Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   115866
Name   oriT_p2-125 in_silico
Organism   Serratia liquefaciens strain FG3
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP033895 (37145..37218 [+], 74 nt)
oriT length   74 nt
IRs (inverted repeats)      30..36, 41..47  (GCAAAAA..TTTTTGC)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 74 nt

>oriT_p2-125
TTCTCACCCCAAAAATCACCACACCCCACGCAAAAATTACTTTTTGCTGATTAGGTTGTTAAAACAGTAACTTA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   10160 GenBank   WP_142816634
Name   traI_EGO53_RS28745_p2-125 insolico UniProt ID   _
Length   1748 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1748 a.a.        Molecular weight: 189738.11 Da        Isoelectric Point: 6.3085

>WP_142816634.1 conjugative transfer relaxase/helicase TraI [Serratia liquefaciens]
MLSLATVKSAGSAGNYYTDKDNYYVIGSMGERWAGEGAAELGLKGEVDQKTFTALLEGRLPDGRDLSRMQ
EGANKHRPGYDLTFSAPKSISVMAMLGGDTRLIDAHNRSVDIAVKQVEALASTRVMTDGKSQTELTGNLV
MALFNHDTSRDQEPQLHTHAVVANLTRHGDDWRTLSSDKVGKTGFIENVYANQIAFGKIYRAALHQEVTA
LGYETEIVGKHGMWELKNVPVGEFSSRTQAIKDAVGEDASLKSRDMAALDTRRSKEKVDPEQRMSEWMHT
LKATGFDIRSYREGADQRAQSGDIPAPAVEAVDISASVGLAIGMLSDRRARFTYSELLATTIGQLPAQPG
VVAQAREGIESAIKNEQLIPLDKEKGLFTSNIHVLDELSVAALTRDLQRAGPIDTFADKAQPRTRAYSDA
VSVLAQDRLPVAIVAGQGGATGQRERVAELAMMAHEQGRKVQIVAADRRSARSLAQDERLSGEHITDRRA
LTEGMTFLPGSTLIVDQGEKLTLKETLTLLDGALRHNVQLLITDSGQRSGTGSVLTVMKETGVNTLSWQQ
GEKTRVDVISEPDRRQRYDRLATDFARSIREGEQSVAQVTGAREQAALTGAVRDALRAERVLGEKEHTIT
ALEPVWLDSRHQQVRDHYRDGMVMERWDAQARRHQRFVIDRVTARNNSLTLRNAQGESQVIRLASLDSSW
SLLRATQIPVSEGDRLAVLGKTPGARLKGGDTVTVTGFDDKGINVTLPGRKGTVTLPSGDSPFTAPKVGQ
GWVGSPGRSVSDNATVFASLSLREMDTTTLNKLAMSGSQVRLYSAQTEAKTTEKLARQSAFSVVSAQIKE
ASGHDRLDDALTHQKNALHTPAQQAIHLAIPALESRNLAFTKPQLMAAASEVAPTGQELAAIEREIDQQT
REGALMSVPVSPGNGLQLLVARTSYNAEKSILRHVLEGKDAVEPLMAQIPVGQLEGLTLGQRNATRMILG
SEDRFTLVQGYAGVGKTTQFRAVMSAIGTLPEEQRPRVIGVAPTHRAVSEMRDAGVPESQTLAAFIHDTQ
QQLRGGEKPDFRNVLFLVDESSMVGNADMARAYGLIAGGGGRAVLSGDTDQLQSIAPGQPFRLLQKRSAI
DVAVMQEIVRQTPALKPAVYSLIDRDIDSALNTIEQVAPVQVPRQVGAWQPESSVVEFGASQEKAIEKGL
ADGSLTPGAQPATLYEAIVRDYIGRTPQAQAQTIVVTTLNADRRALNAQIHEARQAAGELGEQEARLPIL
TSANLRDGELRKMATWQAAHDNLVLLDSTYYRIDSLDKDGQLVTLKDEQGNTRSLSPTQAATEGVTLYRP
DTLTVSTGDRMRFSKSDNERGFVANSVWIVSEIDGDRVTLSDGHQTRTVNPAAERAEQHIDLAYAVTAHG
AQGASEPFAIALQGTEGARKAMVSFESAYVALSRMKQHAQVYTDDRAAWVEAMGKSRARSTAHDILEPRG
DRAVSNAERLMGTAKPLGDVAAGRAVLRQVGLSPDGSMARFISPGRKYPQPHVALPAFDGNGKPAGIWLS
SLMPGEGEVLGLTDQGRVMGSEAATFAGLQVSRNGESLLAADMPAAVKLARENPHSGVVVRLPGSEGRPW
NPGAITGGRVWADGIPDDVVTGTQHGEKLPPEVVAQQAQAEQQRREMEERAAQAVREMARSGDKDREGTD
PVRDVARELERTQEPNPEAVRVPDNHEERRRDDAVAQVVHESVQRERLQQMEREVVRDLDREKTLSGD

  Protein domains


Predicted by InterproScan.

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

(631-710)

TrwC relaxase (TrwC)

(10-283)

DNA helicase TraI (TraI_C)

(1430-1548)

AAA domain (AAA_30)

(968-1156)

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

(573-625)


  Protein structure



No available structure.




T4CP

ID   11868 GenBank   WP_142816633
Name   traD_EGO53_RS28740_p2-125 insolico UniProt ID   _
Length   728 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 728 a.a.        Molecular weight: 80898.55 Da        Isoelectric Point: 5.1556

>WP_142816633.1 type IV conjugative transfer system coupling protein TraD [Serratia liquefaciens]
MSFNAKDMTQGGQIASMRIRMFSQIANIIIYCLVILFAIIVALTFWVKLSWQTFVNGMLHYWCQTLSPMR
DIFKSQPVYTVHYYGKELKYNALQVLQDKYLIWCAEQVWATFLLAAIIAAVVCVVAFFVATWVLGHQGKQ
QSEDEVTGGRELTEDPKRVAKMLKRDGMASDIKIGDLPLIKNSEIQNFCLHGTVGSGKSEAIRRLMNYAR
KRGDMVIVYDRSCEFVKSYYDPATDKILNPLDARCAAWDLWRECLTQPDFDNISNTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDKDRSYSKLVDTLLSIKIEKLRAYLKNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEGNGEPFTIRDWMRGVREDGNNGWLFISSNADTHASLKPVISMWLSIAIRGLLGMGENRDRRV
WIFGDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGDKGAATLFDVMNTRVFFRSPTRKIA
EFAAGEIGEKEILKASEQYSYGVDPVRDGTSVGKDMERVTLVSYSDIQTLPDLSCYVTLPGPYPAVKMSL
KYQPRPKVAPEFIPRTLDEQADARLSLALAAREDESRSLAGLFTPDIPVAAAASVETPVVASAPSAPVAP
AAPVEHPATSSAPAAKSGSSAAAVGVGGTEQELATKAEDAEELPPGIDVSGEVVDWDAFEAWQAEQEGLS
GKDMQRREEVNINVHRSPEKDLEPGDNL

  Protein domains


Predicted by InterproScan.

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

(172-560)

F sex factor protein N terminal (TraD_N)

