Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100323
Name   oriT_pNAH20 in_silico
Organism   Pseudomonas fluorescens
Sequence Completeness      intact
NCBI accession of oriT (coordinates [strand])   NC_012674 (62665..63092 [-], 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_pNAH20
GGTGGTCCTCTCTGAGCCAAATATGGGACTAATTCAGGATAACGATAACTTCCGAAATAGCGTATAGCAAATGCAATACATAAAATGCTTGATTTTATTGGTCTAAATGATAATTTTGTAATACATATGTATAGCGCATGAAATTCATGAATTTGCTCTGTAAGCCGCTCCCAGCGCGGCTTTAACCTACCGCTAGGGGGGTGCGTGTTGTGTATTGAGACTTTGACCCTGTTAAGGGGAAAAGTTGAAGCTCTTGTTAAGGGCGTATCCACTAGTCAGGCCGCAGGCCGTAGGGGGGTAGCACAGATGGTATGCAGAAAGGGTGCAGGAAGGGTGCTAAGAGAGTGCAAGAGGGGTGCAACTTGACTACAGGTAGGGGGCGATTAAGATGCACCTAGAGTGCAATAGGGGTGCAGATAGGGTGCAAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   394 GenBank   YP_002887474
Name   TraC_pNAH20 insolico UniProt ID   C3KFS3
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

>YP_002887474.1 putative TraC protein (plasmid) [Pseudomonas fluorescens]
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 C3KFS3


T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 63478..81415

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HUF66_RS00360 (pNAH20_p66) 58545..58874 + 330 WP_011117442 TrfB-related DNA-binding protein -
HUF66_RS00365 58867..59139 + 273 WP_019694539 hypothetical protein -
HUF66_RS00370 59406..59669 + 264 WP_019694540 hypothetical protein -
HUF66_RS00375 (pNAH20_p68) 60180..60965 - 786 WP_011117444 SprT-like domain-containing protein -
HUF66_RS00380 61103..61489 - 387 WP_019694541 hypothetical protein -
HUF66_RS00385 (pNAH20_p70) 61493..62212 - 720 WP_011117446 StbB family protein -
HUF66_RS00390 (pNAH20_p71) 62209..62664 - 456 WP_011117447 hypothetical protein -
HUF66_RS00395 (pNAH20_p72) 63093..63485 + 393 WP_011117448 hypothetical protein -
HUF66_RS00400 (pNAH20_p73) 63478..65034 + 1557 WP_011117449 type IV secretion system DNA-binding domain-containing protein virb4
HUF66_RS00405 (pNAH20_p74) 65045..67990 + 2946 WP_011117450 MobF family relaxase -
HUF66_RS00410 (pNAH20_p75) 68124..68648 + 525 WP_168940516 hypothetical protein -
HUF66_RS00415 (pNAH20_p76) 68977..69615 - 639 WP_011117452 hypothetical protein -
HUF66_RS00420 (pNAH20_p77) 69663..70145 - 483 WP_011117453 hypothetical protein -
HUF66_RS00425 (pNAH20_p78) 70160..70765 - 606 WP_011117454 phospholipase D family protein -
HUF66_RS00430 (pNAH20_p79) 70755..71105 - 351 WP_228409388 TrbM/KikA/MpfK family conjugal transfer protein -
HUF66_RS00435 (pNAH20_p80) 71114..72019 - 906 WP_011117456 lytic transglycosylase domain-containing protein virB1
HUF66_RS00440 (pNAH20_p81) 72003..73031 - 1029 WP_011117457 P-type DNA transfer ATPase VirB11 virB11
HUF66_RS00445 (pNAH20_p82) 73041..74324 - 1284 WP_011117458 TrbI/VirB10 family protein virB10
HUF66_RS00450 (pNAH20_p83) 74327..75118 - 792 WP_011117459 TrbG/VirB9 family P-type conjugative transfer protein virB9
HUF66_RS00455 (pNAH20_p84) 75143..75808 - 666 WP_011117460 type IV secretion system protein virB8
HUF66_RS00460 (pNAH20_p85) 75812..76675 - 864 WP_011117461 type IV secretion system protein virB6
HUF66_RS00465 (pNAH20_p86) 76663..77067 - 405 WP_011117462 hypothetical protein -
HUF66_RS00470 (pNAH20_p87) 77060..77272 - 213 WP_011117463 hypothetical protein -
HUF66_RS00475 (pNAH20_p88) 77300..77989 - 690 WP_011117464 type IV secretion system protein virB5
HUF66_RS00480 (pNAH20_p89) 77986..80628 - 2643 WP_019694561 hypothetical protein virb4
HUF66_RS00490 (pNAH20_p91) 80954..81415 - 462 WP_011117467 TrbC/VirB2 family protein virB2
HUF66_RS00495 (pNAH20_p92) 81632..82612 - 981 WP_012727771 IS5-like element IS1384 family transposase -
HUF66_RS00500 (pNAH20_p93) 82652..82903 - 252 WP_238838938 hypothetical protein -

Host bacterium

ID   784 GenBank   NC_012674
Plasmid name   pNAH20 Incompatibility group   _
Plasmid size   83042 bp Coordinate of oriT [Strand]   62665..63092 [-]
Host baterium   Pseudomonas fluorescens

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, nahAb, nahG
Symbiosis gene   -
Anti-CRISPR   -