Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   121813
Name   oriT_p2562_3 in_silico
Organism   Klebsiella michiganensis strain 2563
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP116217 (89271..89352 [-], 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_p2562_3
CGGGACAGGATATGTTTTGTATTACCGCCACCACGGTGGCAGCAATCCAAAACTCCTGGTCAGGGCGAAGCCCCGACACCCC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   13770 GenBank   WP_064357930
Name   traI_PHA56_RS31425_p2562_3 insolico UniProt ID   _
Length   642 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 642 a.a.        Molecular weight: 74304.29 Da        Isoelectric Point: 8.8672

>WP_064357930.1 MULTISPECIES: TraI/MobA(P) family conjugative relaxase [Enterobacterales]
MNAIIPPKRRDKKSSFVQLVAYVSVRDDVPLKDELKEDQRFQRPSRSRQAIFDRLVDYMNRSEGTITEQI
TDMSPEGDVRCSVDGVICQHNLMSVETAAMEMNSIAMQNLHVKDAVYHYILSWQEDENPSDDQVFDSVKY
SLKRLGMEENQYVAGIHRDTDNLHVHVAANRVHPVSYRAANVWNDADKLQRTCRELELKHGFKVDNGSWV
RDADNNIVRARKGYRNAPRSARQLEHFSDKESLHHFAVQHVRKPVNAMFREKNASWEKLHQVMNDAGLML
ETSGKGLIVRDVCGDEKLAVKSSRVHPSMTLSRLEPALGTFVPSPRSAEMVKQSVQTPYSDKLHVRDRGA
RAKRRQARADARIDLRERYGKYRNAWKKPDLHAAERFRAVSAAFKEQKTHIRDNEKDAHMRKLMYHIVEF
EREKSMAALRIALKAERQKLYDEGMMRPLTYRAWTEQQALHGDQAALSQLRGWSYRQNRKNRTPQASENI
IYCAPADDTSLLKADGYEARLHRDGAVVYSRQGQDAIIDRGDRVEVINPYDDGDLNTRIAVDMVAWKSGE
RVEFSRDGCFAYAAGDAVAAHNLHHRDSIIVPSDREQYDYTREKFNQLKGRYTDSEREALRQQYDERYYD
DVRNNDDSSYKP

  Protein domains


Predicted by InterproScan.

Relaxase/Mobilisation nuclease domain (Relaxase)

(52-310)


  Protein structure



No available structure.




T4CP

ID   16095 GenBank   WP_064357960
Name   trbC_PHA56_RS31285_p2562_3 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: 82695.78 Da        Isoelectric Point: 6.0387

>WP_064357960.1 MULTISPECIES: F-type conjugative transfer protein TrbC [Enterobacterales]
MQQKQKPVDAARLQRQVHQSMVEEMAYRTGPLLLAIIAIFGAAIVWPVLLWAAIPVMLVWVPMFMLNEFR
MPARMPMDMDRLDPSTETMRPGKLLGFLPVTKLNRHMEKAAGVFYTGYERTLDGGREIWLRMDDLTRHLI
LMATTGAGKTEMLLGFVLNALCWAKGLIFSDGKAQNDVWFAVASLSRRFGREDDLRLLNYITGGQSRSQR
LLENDKSRQQSNNTNPFALAQETYITQLMDSMMPEAGNDRTWQEKAKGMNQVLTKALIYKSRKEQKVMSQ
RLIQEYLSLDKFAELYLQAEAEEWHEEIRTGLRNYLSTSVPGFDMSLITKPSEWSQEARNQHGYLTSQYN
RMLSLFSDTYGHVFSSGAGDIDLRDVVHNDRILVILIPALELSASEALTLGRLTTSQLAMILSQDLGERM
EGKAEDILVIKKFRDRFPFLWLADEVGSYYSDTIGQLATQVRSLGYALVLAGQDLQKLKTAVGDKLWTLL
GNMFTRIFGTIIDPTETAEFAAKSAGMEYQAIQDSMEYRAGAIGGSYADTGRVTVQEKPKLPFDELQALN
QGEQATVFKGAVIRNNALYIADDDKITDKDVRINRFVEVEWPTYDSLSHLLPAKVRRDRPRPASINRIMA
IVKNDNIRHAPDSMIIQDGVLYAIADEAMYFDEVSPVPPDTVRRATQLLSLAASVLTETRGRYSVEYPEP
EKLSVKKDELEKYQHIHQSAVTQQVDGFVY

  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: 57431..79156

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
PHA56_RS31270 (PHA56_31270) 53189..53686 - 498 WP_159041655 RepA family replication protein -
PHA56_RS31275 (PHA56_31275) 54395..54646 - 252 WP_064357964 hypothetical protein -
PHA56_RS31280 (PHA56_31280) 54658..55191 - 534 WP_096807525 phospholipase D family protein -
PHA56_RS31285 (PHA56_31285) 55237..57429 - 2193 WP_064357960 F-type conjugative transfer protein TrbC -
PHA56_RS31290 (PHA56_31290) 57431..58522 - 1092 WP_064357959 thioredoxin fold domain-containing protein trbB
PHA56_RS31295 (PHA56_31295) 58533..59951 - 1419 WP_071887238 hypothetical protein trbA
PHA56_RS31300 (PHA56_31300) 60053..60676 - 624 WP_064357957 plasmid IncI1-type surface exclusion protein ExcA -
PHA56_RS31305 (PHA56_31305) 60742..62886 - 2145 WP_064357955 DotA/TraY family protein traY
PHA56_RS31310 (PHA56_31310) 62928..63509 - 582 WP_064357954 conjugal transfer protein TraX -
PHA56_RS31315 (PHA56_31315) 63506..64702 - 1197 WP_064357952 conjugal transfer protein TraW traW
PHA56_RS31320 (PHA56_31320) 64712..67759 - 3048 WP_189095616 ATP-binding protein traU
PHA56_RS31325 (PHA56_31325) 67769..68332 - 564 WP_064357949 hypothetical protein traT
PHA56_RS31330 (PHA56_31330) 68376..68777 - 402 WP_032440588 DUF6750 family protein traR
PHA56_RS31335 (PHA56_31335) 68833..69366 - 534 WP_064357947 conjugal transfer protein TraQ traQ
PHA56_RS31340 (PHA56_31340) 69376..70095 - 720 WP_064357945 conjugal transfer protein TraP traP
PHA56_RS31345 (PHA56_31345) 70102..71430 - 1329 WP_064357943 conjugal transfer protein TraO traO
PHA56_RS31350 (PHA56_31350) 71434..72537 - 1104 WP_081042499 DotH/IcmK family type IV secretion protein traN
PHA56_RS31355 (PHA56_31355) 72548..73216 - 669 WP_196548568 DotI/IcmL/TraM family protein traM
PHA56_RS31360 (PHA56_31360) 73290..73643 - 354 WP_064357942 hypothetical protein traL
PHA56_RS31365 (PHA56_31365) 73677..76892 - 3216 WP_271293008 LPD7 domain-containing protein -
PHA56_RS31370 (PHA56_31370) 76910..77176 - 267 WP_189095618 IcmT/TraK family protein traK
PHA56_RS31375 (PHA56_31375) 77173..78360 - 1188 WP_081042498 plasmid transfer ATPase TraJ virB11
PHA56_RS31380 (PHA56_31380) 78338..79156 - 819 WP_064357938 type IV secretory system conjugative DNA transfer family protein traI
PHA56_RS31385 (PHA56_31385) 79153..79617 - 465 WP_225546581 DotD/TraH family lipoprotein -
PHA56_RS31390 (PHA56_31390) 79643..80122 - 480 WP_064357937 lytic transglycosylase domain-containing protein -
PHA56_RS31395 (PHA56_31395) 80854..81081 - 228 WP_032440573 hypothetical protein -
PHA56_RS31400 (PHA56_31400) 81691..82533 + 843 WP_032440572 helix-turn-helix domain-containing protein -
PHA56_RS31405 (PHA56_31405) 82593..83522 + 930 WP_064357981 glycosyltransferase family 9 protein -
PHA56_RS31410 (PHA56_31410) 83515..84009 + 495 WP_064357935 molybdopterin-dependent oxidoreductase -

Host bacterium

ID   22240 GenBank   NZ_CP116217
Plasmid name   p2562_3 Incompatibility group   IncFII
Plasmid size   105902 bp Coordinate of oriT [Strand]   89271..89352 [-]
Host baterium   Klebsiella michiganensis strain 2563

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -