Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   200409
Name   oriT_Tn6585 in_silico
Organism   Pseudomonas aeruginosa strain SE5331
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   CP046402 (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_Tn6585
GGGAACTGCTGGACCAACTCGGCGTAGCACTCCAGCGGAGCGCGATAGAGGATGGCGAACTGCTTGCGCGACAGCGATGTGCGCTGCCAGATGTGTTCCAGCAGCTTTTGCCGGCGCGGTATCGCCAGTAGGGATGCGGCCGACTCGGGCCGCAGCAGCCCTTTCGGAAGATCAGTGGCTGGCGTTGGCGACGGAGCGGCAGCGACCGAGGCCCGTTTTCGCTGGAACAGGGAGAGCATGAGGGTGTCCTGATGGCGGGCCGACCGGGAGGCCTTTTTGCTTTTTCGAGGTAGGGCCTTTCCCCTTGCACTCCATTCCCTTCCCCTTTCGGCCTTTTGGCCCTTAACAGCCTTTGGGTATAGGGCGCCAGGCGTTGATCGTCCACCACCAATGCGGGTTGCAGCGGGGCCGGATTGATGCGGGAAGGCGGGCTGTTCCCAGCCTACGATGGGCCGATTCTTGGACTCGGGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   14437 GenBank   QLF17370
Name   rlx_GNT44_25725_Tn6585 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

>QLF17370.1 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   16970 GenBank   QLF17348
Name   traD_GNT44_25615_Tn6585 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

>QLF17348.1 type IV conjugative transfer system coupling protein TraD [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: 5385271..5406847

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
GNT44_25570 5380372..5381022 + 651 QLF17339 hypothetical protein -
GNT44_25575 5381087..5382208 + 1122 QLF17340 class I SAM-dependent methyltransferase -
GNT44_25580 5382309..5382620 + 312 QLF17341 hypothetical protein -
GNT44_25585 5382758..5385037 + 2280 QLF17342 DEAD/DEAH box helicase -
GNT44_25590 5385271..5385849 + 579 QLF17343 PilL N-terminal domain-containing protein tfc2
GNT44_25595 5385846..5386487 + 642 QLF17344 hypothetical protein -
GNT44_25600 5386502..5387239 + 738 QLF17345 TIGR03759 family integrating conjugative element protein tfc3
GNT44_25605 5387221..5387826 + 606 QLF17346 transglycosylase SLT domain-containing protein virB1
GNT44_25610 5387823..5388371 + 549 QLF17347 integrating conjugative element protein tfc5
GNT44_25615 5388376..5390562 + 2187 QLF17348 type IV conjugative transfer system coupling protein TraD -
GNT44_25620 5390559..5391308 + 750 QLF17349 TIGR03747 family integrating conjugative element membrane protein tfc7
GNT44_25625 5391309..5392679 - 1371 QLF17350 hypothetical protein -
GNT44_25630 5392841..5393221 + 381 QLF17351 RAQPRD family integrative conjugative element protein tfc8
GNT44_25635 5393218..5393451 + 234 QLF17352 TIGR03758 family integrating conjugative element protein tfc9
GNT44_25640 5393468..5393827 + 360 QLF17353 TIGR03745 family integrating conjugative element membrane protein tfc10
GNT44_25645 5393840..5394250 + 411 QLF17354 TIGR03750 family conjugal transfer protein tfc11
GNT44_25650 5394247..5394936 + 690 QLF17355 TIGR03746 family integrating conjugative element protein tfc12
GNT44_25655 5394933..5395865 + 933 QLF17356 TIGR03749 family integrating conjugative element protein tfc13
GNT44_25660 5395855..5397273 + 1419 QLF17357 TIGR03752 family integrating conjugative element protein tfc14
GNT44_25665 5397254..5397694 + 441 QLF17358 TIGR03751 family conjugal transfer lipoprotein tfc15
GNT44_25670 5397694..5400564 + 2871 QLF17359 F-type type IV secretion, ATPase/inner membrane complex component TivF15 virb4
GNT44_25675 5400580..5401332 + 753 QLF17360 DsbA family protein -
GNT44_25680 5401519..5402013 + 495 QLF17361 DNA repair protein RadC -
GNT44_25685 5402157..5402603 + 447 QLF17362 TIGR03757 family integrating conjugative element protein tfc24
GNT44_25690 5402600..5403547 + 948 QLF17363 TIGR03756 family integrating conjugative element protein tfc23
GNT44_25695 5403558..5404952 + 1395 QLF17364 integrating conjugative element protein tfc22
GNT44_25700 5404949..5405308 + 360 QLF17365 hypothetical protein tfc18
GNT44_25705 5405324..5406847 + 1524 QLF17366 F-type type IV secretion, mating pair stabilization protein TivF3 tfc19
GNT44_25710 5406854..5407216 - 363 QLF17367 DUF3742 family protein -
GNT44_25715 5407244..5407702 - 459 QLF17368 type II toxin-antitoxin system YhaV family toxin -
GNT44_25720 5407702..5408019 - 318 QLF17369 type II toxin-antitoxin system PrlF family antitoxin -
GNT44_25725 5408331..5410193 + 1863 QLF17370 Relaxase -
GNT44_25730 5410204..5410785 - 582 QRG26621 DUF2130 domain-containing protein -
GNT44_25735 5410971..5411171 - 201 Protein_5101 Tn3 family transposase -

Host bacterium

ID   364 Element type   ICE (Integrative and conjugative element)
Element name   Tn6585 GenBank   CP046402
Element size   7056430 bp Coordinate of oriT [Strand]   47347..47818 [-]
Host bacterium   Pseudomonas aeruginosa strain SE5331 Coordinate of element   5360752..5461449

Cargo genes

Drug resistance gene   blaGES-5, 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   -