Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   108961
Name   oriT_pB-4548_1 in_silico
Organism   Salmonella enterica subsp. enterica serovar Gallinarum strain SCPM-O-B-4548
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP088143 (51168..51429 [-], 262 nt)
oriT length   262 nt
IRs (inverted repeats)      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: 262 nt

>oriT_pB-4548_1
GTCCTCACCACCAAAAGCACCACACCCCACGCAAAATTAAAATTTTGCTGATTTGTTTTTAGTAACAGTGAGTTATGTTCATAATAATGTAATTTAATTTATTTTAATGTATTAAATAGCGGTGCAGGCACGTCGCCGGCACCGCTATGACGACGCTATACAGGGGTAGTACTGACTATTTTTATAAAAAACATTGCATTATATCAGGGGCGCTGCTAGCGTCGCTGTGCCTGTTTTTAAGTAACACCCCTGGGGGCGCTGC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   6007 GenBank   WP_000986920
Name   traI_LRM93_RS22710_pB-4548_1 insolico UniProt ID   A0A5Y3LDY8
Length   1751 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1751 a.a.        Molecular weight: 191121.19 Da        Isoelectric Point: 5.7555

>WP_000986920.1 conjugative transfer relaxase/helicase TraI [Salmonella enterica]
MMSIAQVRSAGSAAGYYSDRDNYYVLGSMEERWAGKGAEQLGLQGAVDKEVFTRVLEGRLPDGADLSRQQ
DGGNKHRPGYDLTFSAPKSVSLMAMLAGDKRLTEAHNQAVDIAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQEPQLHTHAVVANVTLHDGEWKTLSSDKVGKTGFIENIYANQIAFGKIYRAVLKEKVEA
LGYETEVVGKHGMWEMPGVPVEAFSSRSQAIREAVGEDASLKSRDVAALDTRKSKQHVDPAVKMAEWMQT
LKDTGFDISAYREAADRRAEIQAAQPVPSQEQPDIQQAVTQAIAGLSDRKVQFTYTDVLARTVGMLPPEA
GVIEKARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSSDIMKQNRVTVHPEKSVPRTGSYSD
AVSVLARDRPSLAIISGQGGAAGQRERVAELTMMAREQGREVQIIAADRRSQTNLKQDERLSGELITGRR
QLQEGMTFSPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKEAGVNSYRWQ
GGQQTPATVISEPDRNVRYARLAGDFVAAVKTGEESVAQVSGVREQAILAGMIRSELKTQGILGQQDTMM
TALSPVWLDSRNRYLRDMYREGMVMEQWNPEKRSHDRYVIDRVTAQSHSLTLRDAQGGTQMVRISALDSS
WSLFRPEKIPVADGERLMVTGKIPWLRVSGGDRLQVSAVNDGVMTVTVPGRAEPASLPVGDSPFTALKLE
NGWVETPGHSVSDSAKVFASVTQMAMDNATLNGLARSGRDVRLYSSLDEIRTAEKLSRHPSFTVVSEQIK
ARAGEVSLETAISLQKAGLHTPAQQALHLAIPVVESKNLAFSQVELLTEAKSFAAEGTGFADLGREIDAQ
IKRGDLLYVDVAKCYGTDLLISRASYDAEKSILHHILEGKEAVTPLMERVPGELMETLTSGQRAATRMIL
ETKDRFTVVQGYAGVGKTTQFRAVMSAVNLLPEDERPRVVGLGPTHRAVGEMRSAGVEAQTLASFLHDTQ
LQQRSGEAPDFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQARSAA
DVAIMKEIVRQTPELRDAVYSLINRDVNKALSGLENVKPVQVPRLKGAWAPENSVTEFSRLQERELAKAA
QEAEKKGEAFPDVPVTLYEAIVLDYTGRMPEAREQTLIVTHLNEDRRVLNSMIHDVREKAGELGEQQADI
PVLTTANIRDGELRRLSTWEAHPGALALVDNVYHRIAGISKEDGLITLEDKAGNTRLISPREAAAEGVTL
YNPETIRVGAGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGKQTCVVRPGQDRAEQHIDLAYAIT
AHGAQGASETFAIALEGTEGGRKQMAGFESAYVALSRMKQHVQVYTDDRQGWVKAINSAEQKGTAHDVLE
PKSEREMMNAERLFSTARELRDVAVGRAVLRNAGLAQGDSRARFIAPGRKYPQPYVALPAFDRNGKSAGI
WLNPLTTDDGAGLRGFTGEGRVKGSEEAQFVALQGSRNGESLLAGSMQDGVRIARENPDSGVVVRIAGDG
RPWNPVAITGGRVWGDIPDSNVQPGAGNGEPVTAEILAQRQAEEAVRRETERRADEIVRKMAEDKSDLPE
EKTAQAVREIAGQEQDRMTPPEREPALPESVLREPQRERETIREVARENRGRERLQEMVCDLQKEKTPGG
D

  Protein domains


Predicted by InterproScan.

TrwC relaxase (TrwC)

(11-282)

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

(574-626)

AAA domain (AAA_30)

(967-1158)

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

(632-711)

DNA helicase TraI (TraI_C)

(1433-1556)


  Protein structure



No available structure.




Auxiliary protein

ID   3039 GenBank   WP_001676655
Name   WP_001676655_pB-4548_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

ID   3040 GenBank   WP_001151546
Name   WP_001151546_pB-4548_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


T4CP

ID   6497 GenBank   WP_000009313
Name   traD_LRM93_RS22725_pB-4548_1 insolico UniProt ID   _
Length   744 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 744 a.a.        Molecular weight: 84338.18 Da        Isoelectric Point: 5.2353

>WP_000009313.1 type IV conjugative transfer system coupling protein TraD [Salmonella enterica]
MSFNAKDMTQGGQIASMRIRMFSQIANIIFYCLFIFFWILVGLVLWVKLIWQTFVNGCIYWWCTTLEGMR
DLIKSQPVYEIRYYGQTFRMNAAQVLQDKYTVWCGEQLWSAFVLAACVALVICLITFFMVTWILGRQGKQ
QSEDDVTGGHQLTDNPKDVARMLKKDGKASDILIGDLPIIKDSEIQNFLLHGTVSTGKSEIIRRLANYAR
QRGDMVVMYDRSCEFVKSYYDPSIDKILNPCDARCAAWDLWRECLTLPDFDNAANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDSDRSYSKLVDTLLSIKIEKLRTYLRDSPAANLVEEKIEKTAISIRAVLTNYVKA
VRYLQGIERNGEPFTIRDWMRGVREDQKNGWLFISSNADTHSSLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEIVPEARKFGGCYVFGIQSSTQMEDIYGEKAAATLLDVMNTRAFFRSPSYKIA
DYVAHEIGEKEILKASEQYSYGADPVRDGVSTGKEMERVTLVSYSDIQSLPDLTCYVTLPGPYPAVKLAL
KYQERPKVAPEFIPREMNPEAEARLSAVLAAREAEGRQMSSLFEPDTEAVAPAAAEAQAEQPQQPQQPQQ
PQQPQQPQQPQQPQQPQQPQSTVVSDKKSAAAGTAVNTPAGGVGQELKMKQEDEEQPLPPGINASGEVVD
MAVYERWRQEQELNTQQQMQRREEVNINVHRGHGKDEPEPGDHF

  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.



ID   6498 GenBank   WP_000793311
Name   traC_LRM93_RS22820_pB-4548_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: 100401.28 Da        Isoelectric Point: 6.8187

>WP_000793311.1 type IV secretion system protein TraC [Salmonella enterica]
MKNLLDTVTQAANSLLTALKMPDESAQANQILGEMSFPQFSRLLPYRDYNQESGLFMNDATMGFMLEATP
VNGANETIALSLDHLLRTKLPRGIPLCVHLMSSQLVGERIEYGLREFSWSGEQAERLNAITRAYYMKAAE
THFPLPEGMNLPLTLRHYRVFISYCAPSRKKSRADILEMENLVKIIRASLQGAYISTQSVDAKAFINIVG
EMINHNPESLHPTRRRLDPYSDLNYQCVDDSFDLKVRQDYLTLGLRDNGKNSTARIMSFHLARNPEIAFL
WNSADNYSNLLNPELSISCPFILTLTLVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWGD
LRQRLASNQSSVVSYFFNITAFCRDNKEMALETEQDILNSFRKNGFELISPRFNHMRNFLACLPFMAGKG
LFKQLKEAGVVQRAESFNVANLMPLVADNPLTPAGLLAPTYRNQLAFIDIFFRGMNNTNYNMAVCGTSGA
GKTGLIQPLIRSVLDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLRFNPFANITNIDQSAERIRDQLSV
MASPNGNLDEVHEGLLLQAVRAAWLTKKNRARIDDVVYFLENARTSEQYAESPGIRSRLDEMIVLLNQYT
AAGTYGRYFNSDEPSLRDDARMVVLELGGLEDRPSLLVAVMFSLIIYIENRMYRTPRNLKKLNVIDEGWR
LLDFKNRKVGDFIEKGYRTARRHTGAYITITQNIVDFDSDKASSAARAAWGNSSYKIILKQSAKEFAKYN
QLYPDQFPQLHREMIEKFGAAKDQWFSSFLLQVENHSSWHRLFVDPLSRAMYSSDGPDFEFVQQKRKEGL
SIHEAVWQLAWKKSGPEMASLEAWLQEHETFRGTYEYKAETD

  Protein domains


Predicted by InterproScan.

Family of unknown function (DUF5934) (DUF5934)

(289-446)

TraC protein (TraC_F_IV)

(38-276)

TraG P-loop domain (P-loop_TraG)

(467-763)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 24106..51970

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
LRM93_RS22715 (LRM93_22715) 23472..23699 + 228 WP_000450263 toxin-antitoxin system antitoxin VapB -
LRM93_RS22720 (LRM93_22720) 23699..24097 + 399 WP_000911323 tRNA(fMet)-specific endonuclease VapC -
LRM93_RS22725 (LRM93_22725) 24106..26340 - 2235 WP_000009313 type IV conjugative transfer system coupling protein TraD prgC
LRM93_RS22730 (LRM93_22730) 26620..27231 - 612 WP_232520941 hypothetical protein -
LRM93_RS22735 (LRM93_22735) 27351..28082 - 732 WP_000782437 conjugal transfer complement resistance protein TraT -
LRM93_RS22740 (LRM93_22740) 28181..28492 + 312 WP_000522257 hypothetical protein -
LRM93_RS22745 (LRM93_22745) 28495..31314 - 2820 Protein_30 conjugal transfer mating-pair stabilization protein TraG -
LRM93_RS22750 (LRM93_22750) 31311..32693 - 1383 WP_001161718 conjugal transfer pilus assembly protein TraH traH
LRM93_RS22755 (LRM93_22755) 32683..33231 - 549 WP_000059056 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
LRM93_RS22760 (LRM93_22760) 33218..33511 - 294 WP_001233880 type-F conjugative transfer system pilin chaperone TraQ -
LRM93_RS22765 (LRM93_22765) 33887..34231 - 345 WP_001697170 conjugal transfer protein TrbA -
LRM93_RS22770 (LRM93_22770) 34246..34995 - 750 WP_001226834 type-F conjugative transfer system pilin assembly protein TraF traF
LRM93_RS22775 (LRM93_22775) 35008..35223 - 216 WP_000783297 conjugal transfer protein TrbE -
LRM93_RS22780 (LRM93_22780) 35233..35709 - 477 WP_000046068 hypothetical protein -
LRM93_RS22785 (LRM93_22785) 35720..37597 - 1878 WP_000730206 type-F conjugative transfer system mating-pair stabilization protein TraN traN
LRM93_RS22790 (LRM93_22790) 37799..37936 + 138 WP_154071808 hypothetical protein -
LRM93_RS22795 (LRM93_22795) 37957..38586 - 630 WP_000089759 type-F conjugative transfer system pilin assembly protein TrbC trbC
LRM93_RS22800 (LRM93_22800) 38583..38867 - 285 WP_232520943 hypothetical protein -
LRM93_RS22805 (LRM93_22805) 38898..39890 - 993 WP_000833321 conjugal transfer pilus assembly protein TraU traU
LRM93_RS22810 (LRM93_22810) 39887..40519 - 633 WP_000871997 type-F conjugative transfer system protein TraW traW
LRM93_RS22815 (LRM93_22815) 40516..40902 - 387 WP_000105164 type-F conjugative transfer system protein TrbI -
LRM93_RS22820 (LRM93_22820) 40877..43525 - 2649 WP_000793311 type IV secretion system protein TraC virb4
LRM93_RS22825 (LRM93_22825) 43541..43924 - 384 WP_000870324 hypothetical protein -
LRM93_RS22830 (LRM93_22830) 43921..44388 - 468 WP_000549560 hypothetical protein -
LRM93_RS22835 (LRM93_22835) 44381..44602 - 222 WP_001278681 conjugal transfer protein TraR -
LRM93_RS22840 (LRM93_22840) 44737..45252 - 516 WP_001079997 type IV conjugative transfer system lipoprotein TraV traV
LRM93_RS22845 (LRM93_22845) 45249..45473 - 225 WP_077906918 DUF2689 domain-containing protein -
LRM93_RS22850 (LRM93_22850) 45451..46047 - 597 WP_000527895 conjugal transfer pilus-stabilizing protein TraP -
LRM93_RS22855 (LRM93_22855) 46037..47458 - 1422 WP_000146702 F-type conjugal transfer pilus assembly protein TraB traB
LRM93_RS22860 (LRM93_22860) 47458..48198 - 741 WP_001230721 type-F conjugative transfer system secretin TraK traK
LRM93_RS22865 (LRM93_22865) 48185..48751 - 567 WP_000399761 type IV conjugative transfer system protein TraE traE
LRM93_RS22870 (LRM93_22870) 48773..49084 - 312 WP_000012129 type IV conjugative transfer system protein TraL traL
LRM93_RS22875 (LRM93_22875) 49099..49461 - 363 WP_001274198 type IV conjugative transfer system pilin TraA -
LRM93_RS22880 (LRM93_22880) 49503..49730 - 228 WP_001676655 conjugal transfer relaxosome protein TraY -
LRM93_RS22885 (LRM93_22885) 49824..50510 - 687 WP_000336296 PAS domain-containing protein -
LRM93_RS22890 (LRM93_22890) 50703..51083 - 381 WP_001151546 conjugal transfer relaxosome DNA-binding protein TraM -
LRM93_RS22895 (LRM93_22895) 51500..51970 + 471 WP_015056628 transglycosylase SLT domain-containing protein virB1
LRM93_RS22900 (LRM93_22900) 52493..53099 - 607 Protein_61 DUF932 domain-containing protein -
LRM93_RS22905 (LRM93_22905) 53202..53360 - 159 WP_001704449 hypothetical protein -
LRM93_RS23245 53446..53574 - 129 WP_000372430 hypothetical protein -
LRM93_RS22910 (LRM93_22910) 53609..54265 - 657 Protein_64 plasmid SOS inhibition protein A -
LRM93_RS22915 (LRM93_22915) 54268..54369 - 102 Protein_65 conjugation system SOS inhibitor PsiB family protein -
LRM93_RS22920 (LRM93_22920) 54409..56130 - 1722 Protein_66 ParB/RepB/Spo0J family partition protein -
LRM93_RS22925 (LRM93_22925) 56431..56853 + 423 WP_000925628 translesion error-prone DNA polymerase V autoproteolytic subunit -

Host bacterium

ID   9396 GenBank   NZ_CP088143
Plasmid name   pB-4548_1 Incompatibility group   IncFIB
Plasmid size   92906 bp Coordinate of oriT [Strand]   51168..51429 [-]
Host baterium   Salmonella enterica subsp. enterica serovar Gallinarum strain SCPM-O-B-4548

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -