Detailed information of oriT

oriT


The information of the oriT region


oriTDB ID   113566
Name   oriT_pSH275-1 in_silico
Organism   Shigella sonnei strain SH275-1
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_MG299138 (15108..15160 [-], 53 nt)
oriT length   53 nt
IRs (inverted repeats)     _
Location of nic site      _
Conserved sequence flanking the
  nic site  
 
 _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 53 nt

>oriT_pSH275-1
CACACGATTGTAACATGACCGGAACGGTCTTGTGTACAATCGGTATCGTGCCT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


T4CP


ID   10052 GenBank   WP_039022943
Name   t4cp2_HPG28_RS00240_pSH275-1 insolico UniProt ID   _
Length   652 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 652 a.a.        Molecular weight: 73293.90 Da        Isoelectric Point: 9.1581

>WP_039022943.1 MULTISPECIES: type IV secretory system conjugative DNA transfer family protein [Enterobacteriaceae]
MDAKKTGGLILFLLLLLVGVLIASNYLGGYTALRYSSVDMSLLKWDTFHSVISTFSGNPQYKKLVFMAWF
GFSVPLIFFAIFMLIVVIGIMPKKVIYGDARLATDMDLSKSGFFPDKKSPYKHPPILIGKMFKGRYKKQF
IYFAGQQFLILYAPTRSGKGVGIVIPNCVNYPGSMVILDIKLENWFLSAGFRQKELGQKCFLFAPAGYAE
TIDQAIKGQICSHRWNPLDCVSRSDLLRETDLAKIAAILIPASDDPIWSDSARNLFVGLGLYLLDKERFH
LEQKAKGHNVPDVLVSISAILKTSVPDGGKDLAAWMGQEIENRSWISDKTKSFFFKFMSAPDRTRGSIET
NFSSPLSIFSNPITAEATNFSDFDIRDIRKKPMSIYLGLTPDALITHEKIVNLFFSLLVNENCRELPEHN
PDLKYQCLILLDEFTSMGKSEVIERAVGFTAGYNLRFMFILQNEGQGQKSDMYGQEGWTTFTENSAVVLY
YPPKSKNALAKKISEEIGVRDMKISKRSISSGGGKGGSSRTRNDDVIERPVLLPEEIVSLRDKKNKARNI
AIREIITSEFSRPFIANKIIWFEEPEFKRRVDIARNNHVDIPNLFTQEVMDEIAKIAEIYLPKAGGKKVM
VAGGNVITNPDLDNHDKTDVSE

  Protein domains


Predicted by InterproScan.

(127-591)

  Protein structure



No available structure.




T4SS


T4SS were predicted by using oriTfinder2.

Region 1: 34422..58568

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HPG28_RS00175 29747..30400 - 654 WP_170855322 hypothetical protein -
HPG28_RS00180 30412..31536 - 1125 WP_000486716 site-specific integrase -
HPG28_RS00410 31599..31820 + 222 Protein_38 shufflon system plasmid conjugative transfer pilus tip adhesin PilV -
HPG28_RS00190 32484..33770 - 1287 WP_015057162 shufflon system plasmid conjugative transfer pilus tip adhesin PilV -
HPG28_RS00195 33783..34418 - 636 WP_000934977 A24 family peptidase -
HPG28_RS00200 34422..34904 - 483 WP_001258095 lytic transglycosylase domain-containing protein virB1
HPG28_RS00205 34970..35527 - 558 WP_000095048 type 4 pilus major pilin -
HPG28_RS00210 35572..36681 - 1110 WP_000974903 type II secretion system F family protein -
HPG28_RS00215 36672..38210 - 1539 WP_000466225 GspE/PulE family protein virB11
HPG28_RS00220 38235..38729 - 495 WP_000912553 type IV pilus biogenesis protein PilP -
HPG28_RS00225 38713..40035 - 1323 WP_000454142 type 4b pilus protein PilO2 -
HPG28_RS00230 40074..41717 - 1644 WP_001035590 PilN family type IVB pilus formation outer membrane protein -
HPG28_RS00235 41710..42234 - 525 WP_001401691 sigma 54-interacting transcriptional regulator virb4
HPG28_RS00240 42281..44239 - 1959 WP_039022943 type IV secretory system conjugative DNA transfer family protein -
HPG28_RS00245 44255..45310 - 1056 WP_001542006 P-type DNA transfer ATPase VirB11 virB11
HPG28_RS00250 45329..46468 - 1140 WP_001542008 TrbI/VirB10 family protein virB10
HPG28_RS00255 46458..47159 - 702 WP_049824867 TrbG/VirB9 family P-type conjugative transfer protein -
HPG28_RS00260 47225..47959 - 735 WP_000432282 virB8 family protein virB8
HPG28_RS00265 48125..50482 - 2358 WP_065304451 VirB4 family type IV secretion system protein virb4
HPG28_RS00270 50488..50808 - 321 WP_000362080 VirB3 family type IV secretion system protein virB3
HPG28_RS00405 50879..51169 - 291 WP_000865479 conjugal transfer protein -
HPG28_RS00280 51169..51753 - 585 WP_001177114 lytic transglycosylase domain-containing protein virB1
HPG28_RS00285 51774..52172 - 399 WP_001153669 hypothetical protein -
HPG28_RS00290 52291..52728 - 438 WP_000539665 type IV pilus biogenesis protein PilM -
HPG28_RS00295 52734..53969 - 1236 WP_015059538 TcpQ domain-containing protein -
HPG28_RS00300 53972..54271 - 300 WP_000835764 TrbM/KikA/MpfK family conjugal transfer protein -
HPG28_RS00305 54339..54620 - 282 WP_000638823 type II toxin-antitoxin system RelE/ParE family toxin -
HPG28_RS00310 54610..54861 - 252 WP_000121741 type II toxin-antitoxin system Phd/YefM family antitoxin -
HPG28_RS00315 54961..55596 - 636 WP_022645136 hypothetical protein -
HPG28_RS00320 55644..56435 + 792 WP_022645137 DUF5710 domain-containing protein -
HPG28_RS00325 56690..56914 - 225 WP_000713561 EexN family lipoprotein -
HPG28_RS00330 56923..57567 - 645 WP_001310442 type IV secretion system protein -
HPG28_RS00335 57573..58568 - 996 WP_001028541 type IV secretion system protein virB6
HPG28_RS00340 58572..58829 - 258 WP_000739144 hypothetical protein -
HPG28_RS00345 58826..59179 - 354 WP_023154634 hypothetical protein -
HPG28_RS00350 59399..59611 - 213 WP_039022940 hypothetical protein -
HPG28_RS00355 59622..59792 - 171 WP_000550720 hypothetical protein -
HPG28_RS00360 59796..60239 - 444 WP_072037179 NfeD family protein -
HPG28_RS00365 60613..61566 - 954 WP_072109880 SPFH domain-containing protein -
HPG28_RS00370 61593..61769 - 177 WP_000753050 hypothetical protein -
HPG28_RS00375 61762..61977 - 216 WP_001127357 DUF1187 family protein -
HPG28_RS00380 61970..62476 - 507 WP_171265265 CaiF/GrlA family transcriptional regulator -


Host bacterium


ID   14001 GenBank   NZ_MG299138
Plasmid name   pSH275-1 Incompatibility group   IncI2
Plasmid size   63066 bp Coordinate of oriT [Strand]   15108..15160 [-]
Host baterium   Shigella sonnei strain SH275-1

Cargo genes


Drug resistance gene   mcr-1.1
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -