Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100162
Name   oriT_pWW0 in_silico
Organism   Pseudomonas putida
Sequence Completeness      intact
NCBI accession of oriT (coordinates [strand])   NC_003350 (96140..96570 [-], 431 nt)
oriT length   431 nt
IRs (inverted repeats)      R1: 65..73, 76..84  (TGTAATGCA..TGTATTACA)
  IR2: 120..124, 126..130  (TTGTA..TACAA)
  IR3: 188..195, 200..207  (CACCTCCC..GGGAGGTG)
Location of nic site      217..218
Conserved sequence flanking the
  nic site    		  _
Note   _

  oriT sequence  


Download         Length: 431 nt

>oriT_pWW0
GTTGTTCCCTCAAATTCCCCTGGAAAAATGGTGTCTCGCATGACCCAAGGTAACGCAGATTGCTTGTAATGCAAATGTATTACACGTAATGCTTGATTCCAAAGGTCTAAACAGCTACTTTGTATTACAAGCGTATCACATCATAAAAGAAGGCAATACTCCGCAAGCTCAGGCACAGCGCGGCTTCCACCTCCCGCAAGGGAGGTGCGTGTTGTGTATTGAGACTTTGACCCTGTTAAGGGTCGAAGTTGATGCTCTTGTTAAGGGCGTTTTTAGGGCCTAGGCCGAAGGCCGTAGCGAGCGGAGGACAAGGGGTAGGCAATATGGGTGCAGTATGGCTGTAGATTGAGTGCAGAAGGGGTTTAGCTTGACTACTGGTAGGGGGTGAGTAGGATGCAGGGTAAATGCAATGTAGGTGCAGGTAGGGTGCA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file

  Reference


[1] Greated A et al. (2002) Complete sequence of the IncP-9 TOL plasmid pWW0 from Pseudomonas putida. Environ Microbiol. 4(12):856-71. [PMID:12534468]


Relaxase

ID   156 GenBank   NP_542915
Name   TraC_pWW0 insolico UniProt ID   Q8VMG1
Length   978 a.a. PDB ID   
Note   relaxase

  Relaxase protein sequence


Download         Length: 978 a.a.        Molecular weight: 109120.90 Da        Isoelectric Point: 10.0738

>NP_542915.1 putative TraC protein (plasmid) [Pseudomonas putida]
MFNVTLIKGDNQYAAAGYFSNADDYYAKEAPGEWQGIGAELLGLEGAIDQKELARLFDGKLPNGERMAKT
FDKETGTRRMGLDLTFSAPKSVSMQALIAGDKDVMAAHDRAVTKSMEEVERLAQTRLKVNGKTMLERSGN
LVIGKFRHEMSRAKDPQMHTHAVVMNMTRRSDGKWRALRNDDIYKIQPQVDAMYKGILAQELRALGYEIR
VLDNQGNFELAHISRDQIEAFSSRSKVIEDALAKDGKTRADATPLEKQIIAMATRPRKDERDRHLVKEYW
VTKARELGIDFGARSHLDNREYAPRNGGPAEYSLPQGITPGQAVVQYAINHLTEREQVVGENDLRTVALR
RAVGLATPDQVNDEIRRLVKQGTLIESPPTYRMPNGDLDSPVLSPAGWRAHLQELKGWSEKEARQYVDKA
IKRGSLEPAEKRYTTQKALKREKAILAIERTGRGQVTPLMTKEQVAKALEGSTLSPGQFQAVEVIVSTNN
RFVGIQGDAGTGKTYSVDRAVKLIDSVNAAMATNNPQDITGYRVVALAPYGNQVTALKNEGLDAHTLASF
FHTKNKGLDAKTIVILDEAGVVGARQMERLMREIEQSGARLIQLGDTKQTEAIEAGKPFAQLQQSGMQTA
RIKEIQRQKDPELKRAVQHAAEGQPTKSLEHLKHVEELRTASDRHQAIVRDYMALTPDQRKEVLIVAGTN
KDRKEINTMARQALGLFGKGKEFETLNRVDSTDAERRYAPSYKQGMIIQPEKDYKRAGLVRGELYVVDQA
LPGNVLVVKDRSGNRFEFNPRQATKLSVYKLEKPELAVGDLIRINRQDPKLDLTNGDRMRVVSIEGGVVQ
LASLKEVNGQPERTVSLPTNKPLHLEHAYSATVHSAQGLTNDRVMISLNTKSRTTSQNLWYVAISRARHE
ARVYADSIKGLPAAIAKRYDKTTALSLQQERERQRRDSIQPRTVSDGRALERKQRTGLDGPSSGNARI

  Protein domains


Predicted by InterproScan.

UvrD-like helicase C-terminal domain (UvrD_C_2)

(867-913)

AAA domain (AAA_30)

(473-671)

TrwC relaxase (TrwC)

(15-286)


  Protein structure


Source ID Structure
AlphaFold DB Q8VMG1

  Reference


[1] Greated A et al. (2002) Complete sequence of the IncP-9 TOL plasmid pWW0 from Pseudomonas putida. Environ Microbiol. 4(12):856-71. [PMID:12534468]


Auxiliary protein

ID   226 GenBank   NP_542913
Name   TraA_pWW0 insolico UniProt ID   Q8VMG3
Length   127 a.a. PDB ID   _
Note   putative TraA protein

  Auxiliary protein sequence


Download         Length: 127 a.a.        Molecular weight: 14136.97 Da        Isoelectric Point: 4.7483

>NP_542913.1 putative TraA protein (plasmid) [Pseudomonas putida]
MGKTVPIRFNSEQLARVEEAAALAGYKHLSSYIRDRVLAPDKGGRQVDMDSWAEQQRLLGLLENITQEQA
RSRTIQAITVYLLQQGTTKGTINKLRADLQQLISSEDALATLLPDLAEDIERLSGED

  Protein domains



No domain identified.



  Protein structure


Source ID Structure
AlphaFold DB Q8VMG3

  Reference


[1] Greated A et al. (2002) Complete sequence of the IncP-9 TOL plasmid pWW0 from Pseudomonas putida. Environ Microbiol. 4(12):856-71. [PMID:12534468]


T4CP

ID   156 GenBank   NP_542914
Name   TraB_pWW0 insolico UniProt ID   Q8VMG2
Length   516 a.a. PDB ID   _
Note   Type IV secretion-system coupling protein DNA-binding domain; pfam10412

  T4CP protein sequence


Download         Length: 516 a.a.        Molecular weight: 58379.87 Da        Isoelectric Point: 8.2071

>NP_542914.1 putative traB protein (plasmid) [Pseudomonas putida]
MHKQEVDSAAMTAGFGLPIAGWLAGTQLAQLPLAPFPAAFKETLHNGWQEPMVLGMTIAASVAAAGLCYY
LYEYCDDGFRGERFQQWLRGSRIRNWHFVERKVSARNAKTNRERRKKGQEKAEPIMIGKLPMPLHLEDRN
TMICASIGAGKSVTMEGMIASALRRNDRMAVVDPNGTFYSKFSFKGDYILNPFDARSAGWTIFNEIRGVH
DFNRMAKSIIPPQVDPSDEQWCAYARDVLSDTMRKLMETGNANQDTLVNLLVREDGDTIRAFLANTDSEG
YFRDNAEKAIASIQFMMNKYIRPLRYMGKGDFSIYRWVNDPDAGNLFITWREDMRDTMRPLVATWIDTIC
ATILSSEPMTGKRLWLFLDELQSLGKLESFVPAATKGRKHGLRMVGSLQDWSQLNASYGRDDAETLLSCF
RNYVILAAANAKNADMAKEILGNHEVKRFRKSWTAGRMTRAEEIKLEPVVMDSEISNLNDLEAYVKFAED
FPITKIKTPYVDYKERAPAIVIGQAA

  Protein domains


Predicted by InterproScan.

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

(125-498)

  Protein structure


Source ID Structure
AlphaFold DB Q8VMG2

  Reference


[1] Greated A et al. (2002) Complete sequence of the IncP-9 TOL plasmid pWW0 from Pseudomonas putida. Environ Microbiol. 4(12):856-71. [PMID:12534468]


T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 56282..64187

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HXE35_RS00335 (pWWO_p075) 51834..52172 - 339 WP_011005910 2Fe-2S iron-sulfur cluster binding domain-containing protein -
HXE35_RS00340 (pWWO_p076) 52317..53126 - 810 WP_011005911 1,6-dihydroxycyclohexa-2,4-diene-1-carboxylate dehydrogenase -
HXE35_RS00345 (pWWO_p077) 53241..54251 - 1011 WP_011005912 benzoate 1,2-dioxygenase electron transfer component BenC -
HXE35_RS00350 (pWWO_p078) 54261..54749 - 489 WP_011005913 benzoate 1,2-dioxygenase small subunit -
HXE35_RS00355 (pWWO_p079) 54750..56102 - 1353 WP_181408537 benzoate 1,2-dioxygenase large subunit -
HXE35_RS00360 (pWWO_p080) 56282..57031 - 750 WP_011005915 TIGR03747 family integrating conjugative element membrane protein tfc7
HXE35_RS00365 (pWWO_p081) 57028..59184 - 2157 WP_011005916 type IV conjugative transfer system coupling protein TraD -
HXE35_RS00370 59193..59730 - 538 Protein_74 integrating conjugative element protein -
HXE35_RS00375 (pWWO_p082) 60042..61175 - 1134 Protein_75 TIGR03752 family integrating conjugative element protein -
HXE35_RS00380 (pWWO_p083) 61172..62080 - 909 WP_011005918 TIGR03749 family integrating conjugative element protein tfc13
HXE35_RS00385 (pWWO_p084) 62077..62769 - 693 WP_095159412 PFL_4703 family integrating conjugative element protein tfc12
HXE35_RS00390 62766..63176 - 411 WP_045633950 TIGR03750 family conjugal transfer protein tfc11
HXE35_RS00395 (pWWO_p085) 63189..63557 - 369 WP_011005920 TIGR03745 family integrating conjugative element membrane protein tfc10
HXE35_RS00400 (pWWO_p086) 63580..63819 - 240 WP_011005921 TIGR03758 family integrating conjugative element protein tfc9
HXE35_RS00405 (pWWO_p087) 63816..64187 - 372 WP_011005922 RAQPRD family integrative conjugative element protein tfc8
HXE35_RS00695 64314..64514 + 201 WP_223817447 transposase family protein -
HXE35_RS00410 64507..64722 - 216 WP_064481777 hypothetical protein -
HXE35_RS00415 64651..64986 + 336 WP_081262894 transposase -
HXE35_RS00420 65193..65300 - 108 Protein_85 IS5/IS1182 family transposase -
HXE35_RS00425 65419..66194 - 776 Protein_86 transposase -
HXE35_RS00430 (pWWO_p091) 66416..66769 - 354 WP_011005926 hypothetical protein -
HXE35_RS00435 (pWWO_p092) 67174..68571 - 1398 WP_011005927 outer membrane protein transport protein -

Region 2: 96954..112986

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HXE35_RS00560 (pWWO_p118) 92997..93482 - 486 WP_011005946 hypothetical protein -
HXE35_RS00565 (pWWO_p119) 93649..94440 - 792 WP_011005947 SprT-like domain-containing protein -
HXE35_RS00570 (pWWO_p120) 94570..94962 - 393 WP_011005948 hypothetical protein -
HXE35_RS00575 (pWWO_p121) 94966..95685 - 720 WP_011005949 StbB family protein -
HXE35_RS00580 (pWWO_p122) 95682..96137 - 456 WP_011005950 hypothetical protein -
HXE35_RS00585 (pWWO_p123) 96571..96954 + 384 WP_011005951 hypothetical protein -
HXE35_RS00590 (pWWO_p125) 96954..98504 + 1551 WP_011005952 type IV secretion system DNA-binding domain-containing protein virb4
HXE35_RS00595 (pWWO_p126) 98516..101452 + 2937 WP_011005953 MobF family relaxase -
HXE35_RS00600 (pWWO_p127) 101566..102198 - 633 WP_011005954 hypothetical protein -
HXE35_RS00605 (pWWO_p128) 102212..102781 - 570 WP_090315695 phospholipase D family protein -
HXE35_RS00610 (pWWO_p129) 102804..103139 - 336 WP_011005956 TrbM/KikA/MpfK family conjugal transfer protein -
HXE35_RS00615 (pWWO_p130) 103168..104085 - 918 WP_062378601 lytic transglycosylase domain-containing protein virB1
HXE35_RS00620 (pWWO_p131) 104069..105100 - 1032 WP_011005958 P-type DNA transfer ATPase VirB11 virB11
HXE35_RS00625 (pWWO_p133) 105110..106375 - 1266 WP_011005959 TrbI/VirB10 family protein virB10
HXE35_RS00630 (pWWO_p134) 106378..107163 - 786 WP_011005960 TrbG/VirB9 family P-type conjugative transfer protein virB9
HXE35_RS00635 (pWWO_p136) 107189..107869 - 681 WP_011005961 type IV secretion system protein virB8
HXE35_RS00640 (pWWO_p137) 107853..108716 - 864 WP_011005962 type IV secretion system protein virB6
HXE35_RS00645 (pWWO_p139) 108704..109096 - 393 WP_011005963 hypothetical protein -
HXE35_RS00650 (pWWO_p140) 109089..109301 - 213 WP_011005964 hypothetical protein -
HXE35_RS00655 (pWWO_p141) 109330..110019 - 690 WP_011005965 type IV secretion system protein virB5
HXE35_RS00660 (pWWO_p142) 110019..112703 - 2685 WP_011005966 mating pair formation protein virb4
HXE35_RS00665 (pWWO_p143) 112690..112986 - 297 WP_011005967 VirB3 family type IV secretion system protein virB3
HXE35_RS00670 (pWWO_p145) 112995..113456 - 462 WP_011005968 TrbC/VirB2 family protein -
HXE35_RS00675 (pWWO_p146) 113473..113745 - 273 WP_062378608 hypothetical protein -
HXE35_RS00680 (pWWO_p147) 114411..115229 + 819 WP_238838687 ParA family protein -
HXE35_RS00685 (pWWO_p148) 115240..116184 + 945 WP_011005971 ParB/RepB/Spo0J family partition protein -
HXE35_RS00690 (pWWO_p150) 116181..116531 + 351 WP_011005972 TrfB-related DNA-binding protein -

Host bacterium

ID   156 GenBank   NC_003350
Plasmid name   pWW0 Incompatibility group   IncP9
Plasmid size   116580 bp Coordinate of oriT [Strand]   96140..96570 [-]
Host baterium   Pseudomonas putida

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   mercury resistance
Degradation gene   carries the degradative (xyl) genes for toluenes and xylenes within catabolic transposons Tn4651 and Tn4653
Symbiosis gene   -
Anti-CRISPR   -