Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   101673
Name   oriT_p211DT2019_1 in_silico
Organism   Klebsiella michiganensis strain CPE5
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_JACYGO010000002 (134819..134868 [+], 50 nt)
oriT length   50 nt
IRs (inverted repeats)      7..14, 17..24  (GCAAAATT..AATTTTGC)
Location of nic site      33..34
Conserved sequence flanking the
  nic site    		  GGTGTGGTGA
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 50 nt

>oriT_p211DT2019_1
AAATCTGCAAAATTTTAATTTTGCGTGGGGTGTGGTGATTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


T4CP

ID   1122 GenBank   WP_227632020
Name   traD_IY169_RS00535_p211DT2019_1 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: 86021.20 Da        Isoelectric Point: 5.0632

>WP_227632020.1 type IV conjugative transfer system coupling protein TraD [Klebsiella michiganensis]
MSFNAKDMTQGGQIANMRFRMFGQIANIIFYVLFILFWVLCGLMLMYRLSWQTFVNGCVYWWCTTLGPMR
DIIRSQPVYTIQYYGQSLEYTSEQILADKYTIWCGEQLWTSFVFAAVVSLVICIVTFFIASWVLGRQGKQ
QSEDENTGGRQLSDKPKEVARQMKRDGMASDIKIGDLPILKNSEIQNFCLHGTVGSGKSEVIRRLLNYVR
ARGDMAIIYDRSCEFVKSYYDPSLDKILNPLDSRCAAWDLWKECLTLPDFDNISNTLIPMGTKEDPFWQG
SGRTIFAEGAYLMREDKDRSYEKLVDTMLSIKIDKLRAYLQNTPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEKNGEPFTIRDWMRGVREDRPNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGVKPAATLFDVMNTRAFFRSPSKEIA
EFAAGEIGEKEILKASEQYSYGADPVRDGVSTGKEKERETLVSYSDIQTLPDLSCYVTLPGPYPAVKLAL
KYKPRPKIAEGFIPRRLDTRVDARLSALLEEREAEGSLARALFTPDAPASGPADTDSHAGEQPEPVSQPA
PADMTVSPAPVKAPPTTKMPAAEPSVRATEPPVLRVTTVPLIKPKAAAAAAAASTASSAGIPAAAAGGTE
QELAQQSAEQGQDMLPAGMNEDGVIEDMQAYDAWLADEQTLRDMQRREEVNINHSHRHDEQDDVEIGGNF

  Protein domains


Predicted by InterproScan.

Type IV secretion-system coupling protein DNA-binding domain (TrwB_AAD_bind)

(172-560)

F sex factor protein N terminal (TraD_N)

(32-128)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 105430..135420

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
IY169_RS00535 105430..107742 - 2313 WP_227632020 type IV conjugative transfer system coupling protein TraD virb4
IY169_RS30060 107798..107911 - 114 Protein_109 hypothetical protein -
IY169_RS00540 108102..108833 - 732 WP_032415736 conjugal transfer complement resistance protein TraT -
IY169_RS00545 109084..109686 - 603 WP_023280878 hypothetical protein -
IY169_RS00550 109710..112532 - 2823 WP_023320108 conjugal transfer mating-pair stabilization protein TraG traG
IY169_RS00555 112532..113911 - 1380 WP_011977731 conjugal transfer pilus assembly protein TraH traH
IY169_RS00560 113889..114332 - 444 WP_032436741 F-type conjugal transfer protein TrbF -
IY169_RS00565 114377..114934 - 558 WP_004152678 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
IY169_RS00570 114906..115145 - 240 WP_004144400 type-F conjugative transfer system pilin chaperone TraQ -
IY169_RS00575 115156..115908 - 753 WP_004152677 type-F conjugative transfer system pilin assembly protein TraF traF
IY169_RS00580 115929..116255 - 327 WP_004152676 hypothetical protein -
IY169_RS30500 116301..116486 - 186 WP_032436745 hypothetical protein -
IY169_RS00585 116483..116719 - 237 WP_032436746 conjugal transfer protein TrbE -
IY169_RS00590 116751..118706 - 1956 WP_070552831 type-F conjugative transfer system mating-pair stabilization protein TraN traN
IY169_RS00595 118765..119403 - 639 WP_078174825 type-F conjugative transfer system pilin assembly protein TrbC trbC
IY169_RS00600 119416..120375 - 960 WP_015065634 conjugal transfer pilus assembly protein TraU traU
IY169_RS00605 120419..121045 - 627 WP_087749114 type-F conjugative transfer system protein TraW traW
IY169_RS00610 121045..121434 - 390 WP_194854242 type-F conjugative transfer system protein TrbI -
IY169_RS00615 121434..124073 - 2640 WP_016528865 type IV secretion system protein TraC virb4
IY169_RS00620 124145..124543 - 399 WP_165763624 hypothetical protein -
IY169_RS00625 124837..125241 - 405 WP_023292152 hypothetical protein -
IY169_RS00630 125308..125625 - 318 WP_087749117 hypothetical protein -
IY169_RS00635 125626..125844 - 219 WP_004171484 hypothetical protein -
IY169_RS00640 125868..126158 - 291 WP_087749118 hypothetical protein -
IY169_RS00650 127643..127936 - 294 WP_194854241 hypothetical protein -
IY169_RS00655 128091..128660 - 570 WP_102093258 type IV conjugative transfer system lipoprotein TraV traV
IY169_RS00660 128680..128835 - 156 WP_153909149 hypothetical protein -
IY169_RS00665 128873..129286 - 414 Protein_136 conjugal transfer pilus-stabilizing protein TraP -
IY169_RS00670 129279..130703 - 1425 WP_087749120 F-type conjugal transfer pilus assembly protein TraB traB
IY169_RS00675 130703..131443 - 741 WP_004152497 type-F conjugative transfer system secretin TraK traK
IY169_RS00680 131430..131996 - 567 WP_194854240 type IV conjugative transfer system protein TraE traE
IY169_RS00685 132016..132321 - 306 WP_004178059 type IV conjugative transfer system protein TraL traL
IY169_RS00690 132335..132703 - 369 WP_004178060 type IV conjugative transfer system pilin TraA -
IY169_RS00695 132757..133128 - 372 WP_004208838 TraY domain-containing protein -
IY169_RS00700 133212..133907 - 696 WP_087749121 transcriptional regulator TraJ family protein -
IY169_RS00705 134114..134506 - 393 WP_004178062 conjugal transfer relaxosome DNA-binding protein TraM -
IY169_RS00710 135013..135420 + 408 WP_225375048 transglycosylase SLT domain-containing protein virB1
IY169_RS00715 135458..135988 - 531 WP_023292160 antirestriction protein -
IY169_RS00720 136613..137446 - 834 WP_038990979 N-6 DNA methylase -
IY169_RS00725 137493..137723 - 231 WP_038990977 hypothetical protein -
IY169_RS00730 137811..138158 - 348 WP_038990975 hypothetical protein -
IY169_RS00735 138225..138605 - 381 WP_038990973 hypothetical protein -
IY169_RS00740 139510..139629 - 120 WP_223156217 type I toxin-antitoxin system Hok family toxin -
IY169_RS30065 139574..139726 - 153 WP_224230667 DUF5431 family protein -

Host bacterium

ID   2117 GenBank   NZ_JACYGO010000002
Plasmid name   p211DT2019_1 Incompatibility group   IncFIB
Plasmid size   147143 bp Coordinate of oriT [Strand]   134819..134868 [+]
Host baterium   Klebsiella michiganensis strain CPE5

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   silE, silS, silR, silC, silF, silB, silA, silP, pcoA, pcoB, pcoC, pcoD, pcoR, pcoS, pcoE, arsC, arsB, arsR, arsH, pbrA, merE, merD, merA, merP, merT, merR
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -