Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   103714
Name   oriT_pSCD1 in_silico
Organism   Salmonella enterica subsp. enterica serovar Bovismorbificans strain SB699
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP091299 (39026..39295 [+], 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

>oriT_pSCD1
GTCCTCACCACCAAAAGCACCACACCCCACGCAAAATTAAAATTTTGCTGATTTGTTTTTAGTAACAGTGAGTTATGTTCATAATAATGTAATTTAATTTATTTTAATGTATTAAATAGCGGTGCAGGCACGTCGCCGGCACCGCTATGACGACGCTATACAGGGGTAGTACTGACTATTTTTATAAAAAACATTGCATTATATCAGGGGCGCTGCTAGCGTCGCTGTGCCTGTTTTTAAGTAACACCCCTGGGGGCGCTGCCAGGGGTG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2752 GenBank   WP_024798951
Name   traI_L1971_RS00420_pSCD1 insolico UniProt ID   A0A379NF77
Length   1751 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1751 a.a.        Molecular weight: 191019.00 Da        Isoelectric Point: 5.8095

>WP_024798951.1 conjugative transfer relaxase/helicase TraI [Salmonella enterica]
MMSIAQVRSAGSAAGYYSDRDNYYVLGSMEERWAGKGAEQLGLQGAVDKEVFTRVLEGRLPDGADLSRQQ
DGGNKHRPGYDLTFSAPKSVSLMAMLAGDKRLTEAHNQAVDIAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQEPQLHTHAVVANVTLHDGEWKTLSSDKVGKTGFIENIYANQIAFGKIYRAVLKEKVEA
LGYETEVVGKHGMWEMPGVPVEAFSSRSQAIREAVGEDASLKSRDVAALDTRKSKQHVDPAVKMAEWMQT
LKDTGFDISAYREAADRRAEIQAAQPVPSQEQPDIQQAVTQAIAGLSDRKVQFTYTDVLARTVGMLPPEA
GVIEKARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSSDIMKQNRVTVHPEKSVPRTGSYSD
AVSVLARDRPSLAIISGQGGAAGQRERVAELTMMAREQGREVQIIAADRRSQTNLKQDERLSGELITGRR
QLQEGMTFSPGSTVIVDQGEKLSLKETLTLLDGTARHNVQVLITDSGQRTGTGSALMAMKEAGVNSYRWQ
GGQQTPATVISEPDRNVRYARLAGDFVAAVKTGEESVAQVSGVREQAILAGMIRSELKTQGILGQQDTMM
TALSPVWLDSRNRYLRDMYREGMVMEQWNPEKRSHDRYVIDRVTAQSHSLTLRDAQGGTQMVRISALDSS
WSLFRPEKIPVADGERLMVTGKIPGLRVSGGDRLQVSAVNDGVMTVTVPGRAEPASLPVGDSPFTALKLE
NGWVETPGHSVSDSAKVFASVTQMAMDNATLNGLARSGRDVRLYSSLDEIRTAEKLSRHPSFTVVSEQIK
ARAGEVSLETAISLQKAGLHTPAQQALHLAIPVVESKNLAFSQVELLTEAKSFAAEGTGFADLGREIDAQ
IKRGDLLYVDVAKGYGTDLLISRASYDAEKSILHHILEGKEAVTPLMERVPGELMETLTSGQRAATRMIL
ETKDRFTVVQGYAGVGKTTQFRAVMSAVNLLPEDERPRVVGLGPTHRAVGEMRSAGVEAQTLASFLHDTQ
LQQRSGEAPDFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQARSAA
DVAIMKEIVRQTPELRDAVYSLINRDVNKALSGLENVKPVQVPRLKGAWAPENSVTEFSRLQERELAKAA
QEAEKKGEAFPDVPVTLYEAIVRDYTGRMPEAREQTLIVTHLNEDRRVLNSMIHDVREKAGELGEQQADI
PVLTTANIRDGELRRLSTWEAHPGALALVDNVYHRIAGISKEDGLITLEDKAGNTRLISPREAAAEGVTL
YNPETIRVGAGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGKQTCVVRPGQDRAEQHIDLAYAIT
AHGAQGASETFAIALEGTEGGRKQMAGFESAYVALSRMKQHVQVYTDDRQGWVKAINSAEQKGTAHDVLE
PKSEREMMNAERLFSTARELRDVAVGRAVLRNAGLAQGDSRARFIAPGRKYPQPYVALPAFDRNGKSAGI
WLNPLTTDDGAGLRGFTGEGRVKGSEEAQFVALQGSRNGESLLAGSMQDGVRIARENPDSGVVVRIAGDG
RPWNPVAITGGRVWGDIPDSNVQPGAGNGEPVTAEILAQRQAEEAVRRETERRADEIVRKMAEDKSDLPE
EKTAQAVREIAGQEQDRMTPPEREPALPESVLREPQRERETIREVARENRGRERLQEMVCDLQKEKTPGG
D

  Protein domains


Predicted by InterproScan.

TrwC relaxase (TrwC)

(11-282)

AAA domain (AAA_30)

(967-1158)

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

(574-626)

DNA helicase TraI (TraI_C)

(1433-1556)

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

(632-711)


  Protein structure



No available structure.




Auxiliary protein

ID   1163 GenBank   WP_001151546
Name   WP_001151546_pSCD1 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   1164 GenBank   WP_001676655
Name   WP_001676655_pSCD1 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   2589 GenBank   WP_024798976
Name   traC_L1971_RS00310_pSCD1 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: 100353.19 Da        Isoelectric Point: 6.7137

>WP_024798976.1 type IV secretion system protein TraC [Salmonella enterica]
MKNLLDTVTQAANSLLTALKMPDESAQANQILGEMSFPQFSRLLPYRDYNQESGLFMNDATMGFMLEATP
VNGANETIALSLDHLLRTKLPRGIPLCVHLMSSQLVGERIEYGLREFSWSGEQAERLNAITRAYYMKAAE
THFPLPEGMNLPLTLRHYRVFISYCAPSRKKSRADILEMENLVKIIRASLQGAYISTQSVDAKAFINIVG
EMINHNPESLHPTRRRLDPYSDLNYQCVDDSFDLKVRQDYLTLGLRDNGKNSTARIMSFHLARNPEIAFL
WNSADNYSNLLNPELSISCPFILTLTLVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWGD
LRQRLASNQSSVVSYFFNITAFCRDNKEMALETEQDILNSFRKNGFELISPRFNHMRNFLACLPFMAGKG
LFKQLKEAGVVQRAESFNVANLMPLVADNPLTPAGLLAPTYRNQLAFIDIFFRGMNNTNYNMAVCGTSGA
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   2590 GenBank   WP_152280056
Name   traD_L1971_RS00405_pSCD1 insolico UniProt ID   _
Length   741 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 741 a.a.        Molecular weight: 84003.85 Da        Isoelectric Point: 5.2394

>WP_152280056.1 type IV conjugative transfer system coupling protein TraD [Salmonella enterica]
MSFNAKDMTQGGQIASMRIRMFSQIANIIFYCLFIFFWILVGLVLWVKLIWQTFVNGCIYWWCTTLEGMR
DLIKSQPVYEIRYYGQTFRMNAAQVLQDKYTVWCGEQLWSAFVLAACVALVICLITFFMVTWILGRQGKQ
QSEDDVTGGRQLTDNPKDVARMLKKDGKASDILIGDLPIIKDSEIQNFLLHGTVSTGKSEIIRRLANYAR
QRGDMVVMYDRSCEFVKSYYDPSIDKILNPCDARCAAWDLWRECLTLPDFDNAANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDSDRSYSKLVDTLLSIKIEKLRTYLRDSPAANLVEEKIEKTAISIRAVLTNYVKA
VRYLQGIERNGEPFTIRDWMRGVREDQKNGWLFISSNADTHSSLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEIVPEARKFGGCYVFGIQSSTQMEDIYGEKAAATLLDVMNTRAFFRSPSYKIA
DYVAHEIGEKEILKASEQYSYGADPVRDGVSTGKEMERVTLVSYSDIQSLPDLTCYVTLPGPYPAVKLAL
KYQERPKVAPEFIPREMNPEAEARLSAVLAAREAEGRQMSSLFEPDTEAVAPAAAEAQAEQPQQPQQPQQ
PQQPQQPQQPQQPQQPQSTVVSDKKSAAAGTAVNTPAGGVGQELKMKQEDEEQPLPPGINASGEVVDMAV
YERWRQEQELNTQQQMQRREEVNINVHRGHGKDEPEPGDHF

  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: 38485..66337

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
L1971_RS00205 (L1971_00205) 33604..34026 - 423 WP_000925628 translesion error-prone DNA polymerase V autoproteolytic subunit -
L1971_RS00210 (L1971_00210) 34327..36048 + 1722 Protein_41 ParB/RepB/Spo0J family partition protein -
L1971_RS00215 (L1971_00215) 36088..36189 + 102 Protein_42 conjugation system SOS inhibitor PsiB family protein -
L1971_RS00220 (L1971_00220) 36190..36846 + 657 Protein_43 plasmid SOS inhibition protein A -
L1971_RS23195 36881..37009 + 129 WP_000372430 hypothetical protein -
L1971_RS00225 (L1971_00225) 37095..37253 + 159 WP_001704449 hypothetical protein -
L1971_RS00230 (L1971_00230) 37356..38174 + 819 Protein_46 DUF932 domain-containing protein -
L1971_RS00235 (L1971_00235) 38485..38955 - 471 WP_015056628 transglycosylase SLT domain-containing protein virB1
L1971_RS00240 (L1971_00240) 39370..39750 + 381 WP_001151546 conjugal transfer relaxosome DNA-binding protein TraM -
L1971_RS00245 (L1971_00245) 39943..40629 + 687 WP_000336296 PAS domain-containing protein -
L1971_RS00250 (L1971_00250) 40723..40950 + 228 WP_001676655 conjugal transfer relaxosome protein TraY -
L1971_RS00255 (L1971_00255) 40992..41354 + 363 WP_001274198 type IV conjugative transfer system pilin TraA -
L1971_RS00260 (L1971_00260) 41369..41680 + 312 WP_000012129 type IV conjugative transfer system protein TraL traL
L1971_RS00265 (L1971_00265) 41702..42268 + 567 WP_000399761 type IV conjugative transfer system protein TraE traE
L1971_RS00270 (L1971_00270) 42255..42995 + 741 WP_001230721 type-F conjugative transfer system secretin TraK traK
L1971_RS00275 (L1971_00275) 42995..44416 + 1422 WP_000146702 F-type conjugal transfer pilus assembly protein TraB traB
L1971_RS00280 (L1971_00280) 44406..45002 + 597 WP_024799158 conjugal transfer pilus-stabilizing protein TraP -
L1971_RS00285 (L1971_00285) 44980..45204 + 225 WP_077906918 DUF2689 domain-containing protein -
L1971_RS00290 (L1971_00290) 45201..45716 + 516 WP_001079997 type IV conjugative transfer system lipoprotein TraV traV
L1971_RS00295 (L1971_00295) 45851..46072 + 222 WP_001278681 conjugal transfer protein TraR -
L1971_RS00300 (L1971_00300) 46065..46532 + 468 WP_000549560 hypothetical protein -
L1971_RS00305 (L1971_00305) 46529..46912 + 384 WP_000870324 hypothetical protein -
L1971_RS00310 (L1971_00310) 46928..49576 + 2649 WP_024798976 type IV secretion system protein TraC virb4
L1971_RS00315 (L1971_00315) 49551..49937 + 387 WP_000105164 type-F conjugative transfer system protein TrbI -
L1971_RS00320 (L1971_00320) 49934..50566 + 633 WP_000871997 type-F conjugative transfer system protein TraW traW
L1971_RS00325 (L1971_00325) 50563..51555 + 993 WP_000833321 conjugal transfer pilus assembly protein TraU traU
L1971_RS00330 (L1971_00330) 51574..51870 + 297 WP_077914412 hypothetical protein -
L1971_RS00335 (L1971_00335) 51867..52496 + 630 WP_000089759 type-F conjugative transfer system pilin assembly protein TrbC trbC
L1971_RS00340 (L1971_00340) 52517..52654 - 138 WP_154071808 hypothetical protein -
L1971_RS00345 (L1971_00345) 52856..54733 + 1878 WP_237123561 type-F conjugative transfer system mating-pair stabilization protein TraN traN
L1971_RS00350 (L1971_00350) 54744..55220 + 477 WP_237123570 hypothetical protein -
L1971_RS00355 (L1971_00355) 55230..55445 + 216 WP_000783297 conjugal transfer protein TrbE -
L1971_RS00360 (L1971_00360) 55457..56206 + 750 WP_237123651 type-F conjugative transfer system pilin assembly protein TraF traF
L1971_RS00365 (L1971_00365) 56221..56565 + 345 WP_001697170 conjugal transfer protein TrbA -
L1971_RS00370 (L1971_00370) 56941..57234 + 294 WP_001233880 type-F conjugative transfer system pilin chaperone TraQ -
L1971_RS00375 (L1971_00375) 57221..57769 + 549 WP_024798870 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
L1971_RS00380 (L1971_00380) 57759..59141 + 1383 WP_237123578 conjugal transfer pilus assembly protein TraH traH
L1971_RS00385 (L1971_00385) 59138..61957 + 2820 WP_024798871 conjugal transfer mating-pair stabilization protein TraG traG
L1971_RS00390 (L1971_00390) 61960..62271 - 312 WP_000522257 hypothetical protein -
L1971_RS00395 (L1971_00395) 62370..63101 + 732 WP_000782437 conjugal transfer complement resistance protein TraT -
L1971_RS00400 (L1971_00400) 63353..63832 + 480 WP_025649166 hypothetical protein -
L1971_RS00405 (L1971_00405) 64112..66337 + 2226 WP_152280056 type IV conjugative transfer system coupling protein TraD virb4
L1971_RS00410 (L1971_00410) 66346..66744 - 399 WP_000911323 tRNA(fMet)-specific endonuclease VapC -
L1971_RS00415 (L1971_00415) 66744..66971 - 228 WP_000450263 toxin-antitoxin system antitoxin VapB -

Host bacterium

ID   4157 GenBank   NZ_CP091299
Plasmid name   pSCD1 Incompatibility group   IncFII
Plasmid size   104427 bp Coordinate of oriT [Strand]   39026..39295 [+]
Host baterium   Salmonella enterica subsp. enterica serovar Bovismorbificans strain SB699

Cargo genes

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