Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   120010
Name   oriT_pNUITM-VR1_3 in_silico
Organism   Raoultella ornithinolytica strain NUITM-VR1
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_AP025012 (101972..102020 [-], 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    		  GGTGTGGTGA
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 49 nt

>oriT_pNUITM-VR1_3
AATCTGCAAAATTTTAATTTTGCGTGGGGTGTGGTGATTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   12613 GenBank   WP_104443343
Name   traI_LDO46_RS30715_pNUITM-VR1_3 insolico UniProt ID   _
Length   1753 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1753 a.a.        Molecular weight: 190413.40 Da        Isoelectric Point: 6.3185

>WP_104443343.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Klebsiella/Raoultella group]
MMSIGSVKAAGSAGNYYTDKDNYYVIGSMDERWQGKGAEALGIDGKAVDKALFTELLKGKLPDGSDLTRI
QDGANKHRPGYDLTFSAPKSVSVMAMLGGDKRLIDAHNQAVTEAVRQLETLAATRVMTDGKSETVLTGNL
IVAKFNHDTNRNQEPQIHTHAVVINATQNGDKWQSLGTDKIGKTGFIENVYANQIAFGKLYREAFKPLVE
KLGYETEVVGKHGMWEMKGVPVEPFSTRTQEVREAAGPDASLKSRDVAALDTRKSKEAIDPAEKMVEWMN
TLKETGFDIRGYREAADARAAELARAPAAPVNTDGPDITDVVTKAIAGLSDRKVQFTYADLLARTVGQLE
AKDGVFELARKGIDAAIEREQLIPLDREKGLFTSNIHVLDELAVKALSQEVQRQNHVSVTPDASVVRQVP
FSDAVSVLAQDRPVMGIVSGQGGATGQRERVAELTLMAREQGRDVHILAADNRSRDFLAGDVRLAGETVT
GKSALQDGTAFIPGGTLIVDQAEKLSLKETISLLDGAMRHNVQVLLSDSGKRSGTGSALTVLKDSGVNTY
RWQGGHQTTADIISEPDKGARYSRLAQEFAVSVREGQESVAQISGTREQSVLNGLIRDSLRHEGVLGEKD
TTITALTPVWLDSKSRGVRDYYREGMVMERWDPETRTHDRFVIDRVTGSSNMLTLKDREGGRLDLKVSAV
DSQWTLFRAETLPVAEGERLAVLGKIPDTRLKGGESITVMKVEEGQLTVQRPGQKTTQTLAVGAGVFDGI
KIGHGWVESPGRSVSETATVFASVTQRELDNATLNQLAQSGSHLRLYSAQDAARTTEKLSRHTSFSVVSE
QLKTRSGETDLDAAIAQQKAGLRTPAEQAIHLAIPLLESEKLTFSRPQLLATALETGGGKVPMADIDTTI
QTQIRSGQLLNVPVAHGYGNDLLISRQTWDAEKSILTHVLEGKGAVAPLMDRVPASLMTDLTAGQRAATR
MILESTDRFTVVQGYAGVGKTTQFRAVMSAISLLPEETRPRVIGLAPTHRAVGEMQSAGVEARTTASFLH
DTQLLQRNGQTPDFSNTLFLLDESSMVGLADMAKAHSLIVAGGGRAVSSGDNDQLQPIAPGQPFRLMQQR
SAADVAIMKEIVRQVPELRPAVYSLIERDVHRALTTIEQVTPEQVPRKEGVWAPGSSVVEFTQAQEKAIQ
KALSEGETLPAGQPASLYEALVKDYTGRTPEAQSQTLVITHLNKDRRALNSLIHDARRENGETGKEEITL
PVLVTSNIRDGELRKLSTWTAHKEAVALVDNVYHRISKVDKDNQLITLTDSEGKERFISPREASAEGVTL
YRQEKITVSQGDRMRFSKSDPERGYVANSIWEVQSVSGDSVTLSDGKLTRTLTPKADQAQQHIDLAYAIT
AHGAQGASEPYAIALEGVAGGREQMASFESAYVALSRMKQHVQVYTDSREGWIKAIQHSPEKATAHDILE
PRNDRAVKSADLLFGRARPLDETAAGRAALQQSGLAQGSSPGRFISPGKKYPQPHVALPAFDKNGKAAGI
WLSPLTDRDGRLEAIGGEGRIMGNDAARFVALQNSRNGESLLAGNMGEGVRMARDNPDTGVVVRLAGDDR
PWNPGAMTGGRVWADPAPVAPVPQAGADIILPPEVLAQRAAEEQQRREMEKQAEQTAREVAGEARKAGEP
ADRVKEVIGDVIRGLERDRPGTEKTTLPDDPQFRRQEAAIQQVASEGLQRERLQAVERDMVRDLNREKTL
GGD

  Protein domains


Predicted by InterproScan.

TrwC relaxase (TrwC)

(10-284)

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

(635-714)

AAA domain (AAA_30)

(971-1157)

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

(577-629)

DNA helicase TraI (TraI_C)

(1433-1555)


  Protein structure



No available structure.




T4CP

ID   14811 GenBank   WP_032454979
Name   traD_LDO46_RS30710_pNUITM-VR1_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: 86062.11 Da        Isoelectric Point: 5.0175

>WP_032454979.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIANMRFRMFGQIANIIFYVLFILFWVLCGLMLMYRLSWQTFVNGCVYWWCTTLGPMR
DIIRSQPVYTIQYYGQSLEYTSEQILADKYTIWCGEQLWTSFVFAAVVSLVICIVTFFIASWVLGRQGKQ
QSEDENTGGRQLSDKPKEVARQMKRDGMASDIKIGDLPILKNSEIQNFCLHGTVGSGKSEVIRRLLNYVR
ARGDMAIIYDRSCEFVKSYYDPSLDKILNPLDSRCAAWDLWKECLTLPDFDNISNTLIPMGTKEDPFWQG
SGRTIFAEGAYLMREDKDRSYEKLVDTMLSIKIDKLRAYLQNTPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEKNGEPFTIRDWMRGVREDRPNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGVKPAATLFDVMNTRAFFRSPSREIA
EFAAGEIGEKEILKASEQYSYGADPVRDGVSTGKEKERETLVSYSDIQTLPDLSCYVTLPGPYPAVKLAL
KYKPRPKIAEGFIPRTLDARVDARLSALLEAREAEGSLARALFTPDAPEPGPADTDSHAGEQPEPVSQPA
PADMTVSPAPVKAPPTTKRPAEEPSVRATEPSVLRLTTVPLIKPKAAAAAAAAATASSAGTPAAAAGGTE
QELAQQSAEQGQDMLPAGMNEDGVIEDMQAYDAWLADEQTQRDMQRREEVNINHSHRHDEQDEVEIGGNF

  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: 101414..129918

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
LDO46_RS30530 (NUITMVR1_60300) 98983..99382 + 400 Protein_97 hypothetical protein -
LDO46_RS30535 (NUITMVR1_60310) 100198..101019 + 822 WP_032454971 DUF932 domain-containing protein -
LDO46_RS30540 (NUITMVR1_60320) 101052..101381 + 330 WP_011977736 DUF5983 family protein -
LDO46_RS30545 (NUITMVR1_60330) 101414..101899 - 486 WP_001568108 transglycosylase SLT domain-containing protein virB1
LDO46_RS30550 (NUITMVR1_60340) 102331..102714 + 384 WP_224050217 conjugal transfer relaxosome DNA-binding protein TraM -
LDO46_RS30560 (NUITMVR1_60370) 103890..104045 + 156 Protein_103 type IV conjugative transfer system pilin TraA -
LDO46_RS30565 (NUITMVR1_60380) 104059..104364 + 306 WP_004178059 type IV conjugative transfer system protein TraL traL
LDO46_RS30570 (NUITMVR1_60390) 104384..104950 + 567 WP_004144423 type IV conjugative transfer system protein TraE traE
LDO46_RS30575 (NUITMVR1_60400) 104937..105677 + 741 WP_013214019 type-F conjugative transfer system secretin TraK traK
LDO46_RS30580 (NUITMVR1_60410) 105677..107101 + 1425 WP_023284634 F-type conjugal transfer pilus assembly protein TraB traB
LDO46_RS30585 (NUITMVR1_60420) 107215..107799 + 585 WP_032441881 type IV conjugative transfer system lipoprotein TraV traV
LDO46_RS30590 (NUITMVR1_60430) 107931..108341 + 411 WP_004152499 hypothetical protein -
LDO46_RS30595 (NUITMVR1_60440) 108447..108665 + 219 WP_004195235 hypothetical protein -
LDO46_RS30600 (NUITMVR1_60450) 108666..108977 + 312 WP_004195240 hypothetical protein -
LDO46_RS30605 (NUITMVR1_60460) 109044..109448 + 405 WP_004197817 hypothetical protein -
LDO46_RS30610 (NUITMVR1_60470) 109826..110224 + 399 WP_074184101 hypothetical protein -
LDO46_RS30615 (NUITMVR1_60480) 110296..112938 + 2643 WP_032454974 type IV secretion system protein TraC virb4
LDO46_RS30620 (NUITMVR1_60490) 112935..113324 + 390 WP_004167468 type-F conjugative transfer system protein TrbI -
LDO46_RS30625 (NUITMVR1_60500) 113324..113959 + 636 WP_032441885 type-F conjugative transfer system protein TraW traW
LDO46_RS30630 (NUITMVR1_60510) 113994..114395 + 402 WP_004194979 hypothetical protein -
LDO46_RS30635 (NUITMVR1_60520) 114392..115381 + 990 WP_057193347 conjugal transfer pilus assembly protein TraU traU
LDO46_RS30640 (NUITMVR1_60530) 115394..116032 + 639 WP_004193871 type-F conjugative transfer system pilin assembly protein TrbC trbC
LDO46_RS30645 (NUITMVR1_60540) 116091..118046 + 1956 WP_055316764 type-F conjugative transfer system mating-pair stabilization protein TraN traN
LDO46_RS30650 (NUITMVR1_60550) 118078..118332 + 255 WP_224050194 conjugal transfer protein TrbE -
LDO46_RS30655 (NUITMVR1_60560) 118310..118558 + 249 WP_004152675 hypothetical protein -
LDO46_RS30660 (NUITMVR1_60570) 118571..118897 + 327 WP_004144402 hypothetical protein -
LDO46_RS30665 (NUITMVR1_60580) 118918..119670 + 753 WP_004152677 type-F conjugative transfer system pilin assembly protein TraF traF
LDO46_RS30670 (NUITMVR1_60590) 119681..119920 + 240 WP_004144400 type-F conjugative transfer system pilin chaperone TraQ -
LDO46_RS30675 (NUITMVR1_60600) 119892..120449 + 558 WP_055316562 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
LDO46_RS30680 (NUITMVR1_60610) 120495..120938 + 444 WP_032454976 F-type conjugal transfer protein TrbF -
LDO46_RS30685 (NUITMVR1_60620) 120916..122295 + 1380 WP_074184099 conjugal transfer pilus assembly protein TraH traH
LDO46_RS30690 (NUITMVR1_60630) 122295..125144 + 2850 WP_013609534 conjugal transfer mating-pair stabilization protein TraG traG
LDO46_RS30695 (NUITMVR1_60640) 125147..125680 + 534 WP_014343486 conjugal transfer protein TraS -
LDO46_RS30700 (NUITMVR1_60650) 125866..126597 + 732 WP_013023830 conjugal transfer complement resistance protein TraT -
LDO46_RS30705 (NUITMVR1_60660) 126790..127479 + 690 WP_013023831 hypothetical protein -
LDO46_RS30710 (NUITMVR1_60670) 127606..129918 + 2313 WP_032454979 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   20440 GenBank   NZ_AP025012
Plasmid name   pNUITM-VR1_3 Incompatibility group   IncFII
Plasmid size   139908 bp Coordinate of oriT [Strand]   101972..102020 [-]
Host baterium   Raoultella ornithinolytica strain NUITM-VR1

Cargo genes

Drug resistance gene   aph(3'')-Ib, aph(6)-Id, qnrS1, blaNDM-1
Virulence gene   htpB
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -