Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   120784
Name   oriT_pMB5632_3 in_silico
Organism   Klebsiella aerogenes strain 4417
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP103667 (25574..25623 [-], 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    		  TGTGTGGTGA
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 50 nt

>oriT_pMB5632_3
AAATCTGCAAAATTTTAATTTTGCGTAGTGTGTGGTGATTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   13110 GenBank   WP_259418653
Name   traI_M5S98_RS28125_pMB5632_3 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: 190229.94 Da        Isoelectric Point: 6.2218

>WP_259418653.1 conjugative transfer relaxase/helicase TraI [Klebsiella aerogenes]
MLSFSQVKSAGSAGNYYTDKDNYYVIGSMDERWQGKGAEALGLEGKVDKQVFTELLQGKLPDGSDLTRIQ
DGVNKHRPGYDLTFSAPKSVSMLAMLGGDKRLIDAHNRAVTVALNQVESLASTRVKRDGVSETVLTGNLI
IARFNHDTSRAQDPQIHTHSVVINTTQNGDKWQTLASDTVGKTGFSENILANRIALGKIYQNSLRADVES
MGYKTVDAGKNGMWEMEGVPVESFSTRSQELREAAGPDASLKSRDVAALDTRKSKEAIDPAEKMVEWMNT
LKETGFDIRGYREAADARAAELARAPAAPVNTDGPDITDVVTKAIAGLSDRKVQFTYADLLARTVGQLEA
KDGVFELARAGIDAAIEREQLIPLDREKGLFTSNIHVLDELAVKALSQEVQRQNHVSVTPDASVVRQVPF
SDAVSVLAQDRPVMGIVSGQGGATGQRERVAELTLMAREQGRDVHILAADNRSRDFLAGDVRLAGETVTG
KSALQDGTAFIPGGTLIVDQAEKLSLKETISLLDGAMRHNVQVLLSDSGKRSGTGSALTVLKDSGVNTYR
WQGGHQTTADIISEPDKGARYSRLAQEFAVSVREGQESVAQISGAREQSVLNGLIRDSLRHEGVLGEKDT
TITALTPVWLDSKSRGVRDYYREGMVMERWDPETRTHDRFVIDRVTASSNMLTLKDRDGVRLDLKVSAVD
SQWTLFRAETLPVAEGERLAVLGKIPDTRLKGGESITVMKVEDGQLTVQRPGQKTTQTLAVGAGVFDGIK
IGHGWVESPGRSVSETATVFASVTQRELDNATLNQLAQSGSHLRLYSAQDAARTTEKLSRHTAFSVVSEQ
LKTRSGETDLDAAIAQQKAGLRTPAEQAIHLAIPLLESEKLTFSRPQLLATALETGGGKVPMADIDTTIQ
AQIRSGQLLNVPVAHGHGNDLLISRQTWDAEKSILTHVLEGKDAVAPLMDRVPASLMTDLTAGQRAATRM
ILESTDRFTVVQGYAGVGKTTQFRAVMSAISLLPEETRPRVIGLAPTHRAVGEMQSAGVDARTTASFLHD
TQLLQRNGQTPDFSNTLFLLDESSMVGLADMAKAHSLIVAGGGRAVSSGDNDQLQPIAPGQPFRLMQQRS
AADVAIMKEIVRQVPELRPAVYSLIERDVHRALTTIEQVTPEQVPRKEGVWAPGSSVVEFTPAQEKAIQK
ALSEGETLPAGQPATLYEALVKDYTGRTPEAQSQTLIITHLNKDRRALNSLIHDARRENGETGKEEITLP
VLVTSNIRDGELRKLSTWTAHKEAVALVDNVYHRISKVDKDNQLITLTDSEGKERYISPREASAEGVTLY
RQEKITVSQGDRMRFSKSDLERGYVANSIWEVQSVSGDSVTLSDGKTTRTLTPKADQAQQHIDLAYAITA
HGAQGASEPYAIALEGVAGGREQMASFESAYVALSRMKQHVQVYTDSREGWIKAIKHSPEKATAHDILEP
RNDRAVKSADLLFGRARPLDETAAGRAALQQSGLAQGNSPGKFISPGKKYPQPHVALPAFDKNGKAAGIW
LSPLTDRDGRLEAIGGEGRIMGNDAARFVALQNSRNGESLLAGNMGEGVRMARDNPDTGVVVRLAGDDRP
WNPGAITGGRVWADPAPVGPVPQAGADIILPPEVLAQRAAEEQQRREMEKQAEQTAREVAGEVRKAGEPA
DRVKEVIGDVIRGLERDRPGPEKTTLPDDPQFRRQEAAIQQVASESLQRERLQAVERDMVRDLNREKTLG
GD

  Protein domains


Predicted by InterproScan.

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

(576-628)

AAA domain (AAA_30)

(970-1156)

DNA helicase TraI (TraI_C)

(1432-1554)

TrwC relaxase (TrwC)

(10-283)

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

(634-713)


  Protein structure



No available structure.




T4CP

ID   15387 GenBank   WP_023313941
Name   traD_M5S98_RS28120_pMB5632_3 insolico UniProt ID   _
Length   769 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 769 a.a.        Molecular weight: 85666.78 Da        Isoelectric Point: 5.2499

>WP_023313941.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacterales]
MSFNAKDMTQGGQIANMRFRMFGQIANIIFYVLFILFWVLCGLMLMYRLSWQTFVNGCVYWWCTTLGPMR
DIIRSQPVYTIQYYGQSLEYTSEQILADKYTIWCGEQLWTSFVFAAVVSLVICIVTFFIASWVLGRQGKQ
QSEDENTGGRQLSDKPKEVARQMKRDGMASDIKIGDLPILKNSEIQNFCLHGTVGSGKSEVIRRLLNYVR
ARGDMAIIYDRSCEFVKSYYDPSLDKILNPLDSRCAAWDLWKECLTLPDFDNISNTLIPMGTKEDPFWQG
SGRTIFAEGAYLMREDKDRSYEKLVDTMLSIKIDKLRAYLQNTPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEKNGEPFTIRDWMRGVREDRPNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGVKPAATLFDVMNTRAFFRSPSKEIA
EFAAGEIGEKEILKASEQYSYGADPVRDGVSTGKEKERETLVSYSDIQTLPDLSCYVTLPGPYPAVKLAL
KYKPRPKIAEGFIPRTLDARVDARLSALLEAREAEGSLARALFTPDAPASGTADTNSHAGEQPEPVSQPA
PAEVTVSPAPVKAPATTKMPAAEPSARTAEPPVLRVTTVPLIKPKAAAAAAAAATASSAGTPAAAAGGTE
QELAQQSAEQGQDMLPAGMNKDGVIEDMQAYDAWADEQTLRDMQRREEVNINHSHRHDEQDDVEIGGNF

  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: 25016..47859

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
M5S98_RS27935 (M5S98_27935) 20056..20217 + 162 Protein_27 hypothetical protein -
M5S98_RS28700 20148..20384 - 237 WP_306046130 hypothetical protein -
M5S98_RS27940 (M5S98_27940) 20366..21346 - 981 WP_023155665 IS5-like element ISKpn26 family transposase -
M5S98_RS27945 (M5S98_27945) 21439..21651 + 213 WP_019706020 hypothetical protein -
M5S98_RS27950 (M5S98_27950) 21662..21886 + 225 WP_014343499 hypothetical protein -
M5S98_RS27955 (M5S98_27955) 21967..22287 + 321 WP_004152720 type II toxin-antitoxin system RelE/ParE family toxin -
M5S98_RS27960 (M5S98_27960) 22277..22555 + 279 WP_004152721 helix-turn-helix transcriptional regulator -
M5S98_RS27965 (M5S98_27965) 22556..22969 + 414 WP_023287139 type II toxin-antitoxin system HigA family antitoxin -
M5S98_RS27970 (M5S98_27970) 23800..24621 + 822 WP_004152492 DUF932 domain-containing protein -
M5S98_RS27975 (M5S98_27975) 24654..24983 + 330 WP_053390269 DUF5983 family protein -
M5S98_RS27980 (M5S98_27980) 25016..25501 - 486 WP_259418651 transglycosylase SLT domain-containing protein virB1
M5S98_RS27985 (M5S98_27985) 25892..26308 + 417 WP_014343494 conjugal transfer relaxosome DNA-binding protein TraM -
M5S98_RS27990 (M5S98_27990) 26508..27245 + 738 WP_013214018 conjugal transfer protein TrbJ -
M5S98_RS27995 (M5S98_27995) 27360..27566 + 207 WP_171773970 TraY domain-containing protein -
M5S98_RS28000 (M5S98_28000) 27628..27996 + 369 WP_004194426 type IV conjugative transfer system pilin TraA -
M5S98_RS28005 (M5S98_28005) 28010..28315 + 306 WP_004144424 type IV conjugative transfer system protein TraL traL
M5S98_RS28010 (M5S98_28010) 28335..28901 + 567 WP_004144423 type IV conjugative transfer system protein TraE traE
M5S98_RS28015 (M5S98_28015) 28888..29628 + 741 WP_013214019 type-F conjugative transfer system secretin TraK traK
M5S98_RS28020 (M5S98_28020) 29628..31052 + 1425 WP_023287137 F-type conjugal transfer pilus assembly protein TraB traB
M5S98_RS28025 (M5S98_28025) 31124..31708 + 585 WP_023287136 type IV conjugative transfer system lipoprotein TraV traV
M5S98_RS28030 (M5S98_28030) 32031..32198 + 168 WP_259418652 hypothetical protein -
M5S98_RS28035 (M5S98_28035) 32220..33188 + 969 WP_022652343 IS5-like element IS903B family transposase -
M5S98_RS28040 (M5S98_28040) 33241..33315 + 75 Protein_49 hypothetical protein -
M5S98_RS28045 (M5S98_28045) 33316..33627 + 312 WP_013214022 hypothetical protein -
M5S98_RS28050 (M5S98_28050) 33694..34098 + 405 WP_004197817 hypothetical protein -
M5S98_RS28055 (M5S98_28055) 34475..34873 + 399 WP_014343490 hypothetical protein -
M5S98_RS28060 (M5S98_28060) 34945..37584 + 2640 WP_013214024 type IV secretion system protein TraC virb4
M5S98_RS28065 (M5S98_28065) 37584..37973 + 390 WP_013214025 type-F conjugative transfer system protein TrbI -
M5S98_RS28070 (M5S98_28070) 37973..38608 + 636 WP_013214026 type-F conjugative transfer system protein TraW traW
M5S98_RS28075 (M5S98_28075) 38643..39044 + 402 WP_004194979 hypothetical protein -
M5S98_RS28080 (M5S98_28080) 39041..40030 + 990 WP_013214027 conjugal transfer pilus assembly protein TraU traU
M5S98_RS28085 (M5S98_28085) 40043..40681 + 639 WP_004193871 type-F conjugative transfer system pilin assembly protein TrbC trbC
M5S98_RS28090 (M5S98_28090) 40740..42695 + 1956 WP_023287134 type-F conjugative transfer system mating-pair stabilization protein TraN traN
M5S98_RS28095 (M5S98_28095) 42727..42981 + 255 WP_023287133 conjugal transfer protein TrbE -
M5S98_RS28100 (M5S98_28100) 42959..43066 + 108 Protein_61 hypothetical protein -
M5S98_RS28105 (M5S98_28105) 43124..44092 - 969 WP_015958259 IS5 family transposase -
M5S98_RS28110 (M5S98_28110) 44107..44541 + 435 Protein_63 complement resistance protein TraT -
M5S98_RS28115 (M5S98_28115) 44734..45423 + 690 WP_013023831 hypothetical protein -
M5S98_RS28120 (M5S98_28120) 45550..47859 + 2310 WP_023313941 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   21213 GenBank   NZ_CP103667
Plasmid name   pMB5632_3 Incompatibility group   IncR
Plasmid size   120788 bp Coordinate of oriT [Strand]   25574..25623 [-]
Host baterium   Klebsiella aerogenes strain 4417

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   arsH, arsC, arsB
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -