Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   200408
Name   oriT_Tn6584 in_silico
Organism   Pseudomonas aeruginosa strain SE5352
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   CP054843 (47347..47818 [-], 472 nt)
oriT length   472 nt
IRs (inverted repeats)      200..205, 219..224  (CAGCGA..TCGCTG)
 135..141, 148..154  (TGCGGCC..GGCCGCA)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 472 nt

>oriT_Tn6584
GGGAACTGCTGGACCAACTCGGCGTAGCACTCCAGCGGAGCGCGATAGAGGATGGCGAACTGCTTGCGCGACAGCGATGTGCGCTGCCAGATGTGTTCCAGCAGCTTTTGCCGGCGCGGTATCGCCAGTAGGGATGCGGCCGACTCGGGCCGCAGCAGCCCTTTCGGAAGATCAGTGGCTGGCGTTGGCGACGGAGCGGCAGCGACCGAGGCCCGTTTTCGCTGGAACAGGGAGAGCATGAGGGTGTCCTGATGGCGGGCCGACCGGGAGGCCTTTTTGCTTTTTCGAGGTAGGGCCTTTCCCCTTGCACTCCATTCCCTTCCCCTTTCGGCCTTTTGGCCCTTAACAGCCTTTGGGTATAGGGCGCCAGGCGTTGATCGTCCACCACCAATGCGGGTTGCAGCGGGGCCGGATTGATGCGGGAAGGCGGGCTGTTCCCAGCCTACGATGGGCCGATTCTTGGACTCGGGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   14436 GenBank   QQW04969
Name   rlx_HUS10_24715_Tn6584 insolico UniProt ID   _
Length   620 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 620 a.a.        Molecular weight: 67923.42 Da        Isoelectric Point: 7.1518

>QQW04969.1 Relaxase [Pseudomonas aeruginosa]
MLSLFQRKRASVAAAPSPTPATDLPKGLLRPESAASLLAIPRRQKLLEHIWQRTSLSRKQFAILYRAPLE
CYAELVQQFPASEAHHHAYPGGMLDHGLEIVAYSLKLRQSHLLPIGANPEDQAAQSEAWTAAVAYAALLH
DIGKIAVDLHVELADGSTWHPWHGPLQQPYRFRYRDDREYRLHSAATGLLHHQLLDRQILDWLSGYPALW
GPLLYVLAGQYEHAGVLGELVVQADRASVALELGGDPARAMVAPKHALQRKLLDGLRYLLKEELKLNQPE
ASDGWLTEDGLWLVSKTVSDKLRAHLLSQGIDGIPANNTAVFNVLQDHGMLKPTPDGKAVWRATVISTTG
WSHSFTLLRLAPALIWESGERPAPFAGTVAIDATLAENDASAPATPPAVVMKPAQEDQGPRPWEGGSAAA
LAPPPTAHQALPDALEDMLTMVGMGDSSGTQQDAEVVSSMTPATRPEASMPAMVTVSPTSMPTAATSPST
ARPSGEHFMTWLQQGIASRRLIINDAKALVHTVSDTAYLVSPGVFQRYAQEHPQVGAFAKQENQQDWRWV
QKRFERLQLHRKQASGLNIWTCEVTGPRKSRKLHGYLLLQPQSVFGDVPPNNPYLAVLPT

  Protein domains


Predicted by InterproScan.

Putative conjugal transfer nickase/helicase TraI C-term (TraI_2_C)

(494-616)

Putative helicase (TraI_2)

(27-340)


  Protein structure



No available structure.




T4CP

ID   16969 GenBank   QQW04947
Name   cpl_HUS10_24605_Tn6584 insolico UniProt ID   _
Length   728 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 728 a.a.        Molecular weight: 80922.65 Da        Isoelectric Point: 7.3167

>QQW04947.1 Coupling protein [Pseudomonas aeruginosa]
MSGKQPVEVLLRPAVEFYTVAACAGAAFLSLVAPWSLALSPAMGVGSALAFCAYGAIRYRDARVILRYRR
NIRRLPRYVMTSKDVPVSQQRLFVGRGFLWEQKHTHRLMQTYRPEFRRYVELTPAYRLARRLEERLEFAP
FPLSRLPALTGWDVSFNPVRPLPPVGGLPRLHGIEPDEVDVSLPLGERVGHSLVLGTTRVGKTRLAELFV
TQDIRRKNADGEHEVVIVIDPKGDADLLKRVYVEAKRAGREGEFYVFHLGWPDISARYNAVGRFGRISEV
ATRVAGQLSGEGNSAAFREFAWRFVNIIARALVELGQRPDYMLIQRHVINIDALFIEYAQHYFAKTEPKA
WEVIVQIEAKLNEKNIPRNMIGREKRVVALEQYLSQARNYDPVLDGLRSAVRYDKTYFDKIVASLLPLLE
KLTSGKISQLLAPNYSDLADPRPIFDWMQVIRKRAVVYVGLDALSDAEVAAAVGNSMFSDLVSVAGHIYK
HGIDDGLPGASAGTRVPINVHADEFNELMGDEFVPLINKGGGAGLQVTAYTQTLSDIEARIGNRAKAGQV
IGNFNNLFMLRVRETATAELLTRQLPKVEVYTTTIVSGATDSSDIRGATDFTSNTQDRISMSSVPMIEPS
HVVALPKGQCFALLQGGQLWKVRMPLPAPDPDEVMPQDLQQLAGYMRQSYSEATQWWEFTSSPVLQDTAL
PDDLLDEVATADAPASGTGDMARDEAAP

  Protein domains


Predicted by InterproScan.

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

(508-636)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 5234737..5256313

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HUS10_24560 5229838..5230488 + 651 QQW04938 hypothetical protein -
HUS10_24565 5230553..5231674 + 1122 QQW04939 class I SAM-dependent methyltransferase -
HUS10_24570 5231775..5232086 + 312 QQW04940 hypothetical protein -
HUS10_24575 5232224..5234503 + 2280 QQW04941 DEAD/DEAH box helicase -
HUS10_24580 5234737..5235315 + 579 QQW04942 Conjugal transfer protein PilL tfc2
HUS10_24585 5235312..5235953 + 642 QQW04943 hypothetical protein -
HUS10_24590 5235968..5236705 + 738 QQW04944 TIGR03759 family integrating conjugative element protein tfc3
HUS10_24595 5236687..5237292 + 606 QQW04945 transglycosylase SLT domain-containing protein virB1
HUS10_24600 5237289..5237837 + 549 QQW04946 integrating conjugative element protein tfc5
HUS10_24605 5237842..5240028 + 2187 QQW04947 Coupling protein -
HUS10_24610 5240025..5240774 + 750 QQW04948 TIGR03747 family integrating conjugative element membrane protein tfc7
HUS10_24615 5240775..5242145 - 1371 QQW04949 Vacuolar import and degradation protein -
HUS10_24620 5242307..5242687 + 381 QQW04950 RAQPRD family plasmid tfc8
HUS10_24625 5242684..5242917 + 234 QQW04951 TIGR03758 family integrating conjugative element protein tfc9
HUS10_24630 5242934..5243293 + 360 QQW04952 TIGR03745 family integrating conjugative element membrane protein tfc10
HUS10_24635 5243306..5243716 + 411 QQW04953 TIGR03750 family conjugal transfer protein tfc11
HUS10_24640 5243713..5244402 + 690 QQW04954 TIGR03746 family integrating conjugative element protein tfc12
HUS10_24645 5244399..5245331 + 933 QQW04955 TIGR03749 family integrating conjugative element protein tfc13
HUS10_24650 5245321..5246739 + 1419 QQW04956 TIGR03752 family integrating conjugative element protein tfc14
HUS10_24655 5246720..5247160 + 441 QQW04957 TIGR03751 family conjugal transfer lipoprotein tfc15
HUS10_24660 5247160..5250030 + 2871 QQW04958 F-type type IV secretion, ATPase/inner membrane complex component TivF15 virb4
HUS10_24665 5250046..5250798 + 753 QQW04959 DsbA family protein -
HUS10_24670 5250985..5251479 + 495 QQW04960 DNA repair protein RadC -
HUS10_24675 5251623..5252069 + 447 QQW04961 TIGR03757 family integrating conjugative element protein tfc24
HUS10_24680 5252066..5253013 + 948 QQW04962 TIGR03756 family integrating conjugative element protein tfc23
HUS10_24685 5253024..5254418 + 1395 QQW04963 integrating conjugative element protein tfc22
HUS10_24690 5254415..5254774 + 360 QQW04964 hypothetical protein tfc18
HUS10_24695 5254790..5256313 + 1524 QQW04965 F-type type IV secretion, mating pair stabilization protein TivF3 tfc19
HUS10_24700 5256320..5256682 - 363 QQW04966 DUF3742 family protein -
HUS10_24705 5256710..5257168 - 459 QQW04967 type II toxin-antitoxin system YhaV family toxin -
HUS10_24710 5257168..5257485 - 318 QQW04968 type II toxin-antitoxin system PrlF family antitoxin -
HUS10_24715 5257797..5259659 + 1863 QQW04969 Relaxase -
HUS10_24720 5259670..5260251 - 582 QRG26631 hypothetical protein -
HUS10_24725 5260437..5260670 - 234 Protein_4894 Tn3 family transposase -

Host bacterium

ID   363 Element type   ICE (Integrative and conjugative element)
Element name   Tn6584 GenBank   CP054843
Element size   6904218 bp Coordinate of oriT [Strand]   47347..47818 [-]
Host bacterium   Pseudomonas aeruginosa strain SE5352 Coordinate of element   5210218..5310913

Cargo genes

Drug resistance gene   blaGES-1, aph(3')-XV, qacE, floR, tet(G), sul1
Virulence gene   -
Metal resistance gene   merE, merD, merA, merP, merT, merR
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -