Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   120620
Name   oriT_pAUSMDU8141-3 in_silico
Organism   Citrobacter farmeri strain AUSMDU00008141
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP022698 (28285..28334 [-], 50 nt)
oriT length   50 nt
IRs (inverted repeats)      7..14, 17..24  (GCAAAATT..AATTTTGC)
Location of nic site      33..34
Conserved sequence flanking the
  nic site    		  GGTGTGGTGA
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 50 nt

>oriT_pAUSMDU8141-3
AAATCTGCAAAATTTTAATTTTGCGTGGGGTGTGGTGATTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   12989 GenBank   WP_004153015
Name   traI_CI104_RS28460_pAUSMDU8141-3 insolico UniProt ID   A0A8A5TN24
Length   1753 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1753 a.a.        Molecular weight: 190492.51 Da        Isoelectric Point: 6.3661

>WP_004153015.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacterales]
MMSIGSVKSAGSAGNYYTDKDNYYVIGSMDERWQGKGAEALGIDGKAVDKALFTELLKGKLPDGSDLTRI
QDGANKHRPGYDLTFSAPKSVSVMAMLGGDKRLIDAHNQAVTEAVRQLETLAATRVMTDGKSETVLTGNL
IVAKFNHDTNRNQEPQIHTHAVVINATQNGDKWQSLGTDKIGKTGFIENVYANQIAFGKLYREAFKPLVE
KLGYETEVVGKHGMWEMKGVPVEPFSTRSQEVREAAGPDASLKSRDVAALDTRKSKEAIDPAEKMVEWMN
TLKETGFDIRGYREAADARAAELARAPAAPVNTDGPDITDVVTKAIAGLSDRKVQFTYADLLARTVGQLE
AKDGMFELARKGIDAAIEREQLIPLDREKGLFTSNIHVLDELAVKALSQEVQRHNHVSVTPDASVVRQVP
FSDAVSVLAQDRPVMGIVSGQGGASGQRERVAELTLMAREQGRDVHILAADNRSRDFLAGDVRLAGETVT
GKSALQDGTAFIPGGTLIVDQAEKLSLKETISLLDGAMRHNVQVLLSDSGKRSGTGSALTVLKDSGVNTY
RWQGGHQTTADIISEPDKGARYSRLAQEFAVSVREGQKSVAQISGTREQSVLNGLIRDSLRQEGVLGEKD
TTITALTPVWLDSKSRGVRDYYREGMVMERWDPETRTHDRFVIDRVTASSNMLTLKDREGGRLDLKVSAV
DSQWTLFRAETLPVAEGERLAVLGKIPDTRLKGGESITVMKVEEGQLTVQRPGQKTTQTLAVGAGVFDGI
KIGHGWVESPGRSVSETATVFASVTQRELDNATLNQLAQSGSHLRLYSAQDAARTTEKLSRHTSFSVVSE
QLKTRSGETDLDAAIAQQKAGLRTPAEQAIHLAIPLLESEKLTFSRPQLLATALETGGGKVPMADIDTTI
QTQIRSGQLLNAPVAHGYGNDLLISRQTWDAEKSILTHVLEGKGAVAPLMDRVPASLMTDLTAGQRAATR
MILESTDRFTVVQGYAGVGKTTQFRAVMSAISLLPEETRPRVIGLAPTHRAVGEMQSAGVEARTTASFLH
DTQLLQRNGQTPDFSNTLFLLDESSMVGLADMAKAHSLIVAGGGRAVSSGDNDQLQPIAPGQPFRLMQQR
SAADVAIMKEIVRQVPELRPAVYSLIERDVHRALTTIEQVTPEQVPRKEGVWAPGSSVVEFTQAQEKAIQ
KALSEGETLPAGQPASLYEALVKDYTGRTPEAQSQTLVITHLNKDRRALNSLIHDARRENGETGKEEITL
PVLVTSNIRDGELRKLSTWTAHKEAVALVDNVYHRISKVDKDNQLITLTDSEGKERFISPREASAEGVTL
YRQEKITVSQGDRMRFSKSDPERGYVANSIWEVQSVSGDSVTLSDGKLTRTLTPKADQAQQHIDLAYAIT
AHGAQGASEPYAIALEGVAGGREQMASFESAYVALSRMKQHVQVYTDSREGWIKAIQHSPEKATAHDILE
PRNDRAVKSADLLFGRARPLDETAAGRAALQQSGLAQGSSPGKFISPGKKYPQPHVALPAFDKNGKAAGI
WLSPLTDRDGRLEAIGGEGRIMGNEDARFVALQNSRNGESLLAGNMGEGVRMARDNPDTGVVVRLAGDDR
PWNPGAMTGGRVWAEPAPVAPVPQAGADIILPPEVLAQRAAEEQQRREMEKQAEQTAREVAGEARKAGEP
ADRVKEVIGDVIRGLERDRPGTEKTTLPDDPQFRRQEAAIQQVASESLQRERLQAVERDMVRDLNREKTL
GGD

  Protein domains


Predicted by InterproScan.

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

(635-714)

DNA helicase TraI (TraI_C)

(1433-1555)

TrwC relaxase (TrwC)

(10-284)

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

(577-629)

AAA domain (AAA_30)

(971-1157)


  Protein structure



No available structure.




T4CP

ID   15252 GenBank   WP_004152620
Name   traD_CI104_RS28455_pAUSMDU8141-3 insolico UniProt ID   _
Length   770 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 770 a.a.        Molecular weight: 85871.84 Da        Isoelectric Point: 5.0101

>WP_004152620.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacterales]
MSFNAKDMTQGGQIANMRFRMFGQIANIIFYVLFILFWVLCGLMLMYRLSWQTFVNGCVYWWCTTLGPMR
DIIRSQPVYTIQYYGQSLEYTSEQILADKYTIWCGEQLWTGFAFAAVVSLVICIVTFFIASWVLGRQGKQ
QSEDENTGGRQLSDKPKEVARQMKRDGVASDIKIGDLPILKNSEIQNFCLHGTVGSGKSEVIRRLLNYVR
ARGDMAIIYDRSCEFVKSYYDPSLDKILNPLDSRCAAWDLWKECLTLPDFDNISNTLIPMGTKEDPFWQG
SGRTIFAEGAYLMREDDDRSYEKLVDTMLSIKIDKLRAYLQNTPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEKNGEPFTIRDWMRGVREDRPNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGVKPAATLFDVMNTRAFFRSPSKEIA
EFAAGEIGEKEILKASEQYSYGADPVRDGVSTGKEKERETLVSYSDIQTLPDLSCYVTLPGPYPAVKLAL
KYKPRPKIAEGFIPRTLDARVDARLSALLEAREAEGSLARALFTPDTPEPGPADTDSHASEQPEPVSPPA
PAVMTVTPAPVKSPPTTKRPAAEPSVRATEPPVLRGTTVPLIKPKAAAAATAASTASSAGAPAAAAGGTE
QELAQQSAEQGQDMLPAGMNEDGVIEDMQAYDAWLADEQTQRDMQRREEVNINHSHRHDEQDDVEIGGNF

  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: 27727..58072

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
CI104_RS28215 (CI104_28215) 22829..23179 + 351 WP_004153414 hypothetical protein -
CI104_RS28230 (CI104_28230) 23809..24162 + 354 WP_004152748 hypothetical protein -
CI104_RS28235 (CI104_28235) 24219..24566 + 348 WP_004152749 hypothetical protein -
CI104_RS28240 (CI104_28240) 24661..24807 + 147 WP_004152750 hypothetical protein -
CI104_RS28245 (CI104_28245) 24858..25691 + 834 WP_004152751 N-6 DNA methylase -
CI104_RS28265 (CI104_28265) 26511..27332 + 822 WP_004152492 DUF932 domain-containing protein -
CI104_RS28270 (CI104_28270) 27365..27694 + 330 WP_011977736 DUF5983 family protein -
CI104_RS28275 (CI104_28275) 27727..28212 - 486 WP_001568108 transglycosylase SLT domain-containing protein virB1
CI104_RS28280 (CI104_28280) 28634..29032 + 399 WP_004152493 conjugal transfer relaxosome DNA-binding protein TraM -
CI104_RS28285 (CI104_28285) 29206..29892 + 687 WP_004152494 transcriptional regulator TraJ family protein -
CI104_RS28290 (CI104_28290) 29971..30357 + 387 WP_004152495 TraY domain-containing protein -
CI104_RS28295 (CI104_28295) 30411..30779 + 369 WP_004152496 type IV conjugative transfer system pilin TraA -
CI104_RS28300 (CI104_28300) 30793..31098 + 306 WP_004144424 type IV conjugative transfer system protein TraL traL
CI104_RS28305 (CI104_28305) 31118..31684 + 567 WP_004144423 type IV conjugative transfer system protein TraE traE
CI104_RS28310 (CI104_28310) 31671..32411 + 741 WP_004152497 type-F conjugative transfer system secretin TraK traK
CI104_RS28315 (CI104_28315) 32411..33835 + 1425 WP_004155033 F-type conjugal transfer pilus assembly protein TraB traB
CI104_RS28320 (CI104_28320) 33949..34533 + 585 WP_004161368 type IV conjugative transfer system lipoprotein TraV traV
CI104_RS28325 (CI104_28325) 34665..35075 + 411 WP_004152499 hypothetical protein -
CI104_RS28330 (CI104_28330) 35181..35399 + 219 WP_004152501 hypothetical protein -
CI104_RS28335 (CI104_28335) 35400..35711 + 312 WP_004152502 hypothetical protein -
CI104_RS28340 (CI104_28340) 35778..36182 + 405 WP_004152503 hypothetical protein -
CI104_RS29410 (CI104_28345) 36225..36614 + 390 WP_004153076 hypothetical protein -
CI104_RS28350 (CI104_28350) 36622..37020 + 399 WP_011977783 hypothetical protein -
CI104_RS28355 (CI104_28355) 37092..39731 + 2640 WP_004152505 type IV secretion system protein TraC virb4
CI104_RS28360 (CI104_28360) 39731..40120 + 390 WP_004152506 type-F conjugative transfer system protein TrbI -
CI104_RS28365 (CI104_28365) 40120..40746 + 627 WP_004152507 type-F conjugative transfer system protein TraW traW
CI104_RS28370 (CI104_28370) 40788..41177 + 390 WP_004152508 hypothetical protein -
CI104_RS28375 (CI104_28375) 41174..42163 + 990 WP_011977785 conjugal transfer pilus assembly protein TraU traU
CI104_RS28380 (CI104_28380) 42176..42814 + 639 WP_004152672 type-F conjugative transfer system pilin assembly protein TrbC trbC
CI104_RS28385 (CI104_28385) 42873..44828 + 1956 WP_004152673 type-F conjugative transfer system mating-pair stabilization protein TraN traN
CI104_RS28390 (CI104_28390) 44860..45114 + 255 WP_004152674 conjugal transfer protein TrbE -
CI104_RS28395 (CI104_28395) 45092..45340 + 249 WP_004152675 hypothetical protein -
CI104_RS28400 (CI104_28400) 45353..45679 + 327 WP_004152676 hypothetical protein -
CI104_RS28405 (CI104_28405) 45700..46452 + 753 WP_004152677 type-F conjugative transfer system pilin assembly protein TraF traF
CI104_RS28410 (CI104_28410) 46463..46702 + 240 WP_004144400 type-F conjugative transfer system pilin chaperone TraQ -
CI104_RS28415 (CI104_28415) 46674..47231 + 558 WP_004152678 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
CI104_RS28420 (CI104_28420) 47277..47720 + 444 WP_004152679 F-type conjugal transfer protein TrbF -
CI104_RS28425 (CI104_28425) 47698..49077 + 1380 WP_004165169 conjugal transfer pilus assembly protein TraH traH
CI104_RS28430 (CI104_28430) 49077..51926 + 2850 WP_004152624 conjugal transfer mating-pair stabilization protein TraG traG
CI104_RS28435 (CI104_28435) 51939..52487 + 549 WP_004152623 conjugal transfer entry exclusion protein TraS -
CI104_RS28440 (CI104_28440) 52671..53402 + 732 WP_004152622 conjugal transfer complement resistance protein TraT -
CI104_RS28445 (CI104_28445) 53704..54908 + 1205 WP_085956494 IS3 family transposase -
CI104_RS29340 54942..55631 + 690 WP_004198206 hypothetical protein -
CI104_RS28455 (CI104_28455) 55760..58072 + 2313 WP_004152620 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   21049 GenBank   NZ_CP022698
Plasmid name   pAUSMDU8141-3 Incompatibility group   IncR
Plasmid size   107249 bp Coordinate of oriT [Strand]   28285..28334 [-]
Host baterium   Citrobacter farmeri strain AUSMDU00008141

Cargo genes

Drug resistance gene   blaKPC-2, blaOXA-9, blaTEM-1A
Virulence gene   -
Metal resistance gene   merE, merD, merA
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   AcrIE9