Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100289
Name   oriT_pSMS35_130 in_silico
Organism   Escherichia coli SMS-3-5
Sequence Completeness      intact
NCBI accession of oriT (coordinates [strand])   NC_010488 (36948..37409 [+], 462 nt)
oriT length   462 nt
IRs (inverted repeats)      142..151, 154..163  (ATAGGGTCGT..ACGACCCTAT)
 231..238, 241..248  (GCAAAAAC..GTTTTTGC)
Location of nic site      257..258
Conserved sequence flanking the
  nic site    		  GTGGGGTGT|GG
Note   predicted by the oriTfinder

  oriT sequence  


Download         Length: 462 nt

>oriT_pSMS35_130
AAGAAGAGCACCCCTAGCAGCGCCCCTAGGGTCATACTATAAAAAAACGCACGGCGCTGCTAGGGGCGGCCCTAATATATCCAAATGTTTTTCATAAAATTTGTCAGTACTGACCCTAACAAGGGTCGCCATAGGGTCGCCATAGGGTCGTCAACGACCCTATTTAATAATGTAAAATAAATTAAAATACATTATTTAAAACATAAGCTAATGATTCAAAAAGCAAATCAGCAAAAACTTGTTTTTGCGTGGGGTGTGGTGCTTTTGGTGGTGAGAACCACCAACCTGTTGAGCCTTTTTGTGGAGTGGGTTAAATTATTTACGGATAAAGTCACCAGAGGTGGAAAAATGAAAAAATGGATGTTAGCCATCTGCCTGATGTTTATAAATGAGATCTGCCAGGCCACTGATTGCTTTGATCTTGCAGGCCGGGATTACAAAATAGATCCTGATTTACTGAGA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   360 GenBank   WP_000986979
Name   TraI_pSMS35_130 insolico UniProt ID   B1LRJ1
Length   1756 a.a. PDB ID   
Note   putative relaxase

  Relaxase protein sequence


Download         Length: 1756 a.a.        Molecular weight: 192104.07 Da        Isoelectric Point: 6.0923

>WP_000986979.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacteriaceae]
MMSIAQVRSAGSAGNYYTDKDNYYVLGSMGERWAGRGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQ
DGSNKHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQEPQLHTHAVVANVTQHNGEWKTLSSDKVGKTGFIENVYANQIAFGRLYREKLKEQVEA
LGYETEVVGKHGMWEMPGVPVEAFSGRSQTIREAVGEDASLKSRDVAALDTRKSKQHVDPEIKMTEWMQT
LKETGFDIRAYRDAAEQRAYTRTQTPGPASQDGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE
AGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS
DAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMAREQGREVQIIAADRRSQMNLKQDERLSGELITGR
RQLLEGMAFTPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKDAGVNTYRW
QGGEQRPATIISEPDRNVRYARLAGDFAASVKAGEESVAQVSGVREQAILTQAIRSELKTQGVLGHQEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDAQGETQVVRISSLDS
SWSLFRPEKMPVADGERLRVTGKIPGLRVSGGDRLQVASVSEDAMTVVVPGRAEPASLPVADSPFTALKL
ENGWVETPGHSVSDSAKVFAAVTQMAMDNATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI
KAHAGETSLETSISLQKAGLHTPAQQAIHLALPVLESKKLAFSMVDLLTEAKSFAAEGTGFTELGGEINA
QIKRGDLLYVDVAKGYGTGLLVSRASYEAEKSILRHILEGKEAVTPLMERVPGELMEKLTSGQRAATRMI
LETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPESMRPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT
QLQQRSGETPDFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA
ADVAIMKEIVRQTPELREAVYNLINRDVERALSGLERVKPSQVPRLEGAWAPEHSVMEFSHSQEAKLAEA
QQKAMLKGEAFPDVPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDAREKAGELGKEQVM
VPVLNTANIRDGELRRLSTWETHRDALVLVDNVYHRIAGISKDDGLITLEDAEGNTRLISPREAVAEGVT
LYTPDTIRVGTGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGQQTRVIRPGQERAEQHIDLAYAI
TAHGAQGASETFAIALEGTEGNRKQMAGFESAYVALSRMKQHVQVYTDNRQGWTDAINNAVQKGTAHDVF
EPKPDREVMNAERLFSTARELRDVAAGRAVLRQAGLAGGDSPARFIAPGRKYPQPYVALPAFDRNGKSAG
IWLNPLTTDDGNGLRGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQEGVRIARDNPDSGVVVRIAGE
GRPWNPGAITGGRVWGDIPDNSVQPGAGNGEPVTAEVLAQRQAEEAIRRETERRADEIVRKMAENKPDLP
DGKTEQAVREIAGQERDRAAITEREAALPESVLRESQREREAVREVARENLLQERLQQMERDMVRDLQKE
KTLGGD

  Protein domains


Predicted by InterproScan.

TrwC relaxase (TrwC)

(10-283)

DNA helicase TraI (TraI_C)

(1434-1557)

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

(575-627)

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

(633-712)

AAA domain (AAA_30)

(969-1156)


  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 11124..37805

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
ECSMS35_RS24985 (EcSMS35_A0011) 11124..13295 - 2172 WP_000009362 type IV conjugative transfer system coupling protein TraD virb4
ECSMS35_RS24990 (EcSMS35_A0012) 13548..14279 - 732 WP_000850422 conjugal transfer complement resistance protein TraT -
ECSMS35_RS24995 (EcSMS35_A0013) 14311..14814 - 504 WP_000605510 hypothetical protein -
ECSMS35_RS25000 (EcSMS35_A0014) 14829..17651 - 2823 WP_001007026 conjugal transfer mating-pair stabilization protein TraG traG
ECSMS35_RS25005 (EcSMS35_A0015) 17648..19021 - 1374 WP_001137358 conjugal transfer pilus assembly protein TraH traH
ECSMS35_RS25010 (EcSMS35_A0016) 19021..19383 - 363 WP_001443292 P-type conjugative transfer protein TrbJ -
ECSMS35_RS25015 (EcSMS35_A0017) 19313..19858 - 546 WP_000052618 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
ECSMS35_RS25020 (EcSMS35_A0018) 19845..20129 - 285 WP_000624110 type-F conjugative transfer system pilin chaperone TraQ -
ECSMS35_RS25025 (EcSMS35_A0019) 20248..20595 - 348 WP_001287893 conjugal transfer protein TrbA -
ECSMS35_RS25030 (EcSMS35_A0020) 20611..21354 - 744 WP_001030378 type-F conjugative transfer system pilin assembly protein TraF traF
ECSMS35_RS25035 (EcSMS35_A0021) 21347..21604 - 258 WP_000864325 conjugal transfer protein TrbE -
ECSMS35_RS25040 (EcSMS35_A0022) 21631..23439 - 1809 WP_000821821 type-F conjugative transfer system mating-pair stabilization protein TraN traN
ECSMS35_RS25045 (EcSMS35_A0023) 23436..24074 - 639 WP_001104248 type-F conjugative transfer system pilin assembly protein TrbC trbC
ECSMS35_RS25050 (EcSMS35_A0024) 24102..24554 - 453 WP_000069427 hypothetical protein -
ECSMS35_RS25055 (EcSMS35_A0025) 24584..25045 - 462 WP_000277845 hypothetical protein -
ECSMS35_RS25060 (EcSMS35_A0026) 25071..26063 - 993 WP_000830839 conjugal transfer pilus assembly protein TraU traU
ECSMS35_RS25065 (EcSMS35_A0027) 26060..26692 - 633 WP_001203745 type-F conjugative transfer system protein TraW traW
ECSMS35_RS25070 (EcSMS35_A0028) 26689..27075 - 387 WP_000214084 type-F conjugative transfer system protein TrbI -
ECSMS35_RS25075 (EcSMS35_A0029) 27072..29699 - 2628 WP_001064268 type IV secretion system protein TraC virb4
ECSMS35_RS27735 (EcSMS35_A0030) 29859..30080 - 222 WP_001278689 conjugal transfer protein TraR -
ECSMS35_RS25085 (EcSMS35_A0031) 30215..30730 - 516 WP_000809906 type IV conjugative transfer system lipoprotein TraV traV
ECSMS35_RS25090 (EcSMS35_A0032) 30727..30978 - 252 WP_001038341 conjugal transfer protein TrbG -
ECSMS35_RS25095 (EcSMS35_A0033) 30975..31292 - 318 WP_001057292 conjugal transfer protein TrbD virb4
ECSMS35_RS25100 (EcSMS35_A0034) 31289..31861 - 573 WP_000002780 conjugal transfer pilus-stabilizing protein TraP -
ECSMS35_RS25105 (EcSMS35_A0035) 31851..33278 - 1428 WP_000146685 F-type conjugal transfer pilus assembly protein TraB traB
ECSMS35_RS25110 (EcSMS35_A0036) 33278..34006 - 729 WP_001230787 type-F conjugative transfer system secretin TraK traK
ECSMS35_RS25115 (EcSMS35_A0037) 33993..34559 - 567 WP_000399792 type IV conjugative transfer system protein TraE traE
ECSMS35_RS25120 (EcSMS35_A0038) 34581..34892 - 312 WP_000012106 type IV conjugative transfer system protein TraL traL
ECSMS35_RS25125 (EcSMS35_A0039) 34907..35266 - 360 WP_000340272 type IV conjugative transfer system pilin TraA -
ECSMS35_RS25130 (EcSMS35_A0040) 35300..35527 - 228 WP_001254386 conjugal transfer relaxosome protein TraY -
ECSMS35_RS25135 (EcSMS35_A0041) 35621..36307 - 687 WP_000332484 PAS domain-containing protein -
ECSMS35_RS25140 (EcSMS35_A0042) 36498..36881 - 384 WP_000124981 conjugal transfer relaxosome DNA-binding protein TraM -
ECSMS35_RS25145 (EcSMS35_A0043) 37158..37805 + 648 WP_000614936 transglycosylase SLT domain-containing protein virB1
ECSMS35_RS25150 (EcSMS35_A0045) 38102..38923 - 822 WP_001234469 DUF932 domain-containing protein -
ECSMS35_RS25155 (EcSMS35_A0046) 39046..39333 - 288 WP_000107535 hypothetical protein -
ECSMS35_RS28535 (EcSMS35_A0047) 39358..39564 - 207 WP_000547939 hypothetical protein -
ECSMS35_RS30000 39634..39807 + 174 Protein_46 hypothetical protein -
ECSMS35_RS30005 (EcSMS35_A0049) 39805..40035 - 231 WP_001426396 hypothetical protein -
ECSMS35_RS25165 (EcSMS35_A0050) 40255..40380 - 126 WP_001372321 type I toxin-antitoxin system Hok family toxin -
ECSMS35_RS30010 40322..40471 - 150 Protein_49 plasmid maintenance protein Mok -
ECSMS35_RS29575 40493..40681 + 189 WP_001299721 hypothetical protein -
ECSMS35_RS25175 (EcSMS35_A0052) 40650..41412 - 763 Protein_51 plasmid SOS inhibition protein A -
ECSMS35_RS25180 (EcSMS35_A0053) 41409..41843 - 435 WP_000845895 conjugation system SOS inhibitor PsiB -

Host bacterium

ID   751 GenBank   NC_010488
Plasmid name   pSMS35_130 Incompatibility group   IncFIB
Plasmid size   130440 bp Coordinate of oriT [Strand]   36948..37409 [+]
Host baterium   Escherichia coli SMS-3-5

Cargo genes

Drug resistance gene   sitABCD, catA2, dfrA14, sul2, aph(3'')-Ib, aph(6)-Id, blaTEM-1B, aadA2, tet(A), aph(3')-Ia
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -