Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   106433
Name   oriT_pGMI14-001 in_silico
Organism   Salmonella enterica subsp. enterica serovar Typhimurium strain CFSAN018746
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP028200 (9742..10010 [+], 269 nt)
oriT length   269 nt
IRs (inverted repeats)      245..253, 261..269  (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: 269 nt

>oriT_pGMI14-001
GTCCTCACCACCAAAAGCACCACACCCCACGCAAAATTAAAATTTTTCTGATTTGTTTTTAGTAACAGTGAGTTATGTTCATAATAATGTAATTTAATTTATTTTAATGTATTAAATAGCGGTGCAGGCACGTCGCCGGCACCGCTATGACGACGCTATACAGGGGTAGTACTGACTATTTTTATAAAAAACATTGCATTATATCAGGGGCGCTGCTAGCGTCGCTGTGCCTGTTTTTAAGTAACACCCCTGGGGCGCTGCCAGGGGTG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   4290 GenBank   WP_000986921
Name   traI_C6650_RS23750_pGMI14-001 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   1907 GenBank   WP_001151546
Name   WP_001151546_pGMI14-001 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   1908 GenBank   WP_001676655
Name   WP_001676655_pGMI14-001 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   4311 GenBank   WP_000793310
Name   traC_C6650_RS23655_pGMI14-001 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   4312 GenBank   WP_000009320
Name   traD_C6650_RS23735_pGMI14-001 insolico UniProt ID   _
Length   747 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 747 a.a.        Molecular weight: 84627.41 Da        Isoelectric Point: 5.1045

>WP_000009320.1 type IV conjugative transfer system coupling protein TraD [Salmonella enterica]
MSFNAKDMTQGGQIASMRIRMFSQIANIIFYCLFIFFWILVGLVLWVKLSWQTFVNGGIYWWCTTLEGMR
DLIKSQPVYEIRYYGQTFRMNAAQVLQDKYTVWCGEQLWSAFVLAACVALVICLITFFMTTWILGRQGKQ
QSEDDVTGGRQLTDNPKDVARMLKKDGKASDILIGDLPIIKDSEIQNFLLHGTVSTGKSEIIRRLANYAR
QRGDMVVMYDRSCEFVKSYYDPSIDKILNPCDARCAAWDLWRECLTLPDFDNAANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDSDRSYSKLVDTLLSIKIEKLRTYLRDSPAANLVEEKIEKTAISIRAVLTNYVKA
VRYLQGIERNGEPFTIRDWMRGVREDQKNGWLFISSNADTHSSLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEIVPEARKFGGCYVFGIQSSTQMEDIYGEKAAATLLDVMNTRAFFRSPSYKIA
DYVAHEIGEKEILKASEQYSYGADPVRDGVSTGKEMERVTLVSYSDIQSLPDLTCYVTLPGPYPAVKLAL
KYQERPKVAPEFIPREMNPEAEARLSAVLAAREAEVRQMSSLFEPDTEAVAPTAAEAQAEQPQQPQQPQQ
PQQPQQPQQPQQPQQPQQPQQPQPTVVSDKKSAAAGTAVNTPAGGVGQELKMKPEDEEQPLPPGINASGE
VVDMAAYERWRQEQEVNTQQQMQRREEVNINVHRGHGKDEPEPGDDF

  Protein domains


Predicted by InterproScan.

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

(173-560)

F sex factor protein N terminal (TraD_N)

(32-128)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 9201..35637

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
C6650_RS23555 (C6650_24900) 4357..6354 + 1998 WP_000117513 ParB/RepB/Spo0J family partition protein -
C6650_RS23560 (C6650_24895) 6394..6828 + 435 WP_010999943 conjugation system SOS inhibitor PsiB -
C6650_RS23565 (C6650_24890) 6825..7562 + 738 WP_000581933 plasmid SOS inhibition protein A -
C6650_RS24175 7597..7725 + 129 WP_000372429 hypothetical protein -
C6650_RS23570 (C6650_25650) 7811..7969 + 159 WP_001704449 hypothetical protein -
C6650_RS23575 (C6650_24885) 8072..8890 + 819 Protein_12 DUF932 domain-containing protein -
C6650_RS23580 (C6650_24880) 9201..9671 - 471 WP_001526856 transglycosylase SLT domain-containing protein virB1
C6650_RS23585 (C6650_24870) 10085..10465 + 381 WP_001151546 conjugal transfer relaxosome DNA-binding protein TraM -
C6650_RS23590 (C6650_24865) 10658..11344 + 687 WP_000336297 PAS domain-containing protein -
C6650_RS23595 (C6650_24860) 11438..11665 + 228 WP_001676655 conjugal transfer relaxosome protein TraY -
C6650_RS23600 (C6650_24855) 11707..12069 + 363 WP_001274201 type IV conjugative transfer system pilin TraA -
C6650_RS23605 (C6650_24850) 12084..12395 + 312 WP_000012129 type IV conjugative transfer system protein TraL traL
C6650_RS23610 (C6650_24845) 12417..12983 + 567 WP_000399769 type IV conjugative transfer system protein TraE traE
C6650_RS23615 (C6650_25440) 12970..13710 + 741 WP_001230719 type-F conjugative transfer system secretin TraK traK
C6650_RS23620 (C6650_25435) 13710..15131 + 1422 WP_000146700 F-type conjugal transfer pilus assembly protein TraB traB
C6650_RS23625 (C6650_25430) 15121..15717 + 597 WP_000527896 conjugal transfer pilus-stabilizing protein TraP -
C6650_RS23630 (C6650_25425) 15695..15940 + 246 WP_010999944 DUF2689 domain-containing protein virb4
C6650_RS23635 (C6650_25420) 15937..16452 + 516 WP_001079995 type IV conjugative transfer system lipoprotein TraV traV
C6650_RS23640 (C6650_25415) 16587..16808 + 222 WP_001278699 conjugal transfer protein TraR -
C6650_RS23645 (C6650_25410) 16801..17268 + 468 WP_000549562 hypothetical protein -
C6650_RS23650 (C6650_25405) 17385..17648 + 264 WP_001239256 hypothetical protein -
C6650_RS23655 (C6650_25400) 17664..20312 + 2649 WP_000793310 type IV secretion system protein TraC virb4
C6650_RS23660 (C6650_25395) 20287..20673 + 387 WP_000105164 type-F conjugative transfer system protein TrbI -
C6650_RS23665 (C6650_25390) 20670..21302 + 633 WP_000871995 type-F conjugative transfer system protein TraW traW
C6650_RS23670 (C6650_25385) 21299..22291 + 993 WP_000833320 conjugal transfer pilus assembly protein TraU traU
C6650_RS23675 (C6650_25380) 22310..22618 + 309 WP_010999945 hypothetical protein -
C6650_RS23680 (C6650_25375) 22603..23241 + 639 WP_000554823 type-F conjugative transfer system pilin assembly protein TrbC trbC
C6650_RS23685 (C6650_25370) 23278..23697 + 420 WP_001229397 HNH endonuclease signature motif containing protein -
C6650_RS23690 (C6650_25365) 23694..25520 + 1827 WP_000827528 type-F conjugative transfer system mating-pair stabilization protein TraN traN
C6650_RS23695 (C6650_25360) 25531..25746 + 216 WP_000700023 conjugal transfer protein TrbE -
C6650_RS23700 (C6650_25355) 25758..26507 + 750 WP_001226854 type-F conjugative transfer system pilin assembly protein TraF traF
C6650_RS23705 (C6650_25350) 26721..27014 + 294 WP_001233881 type-F conjugative transfer system pilin chaperone TraQ -
C6650_RS23710 (C6650_25345) 27001..27549 + 549 WP_000055840 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
C6650_RS23715 (C6650_25340) 27539..28921 + 1383 WP_001161719 conjugal transfer pilus assembly protein TraH traH
C6650_RS23720 (C6650_25335) 28918..31740 + 2823 WP_001007086 conjugal transfer mating-pair stabilization protein TraG traG
C6650_RS23725 (C6650_25330) 31756..32250 + 495 WP_010999946 entry exclusion protein -
C6650_RS23730 (C6650_25325) 32286..33017 + 732 WP_000782438 conjugal transfer complement resistance protein TraT -
C6650_RS23735 (C6650_25320) 33394..35637 + 2244 WP_000009320 type IV conjugative transfer system coupling protein TraD prgC
C6650_RS23740 (C6650_25315) 35646..36044 - 399 WP_000911322 type II toxin-antitoxin system VapC family toxin -
C6650_RS23745 (C6650_25310) 36044..36271 - 228 WP_000450265 toxin-antitoxin system antitoxin VapB -

Host bacterium

ID   6870 GenBank   NZ_CP028200
Plasmid name   pGMI14-001 Incompatibility group   IncFII
Plasmid size   95983 bp Coordinate of oriT [Strand]   9742..10010 [+]
Host baterium   Salmonella enterica subsp. enterica serovar Typhimurium strain CFSAN018746

Cargo genes

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