Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100587
Name   oriT_pMC-NDM in_silico
Organism   Escherichia coli strain NMI5428/11
Sequence Completeness      intact
NCBI accession of oriT (coordinates [strand])   NC_025106 (36855..37316 [-], 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_pMC-NDM
AAGAAGAGCACCCCTAGCAGCGCCCCTAGGGTCATACTATAAAAAAACGCACGGCGCTGCTAGGGGCGGCCCTAATATATCCAAATGTTTTTCATAAAATTTGTCAGTACTGACCCTAACAAGGGTCGCCATAGGGTCGCCATAGGGTCGTCAACGACCCTATTTAATAATGTAAAATAAATTAAAATACATTATTTAAAACATAAGCTAATGATTCAAAAAGCAAATCAGCAAAAACTTGTTTTTGCGTGGGGTGTGGTGCTTTTGGTGGTGAGAACCACCAACCTGTTGAGCCTTTTTGTGGAGTGGGTTAAATTATTTACGGATAAAGTCACCAGAGGTGGAAAAATGAAAAAGTGGATGTTAGCCATCTGCCTGATGTTTATAAATGAGATCTGCCAGGCCACTGATTGCTTTGATCTTGCAGGCCGGGATTACAAAATAGATCCTGATTTACTGAGA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   659 GenBank   YP_009066506
Name   TraI_pMC-NDM insolico UniProt ID   I1WZQ7
Length   1756 a.a. PDB ID   
Note   putative relaxase

  Relaxase protein sequence


Download         Length: 1756 a.a.        Molecular weight: 191914.74 Da        Isoelectric Point: 6.1060

>YP_009066506.1 TraI protein (plasmid) [Escherichia coli]
MMSIAQVRSAGSAGNYYTDKDNYYVLGSMGERWAGRGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQ
DGSNRHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQEPQLHTHAVVANVTQHNGEWKTLSSDKVGKTGFIENVYANQIAFGRLYREKLKEQVEA
LGYETEVVGKHGMWEMPGVPVEAFSGRSQAIREAVGEDASLKSRDVAALDTRKSKQHVDPEVRMAEWMQT
LKETGFDIRAYRDAADQRAETRTQAPGAVSQEGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE
NGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS
DAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMVREQGREVQIIAADRRSQMNLKQDERLSGELITGR
RQLLEGMAFTPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKDAGVNTYRW
QGGEQRPATIISEPDRNVRYARLAGDFAASVKAGEESVAQVSGVREQAILTQAIRSELKTQGVLGHQEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDAQGETQVVRISSLDS
SWSLFRPEKMPVADGERLRVTGKISGLRVSGGDRLQVASVSEDAMTVVVPGRAEPASLPVSDSPFTALKL
ENGWVETPGHSVSDSAKVFASVTQMAMDNATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI
KARAGETLLETAISLQKTGLHTPAQQAIHLALPVVESKNLAFSMVDLLTEAKSFAAEGTSFTELGGEINA
QIKRGDLLYVDVAKGYGTGLLVSRASYEAEKSILRHILEGKEAVTPLMERVPGELMEKLTSGQRAATRMI
LETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPESERPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT
QLLQRSGETPNFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA
ADVAIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRLEGAWAPEHSVTEFSHSQEAKLAEA
QQKAMQKGEAFPDVPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDAREKAGELGKEQVM
VPVLNTANIRDGELRRLSTWETHRDALALVDNVYHRIAGISKDDGLITLQDAEGNTRLISPREAVAEGVT
LYTPDTIRVGTGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGQQTRVIRPGQERAEQHIGLAYAI
TAHGAQGASETFAIALEGTEGNRKQMAGFESAYVALSRMKQHVQVYTDNRQGWTDAINNAVQKGTAHDVL
EPKSDREVMNAERLFSTARELRDVVAGRAVLRQAGLAGGDSPARFIAPGRKYPQPYVALPAFDRNGKSAG
IWLNPLTTDDGNGLRGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGVVVRIAGE
GRPWNPGTITGGRVWGDIPDNSVQPGAGNGEPVTAEVLAQRQAEEAIRRETERRADEIVRKMAENKPDLP
DGKTEQAVRDIAGLERDRSAISEREAALPESVLREPQRVREAVREVARENLLQERLQQMERDMVRDLQKE
KTLGGD

  Protein domains


Predicted by InterproScan.

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

(633-712)

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

(575-627)

AAA domain (AAA_30)

(969-1156)

DNA helicase TraI (TraI_C)

(1434-1557)

TrwC relaxase (TrwC)

(10-283)


  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 36459..63317

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
H4J91_RS00205 (D616_p137035) 32426..32860 + 435 WP_000845953 conjugation system SOS inhibitor PsiB -
H4J91_RS00210 (D616_p137036) 32857..33619 + 763 Protein_43 plasmid SOS inhibition protein A -
H4J91_RS00525 33798..33947 + 150 Protein_44 plasmid maintenance protein Mok -
H4J91_RS00215 (D616_p137038) 33889..34014 + 126 WP_001372321 type I toxin-antitoxin system Hok family toxin -
H4J91_RS00530 34234..34464 + 231 WP_001426396 hypothetical protein -
H4J91_RS00535 34462..34635 - 174 Protein_47 hypothetical protein -
H4J91_RS00540 34705..34911 + 207 WP_000547968 hypothetical protein -
H4J91_RS00220 34936..35223 + 288 WP_000107544 hypothetical protein -
H4J91_RS00225 (D616_p137040) 35341..36162 + 822 WP_001234469 DUF932 domain-containing protein -
H4J91_RS00230 (D616_p137041) 36459..37106 - 648 WP_031943493 transglycosylase SLT domain-containing protein virB1
H4J91_RS00235 (D616_p137042) 37383..37766 + 384 WP_000124981 conjugal transfer relaxosome DNA-binding protein TraM -
H4J91_RS00240 (D616_p137043) 37957..38643 + 687 WP_000332484 PAS domain-containing protein -
H4J91_RS00245 (D616_p137044) 38737..38964 + 228 WP_001254386 conjugal transfer relaxosome protein TraY -
H4J91_RS00250 (D616_p137045) 38998..39357 + 360 WP_000340272 type IV conjugative transfer system pilin TraA -
H4J91_RS00255 (D616_p137046) 39372..39683 + 312 WP_000012106 type IV conjugative transfer system protein TraL traL
H4J91_RS00260 (D616_p137047) 39705..40271 + 567 WP_000399792 type IV conjugative transfer system protein TraE traE
H4J91_RS00265 (D616_p137048) 40258..40986 + 729 WP_001230813 type-F conjugative transfer system secretin TraK traK
H4J91_RS00270 (D616_p137049) 40986..42413 + 1428 WP_000146685 F-type conjugal transfer pilus assembly protein TraB traB
H4J91_RS00275 (D616_p137050) 42403..42993 + 591 WP_000002787 conjugal transfer pilus-stabilizing protein TraP -
H4J91_RS00280 (D616_p137051) 42980..43300 + 321 WP_001057287 conjugal transfer protein TrbD virb4
H4J91_RS00285 (D616_p137052) 43293..43544 + 252 WP_001038342 conjugal transfer protein TrbG -
H4J91_RS00290 (D616_p137053) 43541..44056 + 516 WP_015059130 type IV conjugative transfer system lipoprotein TraV traV
H4J91_RS00295 (D616_p137054) 44191..44412 + 222 WP_001278695 conjugal transfer protein TraR -
H4J91_RS00300 (D616_p137055) 44405..44881 + 477 WP_015059129 hypothetical protein -
H4J91_RS00305 44961..45175 + 215 Protein_66 hypothetical protein -
H4J91_RS00310 (D616_p137056) 45203..45565 + 363 WP_000836675 hypothetical protein -
H4J91_RS00315 (D616_p137057) 45691..48321 + 2631 WP_000069764 type IV secretion system protein TraC virb4
H4J91_RS00320 (D616_p137058) 48318..48704 + 387 WP_000214092 type-F conjugative transfer system protein TrbI -
H4J91_RS00325 (D616_p137059) 48701..49333 + 633 WP_001203720 type-F conjugative transfer system protein TraW traW
H4J91_RS00330 (D616_p137060) 49330..50322 + 993 WP_000830839 conjugal transfer pilus assembly protein TraU traU
H4J91_RS00335 (D616_p137061) 50331..50969 + 639 WP_000777692 type-F conjugative transfer system pilin assembly protein TrbC trbC
H4J91_RS00340 (D616_p137062) 50966..52774 + 1809 WP_000821821 type-F conjugative transfer system mating-pair stabilization protein TraN traN
H4J91_RS00345 52801..53058 + 258 WP_000864352 conjugal transfer protein TrbE -
H4J91_RS00350 (D616_p137063) 53051..53794 + 744 WP_001430248 type-F conjugative transfer system pilin assembly protein TraF traF
H4J91_RS00355 (D616_p137064) 53810..54157 + 348 WP_001287891 conjugal transfer protein TrbA -
H4J91_RS00360 (D616_p137065) 54276..54560 + 285 WP_000624109 type-F conjugative transfer system pilin chaperone TraQ -
H4J91_RS00365 (D616_p137066) 54547..55092 + 546 WP_000059821 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
H4J91_RS00370 (D616_p137067) 55022..55384 + 363 WP_010379880 P-type conjugative transfer protein TrbJ -
H4J91_RS00375 (D616_p137068) 55384..56757 + 1374 WP_001137358 conjugal transfer pilus assembly protein TraH traH
H4J91_RS00380 (D616_p137069) 56754..59579 + 2826 WP_001007045 conjugal transfer mating-pair stabilization protein TraG traG
H4J91_RS00385 (D616_p137070) 59576..60085 + 510 WP_031943494 conjugal transfer entry exclusion protein TraS -
H4J91_RS00390 (D616_p137071) 60099..60830 + 732 WP_094658456 conjugal transfer complement resistance protein TraT -
H4J91_RS00395 (D616_p137072) 61083..63317 + 2235 WP_021532655 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   1047 GenBank   NC_025106
Plasmid name   pMC-NDM Incompatibility group   IncFII
Plasmid size   87619 bp Coordinate of oriT [Strand]   36855..37316 [-]
Host baterium   Escherichia coli strain NMI5428/11

Cargo genes

Drug resistance gene   blaNDM-1, sul1, qacE, aadA2, dfrA12, blaTEM-1B, rmtB
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   AcrIF11