Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   108951
Name   oriT_pB-4549_1 in_silico
Organism   Salmonella enterica subsp. enterica serovar Hissar strain SCPM-O-B-4549
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP088139 (90738..91007 [+], 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_pB-4549_1
GTCCTCACCACCAAAAGCACCACACCCCACGCAAAATTAAAATTTTTCTGATTTGTTTTTAGTAACAGTGAGTTATGTTCATAATAATGTAATTTAATTTATTTTAATGTATTAAATAGCGGTGCAGGCACGTCGCCGGCACCGCTATGACGACGCTATACAGGGGTAGTACTGACTATTTTTATAAAAAACATTGCATTATATCAGGGGCGCTGCTAGCGTCGCTGTGCCTGTTTTTAAGTAACACCCCTGGGGGCGCTGCCAGGGGTG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   6001 GenBank   WP_000986921
Name   traI_LRM92_RS24605_pB-4549_1 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   3032 GenBank   WP_001151546
Name   WP_001151546_pB-4549_1 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   3033 GenBank   WP_001676655
Name   WP_001676655_pB-4549_1 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   6489 GenBank   WP_156038187
Name   traC_LRM92_RS24510_pB-4549_1 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: 100470.29 Da        Isoelectric Point: 6.9347

>WP_156038187.1 type IV secretion system protein TraC [Salmonella enterica]
MKNLLDTVTQAANSLLTALKLPDESAQANQILGEMSFPQFSRLLPYRDYNQESGLFMNDATMGFMLEATP
VNGANETIVLSLDHLLRTKLPRGIPLCVHLMSSQLVGERIEYGLRKFSWSGEQAERFNAITRAYYMKAAE
THFPLPEGMNLPLTLRHYRVFISYCAPSRKKSRADILEMENLVKIIRASLQGAYISTQTVDAKAFINIVG
EMINHNPESIHPTRRRLDPYSDLNYQCVDDSFDLKVRQDYLTLGLRDNGKNSTARIMSFHLARNPEIAFL
WNSADNYSNLLNPELSISCPFILTLTLVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWGD
LRQRLASNQSSVVSYFFNITAFYRDNKETALETEQDILNSFRKNGFELISPRFNHMRNFLACLPFMAGKG
LFKQLKEAGVVQRAESFNVTNLMPLVADNPLTPAGLLAPTYRNQLAFIDIFFRGMNNTNYNMAVCGTSGA
GKTGLIQPLIRSVLDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLRFNPFANITNIDQSAERIRDQLSV
MASPNGNLDEVHEGLLLQAVRAAWLTKKNRARIDDVVDFLENARTSEQYAESPGIRSRLDEMIVLLNQYT
AAGTYGRYFNSDEPSLRDDARMVVLELGGLEDRPSLLVAVMFSLIIYIENRMYRTPRNLKKLNVIDEGWR
LLDFKNRKVGDFIEKGYRTARRHTGAYITITQNIVDFDSDKASSAARAAWGNSSYKIILKQSAKEFAKYN
QLYPDQFPQLHREMIEKFGAAKDQWFSSFLLQVENHSSWHRLFVDPLSRAMYSSDGPDFEFVQQKRKEGL
SIHEAVWQLAWKKSGPEMASLEAWLQEHETFRGTYEYKAETD

  Protein domains


Predicted by InterproScan.

TraG P-loop domain (P-loop_TraG)

(468-763)

Family of unknown function (DUF5934) (DUF5934)

(289-446)

TraC protein (TraC_F_IV)

(38-276)

  Protein structure



No available structure.



ID   6490 GenBank   WP_000009318
Name   traD_LRM92_RS24590_pB-4549_1 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: 90197..116553

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
LRM92_RS24410 (LRM92_24405) 85353..87350 + 1998 WP_000117513 ParB/RepB/Spo0J family partition protein -
LRM92_RS24415 (LRM92_24410) 87390..87824 + 435 WP_010999943 conjugation system SOS inhibitor PsiB -
LRM92_RS24420 (LRM92_24415) 87821..88558 + 738 WP_000581933 plasmid SOS inhibition protein A -
LRM92_RS24780 88593..88721 + 129 WP_000372429 hypothetical protein -
LRM92_RS24425 (LRM92_24420) 88807..88965 + 159 WP_001704449 hypothetical protein -
LRM92_RS24430 (LRM92_24425) 89068..89886 + 819 Protein_107 DUF932 domain-containing protein -
LRM92_RS24435 (LRM92_24430) 90197..90667 - 471 WP_001526856 transglycosylase SLT domain-containing protein virB1
LRM92_RS24440 (LRM92_24435) 91082..91462 + 381 WP_001151546 conjugal transfer relaxosome DNA-binding protein TraM -
LRM92_RS24445 (LRM92_24440) 91655..92341 + 687 WP_156038189 PAS domain-containing protein -
LRM92_RS24450 (LRM92_24445) 92435..92662 + 228 WP_001676655 conjugal transfer relaxosome protein TraY -
LRM92_RS24455 (LRM92_24450) 92704..93066 + 363 WP_001274201 type IV conjugative transfer system pilin TraA -
LRM92_RS24460 (LRM92_24455) 93081..93392 + 312 WP_012825259 type IV conjugative transfer system protein TraL traL
LRM92_RS24465 (LRM92_24460) 93414..93980 + 567 WP_000399768 type IV conjugative transfer system protein TraE traE
LRM92_RS24470 (LRM92_24465) 93967..94707 + 741 WP_001230719 type-F conjugative transfer system secretin TraK traK
LRM92_RS24475 (LRM92_24470) 94707..96128 + 1422 WP_000146700 F-type conjugal transfer pilus assembly protein TraB traB
LRM92_RS24480 (LRM92_24475) 96118..96714 + 597 WP_000527896 conjugal transfer pilus-stabilizing protein TraP -
LRM92_RS24485 (LRM92_24480) 96692..96937 + 246 WP_010999944 DUF2689 domain-containing protein virb4
LRM92_RS24490 (LRM92_24485) 96934..97449 + 516 WP_001079995 type IV conjugative transfer system lipoprotein TraV traV
LRM92_RS24495 (LRM92_24490) 97584..97805 + 222 WP_001278699 conjugal transfer protein TraR -
LRM92_RS24500 (LRM92_24495) 97798..98265 + 468 WP_000549562 hypothetical protein -
LRM92_RS24505 (LRM92_24500) 98382..98645 + 264 WP_001239255 hypothetical protein -
LRM92_RS24510 (LRM92_24505) 98661..101309 + 2649 WP_156038187 type IV secretion system protein TraC virb4
LRM92_RS24515 (LRM92_24510) 101284..101670 + 387 WP_000105164 type-F conjugative transfer system protein TrbI -
LRM92_RS24520 (LRM92_24515) 101667..102299 + 633 WP_000871995 type-F conjugative transfer system protein TraW traW
LRM92_RS24525 (LRM92_24520) 102296..103288 + 993 WP_000833320 conjugal transfer pilus assembly protein TraU traU
LRM92_RS24530 (LRM92_24525) 103307..103615 + 309 WP_010999945 hypothetical protein -
LRM92_RS24535 (LRM92_24530) 103600..104238 + 639 WP_000554823 type-F conjugative transfer system pilin assembly protein TrbC trbC
LRM92_RS24540 (LRM92_24535) 104275..104694 + 420 WP_001229397 HNH endonuclease signature motif containing protein -
LRM92_RS24545 (LRM92_24540) 104691..106517 + 1827 WP_000827528 type-F conjugative transfer system mating-pair stabilization protein TraN traN
LRM92_RS24550 (LRM92_24545) 106528..106743 + 216 WP_000700023 conjugal transfer protein TrbE -
LRM92_RS24555 (LRM92_24550) 106755..107504 + 750 WP_001226854 type-F conjugative transfer system pilin assembly protein TraF traF
LRM92_RS24560 (LRM92_24555) 107718..108011 + 294 WP_001233881 type-F conjugative transfer system pilin chaperone TraQ -
LRM92_RS24565 (LRM92_24560) 107998..108546 + 549 WP_000055840 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
LRM92_RS24570 (LRM92_24565) 108536..109918 + 1383 WP_001161719 conjugal transfer pilus assembly protein TraH traH
LRM92_RS24575 (LRM92_24570) 109915..112737 + 2823 WP_001007086 conjugal transfer mating-pair stabilization protein TraG traG
LRM92_RS24580 (LRM92_24575) 112753..113247 + 495 WP_010999946 entry exclusion protein -
LRM92_RS24585 (LRM92_24580) 113283..114014 + 732 WP_000782438 conjugal transfer complement resistance protein TraT -
LRM92_RS24590 (LRM92_24585) 114391..116553 + 2163 WP_000009318 type IV conjugative transfer system coupling protein TraD virb4
LRM92_RS24595 (LRM92_24590) 116562..116960 - 399 WP_000911322 type II toxin-antitoxin system VapC family toxin -
LRM92_RS24600 (LRM92_24595) 116960..117187 - 228 WP_000450265 toxin-antitoxin system antitoxin VapB -

Host bacterium

ID   9386 GenBank   NZ_CP088139
Plasmid name   pB-4549_1 Incompatibility group   IncFIB
Plasmid size   125931 bp Coordinate of oriT [Strand]   90738..91007 [+]
Host baterium   Salmonella enterica subsp. enterica serovar Hissar strain SCPM-O-B-4549

Cargo genes

Drug resistance gene   ant(2'')-Ia, sul1, dfrA23, blaOXA-1, ant(3'')-Ia
Virulence gene   -
Metal resistance gene   merE, merD, merA, merP, merT, merR
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -