Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   103008
Name   oriT_pFB2.2 in_silico
Organism   Pluralibacter gergoviae strain FB2
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP014777 (94544..94592 [-], 49 nt)
oriT length   49 nt
IRs (inverted repeats)      6..13, 16..23  (GCAAAATT..AATTTTGC)
Location of nic site      32..33
Conserved sequence flanking the
  nic site    		  TGTGTGGTGA
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 49 nt

>oriT_pFB2.2
AATCTGCAAAATTTTAATTTTGCGTAGTGTGTGGTGATTTTTTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2257 GenBank   WP_117098435
Name   traI_LG71_RS24960_pFB2.2 insolico UniProt ID   _
Length   1752 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1752 a.a.        Molecular weight: 190192.94 Da        Isoelectric Point: 6.2880

>WP_117098435.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacteriaceae]
MLSFSQVKSAGSAGNYYTDKDNYYVIGSMDERWQGKGAEALGLEGKVDKQVFTELLQGKLPDGSDLTRIQ
DGVNKHRPGYDLTFSAPKSVSMLAMLGGDKRLIDAHNRAVTVALNQVESLASTRVKRDGVSETVLTGNLI
IARFNHDTSRAQDPQIHTHSVVINATQNGDKWQTLASDTVGKTGFSENILANRIALGKIYQNSLRADVES
MGYKTVDAGKNGMWEMEGVPVESFSTRSQELREAAGPDASLKSRDVAALDTRKSKEAIDPAEKMVEWMNT
LKETGFDIRGYREAADARAAELARAPAAPVNTDGPDITDVVTKAIAGLSDRKVQFTYADLLARTVGQLEA
KDGVFELARKGIDAAIEREQLIPLDREKGLFTSNIHVLDELAVKALSQEVQRQNHVSVTPDASVVRQVPF
SDAVSVLAQDRPVMGIVSGQGGATGQRERVAELTLMAREQGRDVHILAADNRSRDFLAGDVRLAGETVTG
KSALQDGTAFIPGGTLIVDQAEKLSLKETISLLDGAMRHNVQVLLSDSGKRSGTGSALTVLKDSGVNTYR
WQGGHQTTADIISEPDKGARYSRLAQEFAVSVREGLESVAQISGTREQSVLNGLIRDSLRNEGVLGEKDT
TITALTPVWLDSKSRGVRDYYREGMVMERWDPETRTHDRFVIDRVTASSNMLTLKDREGGRLDLKVSAVD
SQWTLFRAETLPVAEGERLAVLGKIPDTRLKGGESITVMKVEDGQLTVQRPGQKTTQTLAVGAGVFDGIK
IGHGWVESPGRSVSETATVFASVTQRELDNATLNQLAQSGSHLRLYSAQDAARTTEKLSRHTAFSVVSEQ
LKARSGETDLDAAIAQQKAGLHTPAEQAIHLAIPLLESQDLTFSRPQLLATALETGGGKVSMADIDTTIQ
AQIRSGQLLNVPVAHGHGNDLLISRQTWDAEKSILTRVLEGKDAVAPLMDRVPASLMTDLTAGQRAATRM
ILESTDRFTVVQGYAGVGKTTQFRAVMSAISLLPEETRPRVIGLAPTHRAVGEMQSAGVDARTTASFLHD
TQLLQRNGQTPDFSNTLFLLDESSMVGLADMAKAHSLIVAGGGRAVSSGDNDQLQPIAPGQPFRLMQQRS
AADIAIMKEIVRQVPELRPAVYSLIERDVHRALTTIEQVTPEQVPRKEGVWAPGSSVVEFTPKQEKAIQK
ALSEGKTLPAGQPATLYEALVKDYTGRAPEAQSQTLVITHLNKDRRALNSLIHDARRENGETGKEEITLP
VLVTSNIRDGELRKLSTWTAHKEAVALVDNVYHRISKVDKDNQLITLTDSDGKERYISPREASAEGVTLY
RQEKITVSQGDRMRFSKSDPERGYVANSIWEVQSVAGDSVTLSDGKTTRTLTPKADQAQQHIDLAYAITA
HGAQGASEPYAIALEGVAGGREQMASFESAYVALSRMKQHVQVYTDSREGWIKAIQHSPEKATAHDILEP
RNDRAVKSADLLFGRARPLDETAAGRAALQQSGLAQGNSPGKFISPGKKYPQPHVALPAFDKNGKAAGIW
LSPLTDRDGRLEAIGGEGRIMGNDAARFVALQNSRNGESLLAGNMGEGVRMARDNPDTGVVVRLAGDDRP
WNPGAMTGGRVWAEPAPVAPVPQAGADIILPPEVLAQRAAEEQQRREMEKQAEQTAREVAGEARKAGEPV
DRVKEVIGDVIRGLERDRPGPEKTTLPDDPQFRRQEAAIQQVASESLQRERLQAVERDMVRDLNREKTLG
GD

  Protein domains


Predicted by InterproScan.

TrwC relaxase (TrwC)

(10-283)

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

(576-628)

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

(634-713)

AAA domain (AAA_30)

(970-1156)

DNA helicase TraI (TraI_C)

(1432-1554)


  Protein structure



No available structure.




T4CP

ID   1946 GenBank   WP_020316650
Name   traD_LG71_RS24955_pFB2.2 insolico UniProt ID   _
Length   763 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 763 a.a.        Molecular weight: 85197.99 Da        Isoelectric Point: 4.8865

>WP_020316650.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIANMRFRMFGQIANIIFYVLFILFWVLCGLMLMYRLSWQTFVNGCVYWWCTTLGPMR
DIIRSQPVYTIQYYGQSLEYTSEQILADKYTIWCGEQLWTGFAFAAVVSLVICIVTFFIASWVLGRQGKQ
QSEDENTGGRQLSDKPKEVARQMKRDGVASDIKIGDLPILKNSEIQNFCLHGTVGSGKSEVIRRLLNYVR
ARGDMAIIYDRSCEFVKSYYDPSLDKILNPLDSRCAAWDLWKECLTLPDFDNISNTLIPMGTKEDPFWQG
SGRTIFAEGAYLMREDDDRSYEKLVDTMLSIKIDKLRAYLQNTPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEKNGEPFTIRDWMRGVREDRPNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGVKPAATLFDVMNTRAFFRSPSKEIA
EFAAGEIGEKEILKASEQYSYGADPVRDGVSTGKEKERETLVSYSDIQTLPDLSCYVTLPGPYPAVKLAL
KYKPRPKIAEGFIPRSLDARVDARLSALLEAREAEGSLARALFTPDAPEPGPADTDSHAGEQPEPAEVTV
SPAPVKATQTTKMPAEEPSVRATEPPVLRVTTVPLIKPKAAAAAAAAATASSAGTPAAAAGGTEQELAQQ
SAEQGQDMLPAGMNEDGVIEDMQAYDAWADEQTQRDMQRREEVNINHSHRHDEQDDVEIGGNF

  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)

(172-560)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 96971..122496

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
LG71_RS18865 (LG71_28250) 93424..93954 + 531 WP_015632491 antirestriction protein -
LG71_RS18895 (LG71_28255) 93992..94399 - 408 WP_020805750 transglycosylase SLT domain-containing protein -
LG71_RS18935 (LG71_28260) 94903..95295 + 393 WP_032419915 conjugal transfer relaxosome DNA-binding protein TraM -
LG71_RS18940 (LG71_28265) 95872..96234 + 363 WP_237151240 hypothetical protein -
LG71_RS19030 96320..96520 + 201 WP_048289787 TraY domain-containing protein -
LG71_RS19040 (LG71_28270) 96589..96957 + 369 WP_020316649 type IV conjugative transfer system pilin TraA -
LG71_RS19140 (LG71_28275) 96971..97276 + 306 WP_004178059 type IV conjugative transfer system protein TraL traL
LG71_RS19145 (LG71_28280) 97296..97862 + 567 WP_020316627 type IV conjugative transfer system protein TraE traE
LG71_RS19150 (LG71_28285) 97849..98589 + 741 WP_020316652 type-F conjugative transfer system secretin TraK traK
LG71_RS19230 (LG71_28290) 98589..100013 + 1425 WP_020316642 F-type conjugal transfer pilus assembly protein TraB traB
LG71_RS19240 (LG71_28295) 100006..100602 + 597 WP_023340943 conjugal transfer pilus-stabilizing protein TraP -
LG71_RS19250 100625..101194 + 570 WP_168550213 type IV conjugative transfer system lipoprotein TraV traV
LG71_RS19670 (LG71_28300) 101326..101736 + 411 WP_149999108 hypothetical protein -
LG71_RS19815 (LG71_28305) 101741..102031 + 291 WP_020316639 hypothetical protein -
LG71_RS20910 102055..102273 + 219 WP_004171484 hypothetical protein -
LG71_RS20925 (LG71_28310) 102274..102591 + 318 WP_020316633 hypothetical protein -
LG71_RS20935 (LG71_28315) 102658..103062 + 405 WP_032419926 hypothetical protein -
LG71_RS21335 (LG71_28320) 103059..103349 + 291 WP_032419928 hypothetical protein -
LG71_RS21505 (LG71_28325) 103357..103755 + 399 WP_020316629 hypothetical protein -
LG71_RS21945 (LG71_28330) 103827..106466 + 2640 WP_020316635 type IV secretion system protein TraC virb4
LG71_RS21950 (LG71_28335) 106466..106855 + 390 WP_020316628 type-F conjugative transfer system protein TrbI -
LG71_RS21955 (LG71_28340) 106855..107481 + 627 WP_020314628 type-F conjugative transfer system protein TraW traW
LG71_RS22145 (LG71_28345) 107525..108484 + 960 WP_202386622 conjugal transfer pilus assembly protein TraU traU
LG71_RS22370 (LG71_28350) 108497..109135 + 639 WP_020316653 type-F conjugative transfer system pilin assembly protein TrbC trbC
LG71_RS22480 (LG71_28355) 109194..111149 + 1956 WP_020316657 type-F conjugative transfer system mating-pair stabilization protein TraN traN
LG71_RS22510 (LG71_28360) 111182..111463 + 282 WP_032419932 hypothetical protein -
LG71_RS22515 (LG71_28365) 111453..111680 + 228 WP_012540032 conjugal transfer protein TrbE -
LG71_RS23075 (LG71_28370) 111691..112017 + 327 WP_020316638 hypothetical protein -
LG71_RS23130 (LG71_28375) 112038..112790 + 753 WP_020316647 type-F conjugative transfer system pilin assembly protein TraF traF
LG71_RS23220 (LG71_28380) 112801..113040 + 240 WP_009309875 type-F conjugative transfer system pilin chaperone TraQ -
LG71_RS23250 (LG71_28385) 113012..113569 + 558 WP_020804677 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
LG71_RS23280 (LG71_28390) 113615..114058 + 444 WP_020316643 F-type conjugal transfer protein TrbF -
LG71_RS23980 (LG71_28395) 114036..115415 + 1380 WP_072198238 conjugal transfer pilus assembly protein TraH traH
LG71_RS23985 (LG71_28400) 115415..118237 + 2823 WP_020316632 conjugal transfer mating-pair stabilization protein TraG traG
LG71_RS24795 118261..118863 + 603 WP_048263624 hypothetical protein -
LG71_RS24945 (LG71_28405) 119114..119845 + 732 WP_016831056 conjugal transfer complement resistance protein TraT -
LG71_RS24955 (LG71_28410) 120205..122496 + 2292 WP_020316650 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   3451 GenBank   NZ_CP014777
Plasmid name   pFB2.2 Incompatibility group   -
Plasmid size   147881 bp Coordinate of oriT [Strand]   94544..94592 [-]
Host baterium   Pluralibacter gergoviae strain FB2

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   nirD, ncrC, ncrB, ncrA, arsH, arsC, arsB
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   AcrIE9