(32-128)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 36599..65538

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
EGO53_RS28545 (EGO53_28660) 31869..32333 + 465 WP_142816603 protein TraE -
EGO53_RS28550 (EGO53_28665) 32370..32717 + 348 WP_142816604 hypothetical protein -
EGO53_RS28555 (EGO53_28670) 32807..33070 + 264 WP_042785950 hypothetical protein -
EGO53_RS28560 (EGO53_28675) 33125..33922 + 798 WP_142816605 N-6 DNA methylase -
EGO53_RS29775 33960..34085 + 126 WP_260679915 hypothetical protein -
EGO53_RS28565 (EGO53_28680) 34660..35031 + 372 WP_142816606 dehydrogenase -
EGO53_RS28570 (EGO53_28685) 35088..35915 + 828 WP_042785947 DUF932 domain-containing protein -
EGO53_RS28575 (EGO53_28690) 36017..36313 + 297 WP_142816607 DUF5983 family protein -
EGO53_RS28580 (EGO53_28695) 36599..37075 - 477 WP_142816608 transglycosylase SLT domain-containing protein virB1
EGO53_RS28585 (EGO53_28700) 37496..37891 + 396 WP_142816609 conjugal transfer relaxosome DNA-binding protein TraM -
EGO53_RS28590 (EGO53_28705) 38021..39736 - 1716 WP_142816610 hybrid sensor histidine kinase/response regulator -
EGO53_RS28595 (EGO53_28710) 39733..40227 - 495 WP_142816611 oxidoreductase -
EGO53_RS28600 (EGO53_28715) 40214..41209 - 996 WP_142816612 glycosyltransferase family 9 protein -
EGO53_RS28605 (EGO53_28720) 41212..42054 - 843 WP_142816613 helix-turn-helix domain-containing protein -
EGO53_RS29780 42386..42775 + 390 WP_260679916 TraY domain-containing protein -
EGO53_RS28620 (EGO53_28735) 43007..43336 + 330 WP_244952594 TraY domain-containing protein -
EGO53_RS28625 (EGO53_28740) 43401..43751 + 351 WP_142816614 type IV conjugative transfer system pilin TraA -
EGO53_RS28630 (EGO53_28745) 43901..44206 + 306 WP_142816615 type IV conjugative transfer system protein TraL traL
EGO53_RS28635 (EGO53_28750) 44221..44787 + 567 WP_142816616 type IV conjugative transfer system protein TraE traE
EGO53_RS28640 (EGO53_28755) 44813..45517 + 705 WP_185959447 type-F conjugative transfer system secretin TraK traK
EGO53_RS28645 (EGO53_28760) 45504..46898 + 1395 WP_142816618 F-type conjugal transfer pilus assembly protein TraB traB
EGO53_RS29785 46920..47054 + 135 WP_260679917 hypothetical protein -
EGO53_RS28650 (EGO53_28765) 47051..47437 + 387 WP_142816619 hypothetical protein -
EGO53_RS28655 (EGO53_28770) 47462..48001 + 540 WP_142816676 type IV conjugative transfer system lipoprotein TraV traV
EGO53_RS28660 (EGO53_28775) 48135..48350 + 216 WP_142816620 hypothetical protein virb4
EGO53_RS28665 (EGO53_28780) 48347..48586 + 240 WP_260679918 hypothetical protein -
EGO53_RS28670 (EGO53_28785) 48583..49071 + 489 WP_142816621 conjugal transfer protein TraP -
EGO53_RS28675 (EGO53_28790) 49064..51692 + 2629 Protein_59 type IV secretion system protein TraC -
EGO53_RS29790 51951..52208 + 258 WP_142816622 hypothetical protein -
EGO53_RS28685 (EGO53_28800) 52205..52552 + 348 WP_142816623 type-F conjugative transfer system protein TrbI -
EGO53_RS28690 (EGO53_28805) 52549..53205 + 657 WP_142816624 type-F conjugative transfer system protein TraW traW
EGO53_RS28695 (EGO53_28810) 53258..54205 + 948 WP_185959448 conjugal transfer pilus assembly protein TraU traU
EGO53_RS28700 (EGO53_28815) 54220..54849 + 630 WP_142816626 type-F conjugative transfer system pilin assembly protein TrbC trbC
EGO53_RS28705 (EGO53_28820) 54846..56723 + 1878 WP_142816627 type-F conjugative transfer system mating-pair stabilization protein TraN traN
EGO53_RS28710 (EGO53_28825) 56732..57475 + 744 WP_142816628 type-F conjugative transfer system pilin assembly protein TraF traF
EGO53_RS28715 (EGO53_28830) 57492..57755 + 264 WP_142816629 type-F conjugative transfer system pilin chaperone TraQ -
EGO53_RS28720 (EGO53_28835) 57745..58311 + 567 WP_142816630 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
EGO53_RS28725 (EGO53_28840) 58311..59675 + 1365 WP_142816678 conjugal transfer pilus assembly protein TraH traH
EGO53_RS28730 (EGO53_28845) 59675..62503 + 2829 WP_142816631 conjugal transfer mating-pair stabilization protein TraG traG
EGO53_RS28735 (EGO53_28850) 62512..63027 + 516 WP_142816632 hypothetical protein -
EGO53_RS28740 (EGO53_28855) 63352..65538 + 2187 WP_142816633 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   16299 GenBank   NZ_CP033895
Plasmid name   p2-125 Incompatibility group   -
Plasmid size   125113 bp Coordinate of oriT [Strand]   37145..37218 [+]
Host baterium   Serratia liquefaciens strain FG3

Cargo genes

Drug resistance gene   -
Virulence gene   pilW, fimG, fimD, fimC, fimA
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -