Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   109985
Name   oriT1_pHL21C in_silico
Organism   Salmonella enterica subsp. enterica strain HL21
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP126328 ( 29699..31403 [+], 1705 nt)
oriT length   1705 nt
IRs (inverted repeats)     _
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 1705 nt

>oriT1_pHL21C
GCCGTATGAATGACATCTATTTCCGTCCAATTCATCGAAACCAGTATTTTGAGGAAATGAAAGCATGATAAAGAAAATTAAAGTAATCATGTTGGCGGCAATAGTTACCGGATGTTCATCGCCACCGCCTCCCGTTCCTGTAGAGTGGGATAAAGCCGCCGCCCCATTAAACACCAGTTTACCGCAATGGAGTGACAATAACGTTATAGTTCCTTCCCCGACAGTTAACGGTAAATGGACATCATCAATCAGCGCACAAAGTTTCTACGATACAATATGGACTCCAGCAGTATTTTACGCAGTCGCCCACTCAACACGAACTGTCGTCACTGCACAATCCGGCACTGATTTCTTTAATGCCAAAAACTGGCTTCGCCAGAATGGCGCAAAAGGTGTTATTGAATACCAGCCTGTCTTTAATTGTCTGACGTGCAGAGAAACCACTATTTATTTCTCTCGCTAATCCATTTAAGCAACACAATCTAATAAGGATTTACCATGAAAAAAACCGTTATCGCGGCGGCTGTATTATGCCTGACCGCAGGAATGCCGATTTATTCATTTGCTGCTGACCCGTGCGAAGTTGTTCTTTGCATGTACGGAAAAGCCACGGGTAATAGTGGCGGGAGTGAATGCAGTTCAGCAGAACGTGCATTTTTTAAAATCAACGCATTTAAAAAACACCATCGTTTTAATCCGGGTAAAACATTCGATATGCGAAAAGAATTTTTAGGCAAATGTAAAGCCGCAGCCCCTGAATCAATAAGCAAAATCCTTTCAAAATTTGGCAGAGTGAAAGGATAACTGACATATCCATTTTGATATGAGAGGTTCGAAATGATAAACGAAGATTTATTCATTAAGAATATACACTCAAAGAATCAGGACAGAATATCTGTAGCCCTGGTATATGACACGTTATCAAAAGAAGCCCACAGAGGTTGTGGGCTGTATTACGAAATATACGAAAGCTGTTTTATCGGTCTTTTGCGCGATCATCTTTCAGAACTTAATGAAGCTGACGCAAATAAATTAAGACGCTATGCCGAGAGTAAAGGTACGAAAATTGATGATGCGTCCTACAGTGAAGCACTGGAAGCTGAAAGGGAGTGCAGGGCTGAAATATACCGCGAGCAAATGTAATCACACCAAACAAAGGTGTATTGTACAATACACAGACTAACAGGCGACGGGACTTTAAGGCTTCATTATTTTTGGCTTCAATTTCGAAGAAATTGTTAAGACGAAAAATAATGAAGTGGTACGCGGAAAGAAAATTCAATTTCGAAGAAATTGCTAATTTTCAGGAACCGCGCCCACCTGCGAACATTCGCCCACAGCGAATTGAGCAGGCCGGGGGAGCCGCAAAAATTTTGCCGCCCCAGCGAGCAAAAAGGCACGCCCACGTGCCGTTTTTTGTGGGGGGCTTGCCCCGCACACCGTCGCAGCCAGGTAATATAACCCGCCCCAGCGGGGGATATTACCGATTAGGCGCGACCAACCCCTTTAAAGCAGCGTTCCGATTTTTTTGAGCTTGCGAGGAAAAATAGGCTAAACGCAGCGTCTTAAAGGGGTTGGTCGCGCGTAGCGCAAGACGGTGTGCCGCCTTTGACCTTGGGGGTTTTGGCTCGGCGTCCAGCCGGGACATTACCCCCATGTGTCATGCAGTGAGGGCGTCCAGCCCGAACGTAATGGCACACGCCGT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


T4CP

ID   7281 GenBank   WP_284546350
Name   t4cp2_QN088_RS24455_pHL21C insolico UniProt ID   _
Length   578 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 578 a.a.        Molecular weight: 65626.88 Da        Isoelectric Point: 7.4566

>WP_284546350.1 type IV secretion system DNA-binding domain-containing protein [Salmonella enterica]
MGSHLMQRLNAFADAFSFFLLWLQNSPVILSLLAGLTLPFIFHLPREERKNAPFWLKSVACVSIFFFIFG
TISPLTIQGLSYFFKSLDNNILFRVPLWIMTIIFTAAGLIFHIAARRLLAGEIDNLKHRMIKKSKLERNT
RTDVRKVKELLPDSIEYNPLDYIDLKKGVFIGLNKDDQPQYITIKEFKTQHAAIIGTTGSGKGVTATVLL
YQAILLGEAVFVEDPKDDEWAPHVLREACKKAGKKFTLINLNKLNFQLDLLADISHEQLEELFNAGFSLA
KKGEASDFYRIADRRAARNTSAIYEKGMTLRDLFNTDFVQSLREDVPAFCGELEEIALVNSINATKGFSL
KEVFDEGGCCYIIGSTRNQKIISAQRMILTRLIQIAETRDRINSTPRTVAIFLDELKYHLSRPALEGLGT
ARDKGVHIFMAFQAIDDLRDCPSDLNGDSVIGAIIENAKFKLIYKIQNPETAEWAAKMTGSILVDDEMRK
VRTDLSLTEKVDTDRMIRQAESYYVDSNMFLNLPEKVGFVFTSTELPRATKMFQVQVKKENIELLSFEYK
QATPEKNESQEHKPSINL

  Protein domains


Predicted by InterproScan.

Helicase HerA, central domain (DUF87)

(174-315)

TraM recognition site of TraD and TraG (TraG-D_C)

(399-490)

  Protein structure



No available structure.



ID   7282 GenBank   WP_284546350
Name   t4cp2_QN088_RS24605_pHL21C insolico UniProt ID   _
Length   578 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 578 a.a.        Molecular weight: 65626.88 Da        Isoelectric Point: 7.4566

>WP_284546350.1 type IV secretion system DNA-binding domain-containing protein [Salmonella enterica]
MGSHLMQRLNAFADAFSFFLLWLQNSPVILSLLAGLTLPFIFHLPREERKNAPFWLKSVACVSIFFFIFG
TISPLTIQGLSYFFKSLDNNILFRVPLWIMTIIFTAAGLIFHIAARRLLAGEIDNLKHRMIKKSKLERNT
RTDVRKVKELLPDSIEYNPLDYIDLKKGVFIGLNKDDQPQYITIKEFKTQHAAIIGTTGSGKGVTATVLL
YQAILLGEAVFVEDPKDDEWAPHVLREACKKAGKKFTLINLNKLNFQLDLLADISHEQLEELFNAGFSLA
KKGEASDFYRIADRRAARNTSAIYEKGMTLRDLFNTDFVQSLREDVPAFCGELEEIALVNSINATKGFSL
KEVFDEGGCCYIIGSTRNQKIISAQRMILTRLIQIAETRDRINSTPRTVAIFLDELKYHLSRPALEGLGT
ARDKGVHIFMAFQAIDDLRDCPSDLNGDSVIGAIIENAKFKLIYKIQNPETAEWAAKMTGSILVDDEMRK
VRTDLSLTEKVDTDRMIRQAESYYVDSNMFLNLPEKVGFVFTSTELPRATKMFQVQVKKENIELLSFEYK
QATPEKNESQEHKPSINL

  Protein domains


Predicted by InterproScan.

Helicase HerA, central domain (DUF87)

(174-315)

TraM recognition site of TraD and TraG (TraG-D_C)

(399-490)

  Protein structure



No available structure.



ID   7283 GenBank   WP_284546357
Name   t4cp2_QN088_RS24700_pHL21C insolico UniProt ID   _
Length   912 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 912 a.a.        Molecular weight: 103348.32 Da        Isoelectric Point: 7.4787

>WP_284546357.1 VirB3 family type IV secretion system protein [Salmonella enterica]
MAKLLKAMKRPAALWGVPMVPLLAVTGVTIIVAIWTSVALLFLLPVQFLVMKSLTRNEPMRFNLIAVWLR
AKGKPVANRLFGATTFMPVEHDDVDIKEFLDAMKLNQCATIKKYIPYSSHIHQHVVRSPKSDLYCTWELM
GTPFDCESDETLQFGTNQLHGLIRSFEGMPVTFYIHNDRNTFTDNLHQDSGNPYADEVSRLYYASVGSFR
RNRLFLTVCYRPFVSLEKAERKRMKDSQKLKELDGALLEMLEIKSTLDTALARYGAHSLGTFTEGKMVFS
SQLAFYEYLLTHQWRKVRVTRTPAYDVMGAAALFFSAESGQINHANGTQYFRGLEIKEFSEETATGMMDS
LLYAPCDYVITQSYTCMSREEAKKTIKRTRRLLMSADDDAVSQRLDLDVALDLLTSGKIAYGKHHFSIMV
YSPSLESLVADTNEISNALNNIGITPVPAEISLSAAYMAQLPGNYNLRPRKGELSSQNFVELAALHNFYP
GKRDKAPWGYAMALMRTPSGDGYYINLHNTLADKDEFNEKNPASTCILGTNGSGKTMLMTFFEIMQQKYS
REDSFSPDAKTKRLTTVYLDKDRGAEMNIRALGGRYYRVISGESTGWNPFSLPATKRNINFIKQLMKILC
TRNGATITPRDERRLNDAVNAVMSDEPEYRRFGITRLREQLPEPATKEAQENGLDIRLSQWAQGGEFGWV
FDNESDTFDISNCDNFGIDGTEFLDDASVCAPISFYLLYRITSLLDGRRLVIFMDEFWKWLRDPVFKDFA
YNKLKTIRKLNGMLVVGTQSPAEIIKDDIAPAVIEQCGTQILAANPNADRAHYVDGMKFEPEVFDVVKGL
DPQARQYVVVKNQFKRGDTKRFAARVTLDLSGIGRYTKVMSGDAPNLEIFESIYREGMQPHEWLDTYLAK
AL

  Protein domains


Predicted by InterproScan.

Type IV secretory pathway, VirB3-like protein (VirB3)

(3-79)

TraG P-loop domain (P-loop_TraG)

(535-813)

CagE, TrbE, VirB family, component of type IV transporter system (CagE_TrbE_VirB)

(269-470)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 19828..33356

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
QN088_RS24515 (QN088_24515) 16970..17677 - 708 WP_268866177 RepA protein -
QN088_RS24520 (QN088_24520) 18137..18496 - 360 WP_034950652 helix-turn-helix transcriptional regulator -
QN088_RS24525 (QN088_24525) 18745..19200 + 456 WP_284546355 transcription termination/antitermination NusG family protein -
QN088_RS24530 (QN088_24530) 19272..19487 + 216 WP_004178170 hypothetical protein -
QN088_RS24535 (QN088_24535) 19492..19710 + 219 WP_004178172 hypothetical protein -
QN088_RS24540 (QN088_24540) 19828..20538 + 711 WP_284546356 lytic transglycosylase domain-containing protein virB1
QN088_RS24545 (QN088_24545) 20535..20840 + 306 WP_012457109 TrbC/VirB2 family protein virB2
QN088_RS24550 (QN088_24550) 20853..23589 + 2737 Protein_28 VirB3 family type IV secretion system protein -
QN088_RS24555 (QN088_24555) 23607..24308 + 702 WP_284546359 type IV secretion system protein -
QN088_RS24560 (QN088_24560) 24320..24544 + 225 WP_053271848 EexN family lipoprotein -
QN088_RS24565 (QN088_24565) 24556..25632 + 1077 WP_284546347 type IV secretion system protein virB6
QN088_RS24570 (QN088_24570) 25848..26531 + 684 WP_109176809 type IV secretion system protein virB8
QN088_RS24575 (QN088_24575) 26528..27436 + 909 WP_284546193 P-type conjugative transfer protein VirB9 virB9
QN088_RS24580 (QN088_24580) 27483..28751 + 1269 WP_284546348 VirB10/TraB/TrbI family type IV secretion system protein virB10
QN088_RS24585 (QN088_24585) 28741..29766 + 1026 WP_284546192 P-type DNA transfer ATPase VirB11 virB11
QN088_RS24590 (QN088_24590) 29763..30161 + 399 WP_284546191 cag pathogenicity island Cag12 family protein -
QN088_RS24595 (QN088_24595) 30197..30502 + 306 WP_284546349 conjugal transfer protein -
QN088_RS24600 (QN088_24600) 30536..30841 + 306 WP_032152569 hypothetical protein -
QN088_RS24605 (QN088_24605) 31620..33356 + 1737 WP_284546350 type IV secretion system DNA-binding domain-containing protein virb4
QN088_RS24610 (QN088_24610) 33365..34119 + 755 Protein_40 MobC family replication-relaxation protein -
QN088_RS24615 (QN088_24615) 34156..34629 + 474 WP_284546351 thermonuclease family protein -
QN088_RS24620 (QN088_24620) 34690..35031 + 342 WP_350030269 hypothetical protein -
QN088_RS24625 (QN088_24625) 35068..35301 - 234 WP_004178129 hypothetical protein -
QN088_RS24630 (QN088_24630) 35342..35896 - 555 WP_284546353 chromosome partitioning protein -
QN088_RS24635 (QN088_24635) 36106..36888 - 783 WP_284546354 SprT-like domain-containing protein -
QN088_RS24640 (QN088_24640) 37323..37601 + 279 WP_058216745 type II toxin-antitoxin system HicA family toxin -
QN088_RS24645 (QN088_24645) 37594..37941 + 348 WP_058216744 type II toxin-antitoxin system HicB family antitoxin -
QN088_RS24650 (QN088_24650) 38018..38200 - 183 WP_284546360 colicin release lysis protein -

Host bacterium

ID   10420 GenBank   NZ_CP126328
Plasmid name   pHL21C Incompatibility group   -
Plasmid size   48318 bp Coordinate of oriT [Strand]   5542..7246 [+]; 29699..31403 [+]
Host baterium   Salmonella enterica subsp. enterica strain HL21

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -