Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100497
Name   oriT_p14-120 in_silico
Organism   Salmonella sp. 14
Sequence Completeness      intact
NCBI accession of oriT (coordinates [strand])   NC_019342 (65932..66291 [+], 360 nt)
oriT length   360 nt
IRs (inverted repeats)      280..287, 289..296  (GCAAGATT..AATCTTGC)
Location of nic site      305..306
Conserved sequence flanking the
  nic site    		  GACGGGTGT|GG
Note   predicted by the oriTfinder

  oriT sequence  


Download         Length: 360 nt

>oriT_p14-120
GATTATCAAGAGTCACATGTGAATCGGCCATTTATTTTATTAGAGTCAACATGGATTCACCAACTTCATACAGGCGAATCTGTTATACCGAAATTAAGGATTCGAATCCAGATTCGAATCCTTAATTTTGTCTTAATTTAGTGGTCTGATTCGTAGATGAATCTGGATTCAACTCCTTTACGATTCACTGAAGATTTGCATGTGAATCTAGTATCTATATCGAACATAGAATAACGATAAAAATATTAACATAACATACTGATATAAAAGGATAATCATGCAAGATTAAATCTTGCGACGGGTGTGGGACTTTGATGTTAAGGAGCAGGCATACAGAAATATGCCAGCCAGGAAGAATTC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   568 GenBank   YP_006964311
Name   TraD_p14-120 insolico UniProt ID   I3W357
Length   1767 a.a. PDB ID   
Note   putative relaxase

  Relaxase protein sequence


Download         Length: 1767 a.a.        Molecular weight: 193737.36 Da        Isoelectric Point: 5.0822

>YP_006964311.1 IncF plasmid conjugative transfer protein TraD (plasmid) [Salmonella sp. 14]
MLSISSIKGDAGYYSHEDNYYASGSLDSRWMGEGAEKLGLKGEVASADMDAVRQGRLPDGSDLSRMVDGV
NKHRSGYDLTFSAPKSVSVMALVGEDRRFIEAHNRAVAVVMQEVEQLVSARITQEGKTETVLTGSMVAAL
YNHDTSRDLDPQVHTHALVFNATFADDKWRSLASDTRMKTGFSENLYATKIALGNLYRAALREDIESMGF
ETVAAGKHGLWELKDVPVDIFSSRSQSIRKAAGPDASAKSRDIAALDTRQAKAWADPELLKADWRRRLTD
EKFDIDNYISQAQTRAEPPGPVVGGTEGIRSTGQPASASSAQISELDVQKAVSDTISALSDKKVQFSWSE
MLAGTVSRLPSAPGLFVQARAAIEASIEGQRLIPLDREKGIFTSDIHLLNELSVHQLARTAIQEQTVLVF
PERAQERDIPAGDAVSVLSQDKSPVAILSGRGGAQTLRERTEDVAMMARSQGREVMVIAADGRSGQFLSE
SPHLAGHVMLRSQMNADTLLPVQGTVIVDRAERLSLKETVLLQEKALSAGAQLIFMDTENRQGTGNALSV
LKEADIPQYRFYSTQLPEVRLVSEADKRSRYSQLAQDYVRLSAEGRDVVAQVTGAREQQQLTEVIRDTRR
EAGELGREQVTLRVLEPVWLDSKTRHQRDNYRPGMVMEQWDAEKKTMTRHTIDRVAEATNSLVLLGEDGT
RLTMKVTQLDGSWSLYRSRTLEVSEGDRVRALGRELKGAIKAKEQFTVAGLENGAVRLRSGDRELRLPTE
RAVKLTHDYVEGTGAGTSASRTVLAAVGPRGLNKQALNALAQSGSDIRIYTPREGRQAARKVESVSAVRL
ASDQVRQLTGEANLDTAIQASRERLMSDAEQAVNLAIPRAQQGQVYLSELTLLAEAVKSGQPLADVRTEI
ARQVDSGALIKLDSVAGAGNRVLVPRVAYEMEKTIIRHIAEGKDAVQPLMALTPASVLSGLTAGQREATR
TVLENTDRFMAIQGYAGVGKTTQFRAVMGALNTLSESVRPQVIGLGPTHRAVHEMREAGVEARTLASFLS
ETRQAIQAGETPDFRNVLFLTDESSMVGNRDMAELYQLVAAGGGRMVSSGDTAQLQAVSTGQPFRLVQQR
SAIDTVVMQEIVRQTPALRPAIESIIAGQVEISLRQVDDVTPQQVPRQPGAWVPDNSVMEIRAPKKEQDQ
VQDTPVAGEQTLTPEQLALVRTDIIEAIRDDWMGRTSEAQQQTLVVAELNADRHAINAAIHAARHEKGDT
GAEERTFTVLEPLRVPDNALRAAETFAEYTGAVAMMNERYWTVAEVDTQDAVVTLRNADGESVLISPQQN
TAQDISLFTPRELTISQGDRVRFTRSDTDRGYVANSLWEVAGFTDGGAIRFRQGEQEKIVDPQAMTEDRH
IDLAYALTVYGVQGASERFAIALTGTEGGRKRMASLESTYVTLSRAKEHVQVYTDNLEDWQQQVRQSDGG
KTAHDLLHEKSDRESDTGNRLLATALRLDKTALGRRVLAENGLEGETMARFIAAGKKYPSPYVALPAWTR
HGKAAGALLTEIRIEDDGMRVMLSDESRLRGGDDAQFAGLQASRNGQTLIADDAQTALRLAQENPESGVV
IRLHGEERLLNAARLTGGRITEPDEVERTVRSVAEAESAAKTEDPITLPPDEQQKLAEAQEKAARELAEQ
ARQELLPEMPGEESSRPEPLLSADEERRLRDGTARGERELDEAIQEAVADGRGIRQQVREQMLRTEREWV
VNVPEKDIELEKTLGGD

  Protein domains


Predicted by InterproScan.

single-stranded DNA binding TraI N-terminal subdomain (ssDNA_TraI_N)

(586-638)

DNA helicase TraI (TraI_C)

(1441-1558)

DNA relaxase TraI 2B/2B-like domain (TraI_2B)

(644-723)

TrwC relaxase (TrwC)

(12-279)

AAA domain (AAA_30)

(971-1155)


  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 42778..66822

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HS987_RS00210 (D670_p1061) 42778..45012 - 2235 WP_088546709 type IV conjugative transfer system coupling protein TraD virb4
HS987_RS00215 (D670_p1062) 45163..45900 - 738 WP_088546708 conjugal transfer complement resistance protein TraT -
HS987_RS00220 46078..46638 - 561 WP_088546707 protein traS -
HS987_RS00225 (D670_p1063) 46650..49547 - 2898 WP_015062635 conjugal transfer mating-pair stabilization protein TraG traG
HS987_RS00230 (D670_p1064) 49549..50910 - 1362 WP_015062636 conjugal transfer pilus assembly protein TraH traH
HS987_RS00235 (D670_p1065) 50910..51521 - 612 WP_015062637 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
HS987_RS00240 (D670_p1066) 51543..52322 - 780 WP_015062638 type-F conjugative transfer system pilin assembly protein TraF traF
HS987_RS00245 (D670_p1067) 52319..54148 - 1830 WP_015062639 type-F conjugative transfer system mating-pair stabilization protein TraN traN
HS987_RS00250 (D670_p1068) 54145..54747 - 603 WP_309301465 type-F conjugative transfer system pilin assembly protein TrbC trbC
HS987_RS00255 (D670_p1069) 54756..55124 - 369 WP_015062641 hypothetical protein -
HS987_RS00260 (D670_p1070) 55135..56130 - 996 WP_015062642 conjugal transfer pilus assembly protein TraU traU
HS987_RS00265 (D670_p1071) 56127..56762 - 636 WP_015062643 type-F conjugative transfer system protein TraW traW
HS987_RS00270 (D670_p1072) 56762..57226 - 465 WP_015062644 type-F conjugative transfer system protein TrbI -
HS987_RS00275 (D670_p1073) 57223..59814 - 2592 WP_015062645 type IV secretion system protein TraC virb4
HS987_RS00280 (D670_p1074) 59825..60439 - 615 WP_015062646 type IV conjugative transfer system lipoprotein TraV traV
HS987_RS00285 (D670_p1075) 60550..60774 - 225 WP_008455352 TraR/DksA C4-type zinc finger protein -
HS987_RS00290 (D670_p1076) 60886..62247 - 1362 WP_000024509 F-type conjugal transfer pilus assembly protein TraB traB
HS987_RS00295 (D670_p1077) 62234..62974 - 741 WP_015062647 type-F conjugative transfer system secretin TraK traK
HS987_RS00300 (D670_p1078) 62964..63527 - 564 WP_015062648 type IV conjugative transfer system protein TraE traE
HS987_RS00305 (D670_p1079) 63547..63852 - 306 WP_000398849 type IV conjugative transfer system protein TraL traL
HS987_RS00310 (D670_p1080) 63854..64213 - 360 WP_001054221 type IV conjugative transfer system pilin TraA -
HS987_RS00315 (D670_p1081) 64330..64563 - 234 WP_000662610 TraY domain-containing protein -
HS987_RS00320 (D670_p1082) 64769..65218 - 450 WP_015062649 helix-turn-helix domain-containing protein -
HS987_RS00325 (D670_p1083) 65515..65898 - 384 WP_015062650 conjugal transfer relaxosome DNA-binding protein TraM -
HS987_RS00330 (D670_p1085) 66367..66822 + 456 WP_015062652 transglycosylase SLT domain-containing protein virB1
HS987_RS00335 (D670_p1086) 66833..67419 - 587 Protein_66 antirestriction protein -
HS987_RS00340 (D670_p1088) 68010..68843 - 834 WP_015062654 N-6 DNA methylase -
HS987_RS00345 (D670_p1089) 68890..69036 - 147 WP_001159046 hypothetical protein -
HS987_RS00350 (D670_p1090) 69131..69478 - 348 WP_000550116 hypothetical protein -
HS987_RS00355 (D670_p1091) 69535..69939 - 405 WP_015062655 hypothetical protein -
HS987_RS00720 70591..70741 - 151 Protein_71 hypothetical protein -

Host bacterium

ID   958 GenBank   NC_019342
Plasmid name   p14-120 Incompatibility group   IncFII
Plasmid size   130175 bp Coordinate of oriT [Strand]   65932..66291 [+]
Host baterium   Salmonella sp. 14

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   Cobalt-zinc-cadmium resistance
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -