Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   104500
Name   oriT_STEFF_12|unnamed2 in_silico
Organism   Shigella flexneri strain STEFF_12
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP055221 (67893..67974 [+], 82 nt)
oriT length   82 nt
IRs (inverted repeats)      27..32, 35..40  (GCCACC..GGTGGC)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 82 nt

>oriT_STEFF_12|unnamed2
CGGGACAGGATATGTTTTGTATTACCGCCACCACGGTGGCAGCAATCCAAAACTCCTGGTCAGGGCGAAGCCCCGACACCCC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   3258 GenBank   WP_032440569
Name   Relaxase_HUZ41_RS25550_STEFF_12|unnamed2 insolico UniProt ID   A0A7G3L4G1
Length   642 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 642 a.a.        Molecular weight: 74384.24 Da        Isoelectric Point: 8.3203

>WP_032440569.1 MULTISPECIES: TraI/MobA(P) family conjugative relaxase [Enterobacterales]
MNAIIPPKRRDRKSSFVQLVAYVSVRDDVPLKDELKEDERFQRPSRSRQAIFDRLVDYMNRSEGTIIEQI
SDMTPEGDIRCSVDGVICQHNLMSVETAAMEMNSIAMQNTHVKDAVYHYILSWQEDENPSDDQVFDSVKH
SLKRLGMEEHQYVAAIHRDTDNLHVHIAANRVHPVSYRAANVWNDADKLQRTCRELELKHGFKVDNGSWV
RDADNNIVRARKGYRNAPRSARQLEHFSDKESLHHFAVQHVRKPVNAMFREKNASWEKLHQVMNDAGLML
ETSGKGLIVRDVCGDEKLAVKSSRVHPGMTLSRLEPALGTFVPSPRSAEMVKQSVQTSYSDKLHVRDRGA
RAERRQARADARIDLRERYEKYRNAWKKPDLHAAERFRAVSAAFKEQKTHIRDNEKDAHMRKLMYHIVEF
EREKSMAALRIALKAERQKLYDEGMMRPLTYRAWTEQQALHGDQAALSQLRGWSYRQNRKNRTPQASDNI
IYCAPADDTSLLKADGYEARLHRDGAVVYSRQGQDAIIDRGDRVEVINPYDDGDLNTRIAVDMVAWKSGE
RVEFSRDGSFAYAAGDAVAAHNLHHRDSIIVPSDREQYDYTREKFNQLKGRYTDSEREALRQQYDDRYYD
DVRHNDDSSYKP

  Protein domains


Predicted by InterproScan.

Relaxase/Mobilisation nuclease domain (Relaxase)

(52-307)


  Protein structure


Source ID Structure
AlphaFold DB A0A7G3L4G1


T4CP

ID   3183 GenBank   WP_032440593
Name   trbC_HUZ41_RS25215_STEFF_12|unnamed2 insolico UniProt ID   _
Length   730 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 730 a.a.        Molecular weight: 82679.78 Da        Isoelectric Point: 6.3201

>WP_032440593.1 MULTISPECIES: F-type conjugative transfer protein TrbC [Enterobacterales]
MQQKQKPVDAARLQRQVHQSMVEEMAYRTGPLLLAIIAIFGAAIVWPVLLWAAIPVMLVWVPMFMLNEFR
MPARMPMDMDRLDPSTETMRPGKLLGFLPVTKLNRHMEKAAGVFYTGYERTLDGGREIWLRMDDLTRHLI
LMATTGAGKTEMLLGFVLNALCWAKGLIFSDGKAQNDVWFAVASLSRRFGREDDLRLLNYITGGQSRSQR
LLENDKSRQQSNNTNPFALAQETYITQLMDSMMPEAGNDRTWQEKAKGMNQVLTKALIYKSRKEQKVMSQ
RLIQEYLSLDKFAELYLQAEAEEWHEEIRTGLRNYLSTSVPGFDMSLITKPSEWSQEARNQHGYLTSQYN
RMLSLFSDTYGHVFSSGAGDIDLRDVVHNDRILVILIPALELSASEALTLGRLTTSQLAMILSQDLGERM
EGKAEDILVIKKFRDRFPFLWLADEVGSYYSDTIGQLATQVRSLGYALVLAGQDLQKLKTAVGDKLWTLL
GNMFTRIFGTIIDPTETAEFAAKSAGMEYQAIQDSMEYRAGAIGGSYADTGRVTVQEKPKLPFDELQALN
QGEQATVFKGAVIRNNALYIADDDKITDKDVRINRFVEVEWPTYDSLSHLLPAKVRRDRPRPASINRIMA
IVKNDKIRHAPDSMIIQDGVLYAIADEAMYFDEVAPTPPNTVQRATQLLSLAAAVLTETRGRYRVEYPEP
EKLSVKKDELEKYQHIHQSAVTQQADGFSY

  Protein domains


Predicted by InterproScan.

TraM recognition site of TraD and TraG (TraG-D_C)

(439-560)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 793..17015

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HUZ41_RS25140 (HUZ41_24900) 793..1146 + 354 WP_032440584 hypothetical protein traL
HUZ41_RS25145 (HUZ41_24905) 1182..1886 + 705 WP_045325071 DotI/IcmL/TraM family protein traM
HUZ41_RS25150 (HUZ41_24910) 1897..3000 + 1104 WP_077264204 DotH/IcmK family type IV secretion protein traN
HUZ41_RS25155 (HUZ41_24915) 3004..4344 + 1341 WP_032440586 conjugal transfer protein TraO traO
HUZ41_RS25160 (HUZ41_24920) 4351..5070 + 720 WP_050597333 conjugal transfer protein TraP traP
HUZ41_RS25165 (HUZ41_24925) 5080..5613 + 534 WP_032440587 conjugal transfer protein TraQ traQ
HUZ41_RS25170 (HUZ41_24930) 5669..6070 + 402 WP_032440588 DUF6750 family protein traR
HUZ41_RS25175 (HUZ41_24935) 6114..6677 + 564 WP_045325070 hypothetical protein traT
HUZ41_RS25180 (HUZ41_24940) 6687..9734 + 3048 WP_032440589 conjugal transfer protein traU
HUZ41_RS25185 (HUZ41_24945) 9744..10940 + 1197 WP_032440590 conjugal transfer protein TraW traW
HUZ41_RS25190 (HUZ41_24950) 11027..11518 + 492 WP_162749064 conjugal transfer protein TraX -
HUZ41_RS25195 (HUZ41_24955) 11560..13704 + 2145 WP_032440591 DotA/TraY family protein traY
HUZ41_RS25200 (HUZ41_24960) 13770..14393 + 624 WP_032440592 plasmid IncI1-type surface exclusion protein ExcA -
HUZ41_RS25205 (HUZ41_24965) 14495..15913 + 1419 WP_063666705 hypothetical protein trbA
HUZ41_RS25210 (HUZ41_24970) 15924..17015 + 1092 WP_050597336 thioredoxin fold domain-containing protein trbB
HUZ41_RS25215 (HUZ41_24975) 17017..19209 + 2193 WP_032440593 F-type conjugative transfer protein TrbC -
HUZ41_RS25220 (HUZ41_24980) 19255..19788 + 534 WP_032440594 phospholipase D family protein -
HUZ41_RS25225 (HUZ41_24985) 19800..20051 + 252 WP_113394424 hypothetical protein -
HUZ41_RS25230 (HUZ41_24990) 20626..21252 + 627 WP_254913868 RepA family replication protein -

Host bacterium

ID   4939 GenBank   NZ_CP055221
Plasmid name   STEFF_12|unnamed2 Incompatibility group   IncFII
Plasmid size   82001 bp Coordinate of oriT [Strand]   67893..67974 [+]
Host baterium   Shigella flexneri strain STEFF_12

Cargo genes

Drug resistance gene   blaTEM-1A, blaOXA-9, ant(3'')-Ia, aac(6')-Ib, floR, tet(A), blaLAP-2, qnrS1
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -