (GTH51_23920) 55259..57256 + 1998 WP_022663156 ParB/RepB/Spo0J family partition protein -
GTH51_RS23925 (GTH51_23925) 57296..57730 + 435 WP_010999943 conjugation system SOS inhibitor PsiB -
GTH51_RS23930 (GTH51_23930) 57727..58464 + 738 WP_000581933 plasmid SOS inhibition protein A -
GTH51_RS24475 58499..58627 + 129 WP_000372429 hypothetical protein -
GTH51_RS24190 58713..58871 + 159 WP_001704449 hypothetical protein -
GTH51_RS24195 58974..59792 + 819 Protein_78 DUF932 domain-containing protein -
GTH51_RS23945 (GTH51_23945) 60103..60573 - 471 WP_001526856 transglycosylase SLT domain-containing protein virB1
GTH51_RS23950 (GTH51_23950) 60988..61368 + 381 WP_001151546 conjugal transfer relaxosome DNA-binding protein TraM -
GTH51_RS23955 (GTH51_23955) 61561..62247 + 687 WP_000336297 PAS domain-containing protein -
GTH51_RS23960 (GTH51_23960) 62341..62568 + 228 WP_001676655 conjugal transfer relaxosome protein TraY -
GTH51_RS23965 (GTH51_23965) 62610..62972 + 363 WP_001274201 type IV conjugative transfer system pilin TraA -
GTH51_RS23970 (GTH51_23970) 62987..63298 + 312 WP_000012129 type IV conjugative transfer system protein TraL traL
GTH51_RS23975 (GTH51_23975) 63320..63886 + 567 WP_000399768 type IV conjugative transfer system protein TraE traE
GTH51_RS23980 (GTH51_23980) 63873..64613 + 741 WP_001230719 type-F conjugative transfer system secretin TraK traK
GTH51_RS23985 (GTH51_23985) 64613..66034 + 1422 WP_000146700 F-type conjugal transfer pilus assembly protein TraB traB
GTH51_RS23990 (GTH51_23990) 66024..66620 + 597 WP_000527896 conjugal transfer pilus-stabilizing protein TraP -
GTH51_RS23995 (GTH51_23995) 66598..66843 + 246 WP_010999944 DUF2689 domain-containing protein virb4
GTH51_RS24000 (GTH51_24000) 66840..67355 + 516 WP_001079995 type IV conjugative transfer system lipoprotein TraV traV
GTH51_RS24005 (GTH51_24005) 67490..67711 + 222 WP_001278699 conjugal transfer protein TraR -
GTH51_RS24010 (GTH51_24010) 67704..68171 + 468 WP_000549562 hypothetical protein -
GTH51_RS24015 (GTH51_24015) 68288..68551 + 264 WP_001239255 hypothetical protein -
GTH51_RS24020 (GTH51_24020) 68567..71215 + 2649 WP_000793310 type IV secretion system protein TraC virb4
GTH51_RS24025 (GTH51_24025) 71190..71576 + 387 WP_000105164 type-F conjugative transfer system protein TrbI -
GTH51_RS24030 (GTH51_24030) 71573..72205 + 633 WP_000871995 type-F conjugative transfer system protein TraW traW
GTH51_RS24035 (GTH51_24035) 72202..73194 + 993 WP_000833320 conjugal transfer pilus assembly protein TraU traU
GTH51_RS24040 (GTH51_24040) 73213..73521 + 309 WP_010999945 hypothetical protein -
GTH51_RS24045 (GTH51_24045) 73506..74144 + 639 WP_000554823 type-F conjugative transfer system pilin assembly protein TrbC trbC
GTH51_RS24050 (GTH51_24050) 74181..74600 + 420 WP_001229397 HNH endonuclease signature motif containing protein -
GTH51_RS24055 (GTH51_24055) 74597..76423 + 1827 WP_000827528 type-F conjugative transfer system mating-pair stabilization protein TraN traN
GTH51_RS24060 (GTH51_24060) 76434..76649 + 216 WP_000700023 conjugal transfer protein TrbE -
GTH51_RS24065 (GTH51_24065) 76661..77410 + 750 WP_001226854 type-F conjugative transfer system pilin assembly protein TraF traF
GTH51_RS24070 (GTH51_24070) 77624..77917 + 294 WP_001233881 type-F conjugative transfer system pilin chaperone TraQ -
GTH51_RS24075 (GTH51_24075) 77904..78452 + 549 WP_000055840 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
GTH51_RS24080 (GTH51_24080) 78442..79824 + 1383 WP_001161719 conjugal transfer pilus assembly protein TraH traH
GTH51_RS24085 (GTH51_24085) 79821..82643 + 2823 WP_001007086 conjugal transfer mating-pair stabilization protein TraG traG
GTH51_RS24090 (GTH51_24090) 82659..83153 + 495 WP_010999946 entry exclusion protein -
GTH51_RS24095 (GTH51_24095) 83189..83920 + 732 WP_000782438 conjugal transfer complement resistance protein TraT -
GTH51_RS24100 (GTH51_24100) 84297..86459 + 2163 WP_000009318 type IV conjugative transfer system coupling protein TraD virb4
GTH51_RS24105 (GTH51_24105) 86468..86866 - 399 WP_000911322 type II toxin-antitoxin system VapC family toxin -
GTH51_RS24110 (GTH51_24110) 86866..87093 - 228 WP_000450265 toxin-antitoxin system antitoxin VapB -

Host bacterium

ID   4374 GenBank   NZ_CP047324
Plasmid name   pRM13672 Incompatibility group   IncFII
Plasmid size   93832 bp Coordinate of oriT [Strand]   60644..60913 [+]
Host baterium   Salmonella enterica subsp. enterica serovar Typhimurium strain RM13672

Cargo genes

Drug resistance gene   -
Virulence gene   rck, pefD, pefC, pefA, pefB, spvC, spvB
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -