Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100238
Name   oriT_pDTG1 in_silico
Organism   Pseudomonas putida
Sequence Completeness      intact
NCBI accession of oriT (coordinates [strand])   NC_004999 (63861..64288 [-], 428 nt)
oriT length   428 nt
IRs (inverted repeats)      IR1: 121..126, 127..132  (ATACAT..ATGTAT)
  IR2: 137..142, 144..149  (CATGAA..TTCATG)
  IR3: 162..170, 174..182  (AAGCCGCTC..GCGCGGCTT)
Location of nic site      213..214
Conserved sequence flanking the
  nic site    		  _
Note   predicted by the oriTfinder

  oriT sequence  


Download         Length: 428 nt

>oriT_pDTG1
GGTGGTCCTCTCTGAGCCAAATATGGGACTAATTCAGGATAACGATAACTTCCGAAATAGCGTATAGCAAATGCAATACATAAAATGCTTGATTTTATTGGTCTAAATGATAATTTTGTAATACATATGTATAGCGCATGAAATTCATGAATTTGCTCTGTAAGCCGCTCCCAGCGCGGCTTTAACCTACCGCTAGGGGGGTGCGTGTTGTGTATTGAGACTTTGACCCTGTTAAGGGGAAAAGTTGAAGCTCTTGTTAAGGGCGTATCCACTAGTCAGGCCGCAGGCCGTAGGGGGGTAGCACAGATGGTATGCAGAAAGGGTGCAGGAAGGGTGCTAAGAGAGTGCAAGAGGGGTGCAACTTGACTACAGGTAGGGGGCGATTAAGATGCACCTAGAGTGCAATAGGGGTGCAGATAGGGTGCAAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   309 GenBank   NP_863125
Name   TraC_pDTG1 insolico UniProt ID   Q847F0
Length   981 a.a. PDB ID   
Note   putative relaxase

  Relaxase protein sequence


Download         Length: 981 a.a.        Molecular weight: 108969.65 Da        Isoelectric Point: 9.9827

>NP_863125.1 putative TraC protein (plasmid) [Pseudomonas putida]
MFNVTSIKGSNQYAAAGYYTAADDYYAKESPGEWQGIGAELLGLDGPIDQKELAKLFDGKLPNGELMPKP
VNKETGQIVNRRMGLDLTFSAPKSVSMQALIAGDKDVVAAHDRAVTKAMEHVEKLAQTRRKEHGKSMLER
TGNLIIGKFRHELSRAKDPQLHTHAVVMNATRRADGKWRAIHNDDIFKIQPQIDAMYKGELAKELRELGY
EIRVLDKDGNFELAHISRDQIEAFSSRSKVIEEALAKDGKTRSNATALEKQIIAMATRPRKDERDRHLVK
EYWVIKARDLGIEFGGRSQLDNREYGRRSESIHAEHNLPEGITAGQAVVQYAINHLTEREQVVGESDLRT
AALRRAVGLASPSEVDDEIKRLVKQGTLIESPPTYTMATGKDGTALSPAGWRALLKEQKGWTDKEAQQYV
KMAITRGSLVEAEKRYTTQRALKREKAILAIERSGRGLVAPLLSKEQVAKALEGSTLSAGQYQAVEVIVS
TSNRFVGIQGDAGTGKTYSVDRAVKLIESVNNAMTERTTTTDAVFRVVALAPYGNQVTALKNEGLDAHTL
ASFFHTKDKKLDERTIVVLDEAGVVGARQMEHLMRIIEQSGARLVQLGDTKQTEAIEAGKPFAQLQQNGM
QTARIKEIQRQKNQELKIAVQHAADGNPGKSLEHVNHVEEFREPGQRHQAIVRDYMSLTPEERKEVLIVA
GTNKDRKQINAMTRESLGLVGNGKELPTLNRVDTTQAERRYAPSYKKGMIVQPEKDYIRTGLSRGELYTV
DQALPGNVLVVKDKNGNRVEFNPRKLTKLSVYNLEKPEFSVGDLVRITRNDQKLDLTNGDRMRVVGNANG
VIELASLKEKDGTPERVVALPTNRPLHLEHAYSATVHSAQGLTNDRVMISINTKSRTTSQNLWYVAISRA
RHEARIYTDSIAGLPAAIANRYDKTTALSLQQARERQRNESIKPRTVLDGKALERKQRSALDGPSAGKSG
V

  Protein domains


Predicted by InterproScan.

AAA domain (AAA_30)

(476-667)

UvrD-like helicase C-terminal domain (UvrD_C_2)

(870-916)

TrwC relaxase (TrwC)

(15-288)


  Protein structure


Source ID Structure
AlphaFold DB Q847F0


T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 64674..82611

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HKK40_RS00365 (pDTG1p64) 59741..60070 + 330 WP_011117442 TrfB-related DNA-binding protein -
HKK40_RS00370 60063..60335 + 273 WP_019694539 hypothetical protein -
HKK40_RS00375 60602..60865 + 264 WP_019694540 hypothetical protein -
HKK40_RS00380 (pDTG1p66) 61376..62161 - 786 WP_011117444 SprT-like domain-containing protein -
HKK40_RS00385 62299..62685 - 387 WP_019694541 hypothetical protein -
HKK40_RS00390 (pDTG1p68) 62689..63408 - 720 WP_011117446 StbB family protein -
HKK40_RS00395 (pDTG1p69) 63405..63860 - 456 WP_011117447 hypothetical protein -
HKK40_RS00400 (pDTG1p70) 64289..64681 + 393 WP_011117448 hypothetical protein -
HKK40_RS00405 (pDTG1p71) 64674..66230 + 1557 WP_011117449 type IV secretion system DNA-binding domain-containing protein virb4
HKK40_RS00410 (pDTG1p72) 66241..69186 + 2946 WP_011117450 MobF family relaxase -
HKK40_RS00415 (pDTG1p73) 69320..69844 + 525 WP_168940516 hypothetical protein -
HKK40_RS00420 (pDTG1p74) 70173..70811 - 639 WP_011117452 hypothetical protein -
HKK40_RS00425 (pDTG1p75) 70859..71341 - 483 WP_011117453 hypothetical protein -
HKK40_RS00430 (pDTG1p76) 71356..71961 - 606 WP_011117454 phospholipase D family protein -
HKK40_RS00435 (pDTG1p77) 71951..72301 - 351 WP_228409388 TrbM/KikA/MpfK family conjugal transfer protein -
HKK40_RS00440 (pDTG1p78) 72310..73215 - 906 WP_011117456 lytic transglycosylase domain-containing protein virB1
HKK40_RS00445 (pDTG1p79) 73199..74227 - 1029 WP_011117457 P-type DNA transfer ATPase VirB11 virB11
HKK40_RS00450 (pDTG1p80) 74237..75520 - 1284 WP_011117458 TrbI/VirB10 family protein virB10
HKK40_RS00455 (pDTG1p81) 75523..76314 - 792 WP_011117459 TrbG/VirB9 family P-type conjugative transfer protein virB9
HKK40_RS00460 (pDTG1p82) 76339..77004 - 666 WP_011117460 type IV secretion system protein virB8
HKK40_RS00465 (pDTG1p83) 77008..77871 - 864 WP_011117461 type IV secretion system protein virB6
HKK40_RS00470 (pDTG1p84) 77859..78263 - 405 WP_011117462 hypothetical protein -
HKK40_RS00475 (pDTG1p85) 78256..78468 - 213 WP_011117463 hypothetical protein -
HKK40_RS00480 (pDTG1p86) 78496..79185 - 690 WP_011117464 type IV secretion system protein virB5
HKK40_RS00485 (pDTG1p87) 79182..81824 - 2643 WP_019694561 hypothetical protein virb4
HKK40_RS00495 (pDTG1p89) 82150..82611 - 462 WP_011117467 TrbC/VirB2 family protein virB2
HKK40_RS00500 (pDTG1p90) 82628..82903 - 276 WP_024265231 hypothetical protein -

Host bacterium

ID   700 GenBank   NC_004999
Plasmid name   pDTG1 Incompatibility group   _
Plasmid size   83042 bp Coordinate of oriT [Strand]   63861..64288 [-]
Host baterium   Pseudomonas putida

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   -
Degradation gene   nahAa, nahA2, nahAc, nahB, nahF, nahC, nahE, nahD, nagJ, nahJ, nahK, nahM, nahO, nahL, nahN, nahI, nahH, nahG
Symbiosis gene   -
Anti-CRISPR   -