Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   114026
Name   oriT_pDG3-1g in_silico
Organism   Agrobacterium salinitolerans strain DG3-1
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP074400 (341001..341029 [+], 29 nt)
oriT length   29 nt
IRs (inverted repeats)      14..19, 24..29  (CGTCGC..GCGACG)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 29 nt

>oriT_pDG3-1g
AGGGCGCAATATACGTCGCTGGCGCGACG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   9012 GenBank   WP_217005982
Name   traA_KHC17_RS28135_pDG3-1g insolico UniProt ID   _
Length   1544 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1544 a.a.        Molecular weight: 170896.51 Da        Isoelectric Point: 9.4201

>WP_217005982.1 Ti-type conjugative transfer relaxase TraA [Agrobacterium salinitolerans]
MAIMFIRAQVISRGGGRSIVSAAAYRHRARMVDEQAGASFSYRGGAAELKHEELALPDQIPAWLRTAIDG
KSVAAASEALWNAVDAFETRADAQLARELIVALPEELTRSENIALVREFVRDNLTSRGMIADWVYHDKDG
NPHIHLMTALRPLADDGFGPKKVPVIGTNGEPMRVVTPDRPKGKIVYKLWAGDKETMKSWKIAWAETTNR
HLALAGHDIRLDGRSYAEQGLDGIAQKHLGPEKAALARKGIEMYFAPADLARRHEMADRLLAEPALLLKQ
LANERSTFDERDIARVLHRYVDDPTDFANIRAKLMASNDLVLLKPQQADLQTGEMAEAAVFTTRDILRAE
YDMAQSAEALALRKGFGVAAAKIAAAVRTIETGDAENRFRLDREQVEAVHHIAGDNGIAAVVGLAGAGKS
TLLAAARVAWESDGHRVFGAALAGKAAEGLEDSSGTKSRTLASWEMAWENGRDLLHRQDIFVIDEAGMVS
SHQMACVLRRVEEAGAKVVLVGDAMQLQPIQAGAAFRAISERIGSAELAGVRRQREEWARQASRLFARGQ
VENGLDAYAQRGHIVETGSRDEAVERIVTDWTSARRDLIQQNADKEQPARLRGGELLVLAHTNDDVRRLN
EALRNVMKDEAALTASREFQTARGVREFAGGDRIIFLENARFLEPRARKLGPQYVKNGMLGTVVSTGGLH
SGPLLSVRLDNGRDVVISENSYRNVDHGYAATIHKSQGASVDRTFVLATGMMDQHLAYVSMTRHRDRADL
YAAREDFKPKWEWGMRSPIDHAAGVTGELVGTGNAMFRPQDEGADKSPYADVKTDDGTVHRLWGVSLPKA
LDAAGVSEGDTVTLRKDGVERVTVTVPVIGEKTGKKRLEQRTVDRNVWTAKQIETAEVRQQRIEQESHRP
ELFKQLVERLGRSGAKTTTLDFESEAGYQAHARDFAHRRGIDTLSGVAAWMEAGAGRPLAWLAQKREQVA
KLWERASVALGFAIERERRFSYNEECTENLATQVPADRRYLMAPTTLFSRGVDEDARRAQLRSDRWKERD
AILQPVLQKIYRDPESALARLNALASDARIAPRELAEDLEASPQRLGRLRGSDILVDGRSARSERDTAVL
ALSELLPLARAHATEFRRQAERFGLREEQRRAHMSLSIPALSNQAMGRLAEIEAVRERGGTDAYKTAFTY
AAQDRLLVKEVRAVNDALTARFGWSAFTDKPDAVAERNMIERMPEDLHPDRREKLARLFAVVRRFAEEQH
LAETKDRSRIVAGASVEPGKETVGVLPMLAAVTEFETAIDQEARKRVRAVSHYGQNRTALFGAAERIWRD
PAGAVGKIEELILKGFAGERIAAAVANDPAAYGALRGSGRIMDKLLAVGRERKEALQAISEAASCIRSLG
VSWASAFDAETRAVSEERRCMSVAIPGLSQAAENALSTLVADINRSTGRQKKAGQDAVVRLLDPHIAREF
AEVSRALDERFGRNAILRGERDVINRVSPAQRRAFEAIKERLLVLQRAVREESSQKIIAERQRRSIERGR
IFTR

  Protein domains


Predicted by InterproScan.

MobA/MobL family (MobA_MobL)

(17-249)

BID domain of Bartonella effector protein (Bep) (Bep_C_terminal)

(1053-1125)

BID domain of Bartonella effector protein (Bep) (Bep_C_terminal)

(1306-1399)

AAA domain (AAA_30)

(391-577)


  Protein structure



No available structure.




T4CP

ID   10446 GenBank   WP_217005540
Name   traG_KHC17_RS26585_pDG3-1g insolico UniProt ID   _
Length   639 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 639 a.a.        Molecular weight: 70900.99 Da        Isoelectric Point: 9.3372

>WP_217005540.1 Ti-type conjugative transfer system protein TraG [Agrobacterium salinitolerans]
MKGKARLHPSLLLIIVPIVVTGFSFYVSHWRWPELANGITGKTQYWFLRASPLPVLLLGPLTGLLAVWVL
PLHRRRPVALASFLCFLLMAGFYGLRESGRLLPSLESGVLTWDRALSFVDMIAVVGTAMGFMVVAVAARI
SSIVPERVPRARRGTFGDADWLPMSAAARLFPDDGEIVIGERYRVDKELVHELPFDPNDPATWGRGGRAP
LLTYAQDFDSTHMLFFAGSGGFKTTSNVVPTALRYRGPLICLDPSTEVAPMVVDHRRDKLDREVVVLDPA
NPVMGFNVLDGIEHSLKKEEDIVGIAHMLLSESVRFESSTGSFFQNQAHNLLTGLLAHVMLSPEFAGRRN
LRSLRQIVSEPETSVLAMLRDVQEHSKSAFIRETLGVFVNMTEQTFSGVYSTASKDTQWLSLDNYAALVC
GNTFNSSEIAGGKKDVFINIPASILRSYPGIGRVIIGSLINAMIEADGAFTRRALFVLDEVDLLGYMRVL
EEARDRGRKYGVSMMLMYQSVGQLERHFGKDGAVSWIDGCAFVSYAAIKALDTARNVSAQCGEMTVEVKG
SSRNLGWGTKNSGSRKSESINFQRRPLIMPHEITQSMRKDEQIIIVQGHSPIRCGRAIYFRRKDMDMQAR
PNRFAKLGP

  Protein domains


Predicted by InterproScan.

Type IV secretory system Conjugative DNA transfer (T4SS-DNA_transf)

(166-632)

  Protein structure



No available structure.



ID   10447 GenBank   WP_217005978
Name   traG_KHC17_RS28120_pDG3-1g insolico UniProt ID   _
Length   639 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 639 a.a.        Molecular weight: 70920.99 Da        Isoelectric Point: 9.0337

>WP_217005978.1 Ti-type conjugative transfer system protein TraG [Agrobacterium salinitolerans]
MTGMARLHPSLLLIIVPIVVTGFSFYVSHWRWPELANGITGKTQYWFLRASPLPVLLLGPLAGLLAVWVL
PLHRRRPVALASFLCFLLMAGFYGLREFGRLLPSVESGVLTWDRALSFVDMIAVVGTAMGFMVVAVAARI
SSIVPERVPRARRGTFGDADWLPMSAAARLFPDDGEIVIGERYRVDKELVHELPFDPNDPATWGRGGRAP
LLTYAQDFDSTHMLFFAGSGGFKTTSNVVPTALRYRGPLICLDPSTEVAPMVVDHRRDKLDREVVVLDPA
NPVMGFNVLDGIEHSLKKEEDIVGIAHMLLSESVRFESSTGSFFQNQAHNLLTGLLAHVMLSPEFAGRRN
LRSLRQIVSEPETSVLAMLRDVQEHSRSAFIRETLGVFVNMTEQTFSGVYSTASKDTQWLSLDNYAALVC
GNTFNSSEIAGGKKDVFINIPASILRSYPGIGRVIIGSLINAMIEADGAFTRRALFVLDEVDLLGYMRVL
EEARDRGRKYGVSMMLMYQSVGQLERHFGKDGAVSWIDGCAFVSYAAIKALDTARNVSAQCGEMTVEVKG
SSRNLGWGTKNSGSRKSESINFQRRPLIMPHEITQSMRKDEQIIIVQGHSPIRCGRAIYFRRKDMDMQAR
PNRFAKLGP

  Protein domains


Predicted by InterproScan.

Type IV secretory system Conjugative DNA transfer (T4SS-DNA_transf)

(166-632)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 390214..399130

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
KHC17_RS28335 (KHC17_28335) 386202..386750 + 549 WP_217006041 carboxymuconolactone decarboxylase family protein -
KHC17_RS28340 (KHC17_28340) 386819..387046 + 228 Protein_389 DUF1348 family protein -
KHC17_RS28345 (KHC17_28345) 387071..387418 + 348 WP_217005578 hypothetical protein -
KHC17_RS28350 (KHC17_28350) 387452..388342 + 891 WP_217006043 LysR family transcriptional regulator -
KHC17_RS28355 (KHC17_28355) 388867..389229 - 363 WP_149148713 transcriptional regulator -
KHC17_RS29880 389323..389862 + 540 WP_254229242 hypothetical protein -
KHC17_RS29885 389865..390217 + 353 Protein_394 hypothetical protein -
KHC17_RS28365 (KHC17_28365) 390214..390513 + 300 WP_217006047 TrbC/VirB2 family protein virB2
KHC17_RS28370 (KHC17_28370) 390516..390857 + 342 WP_149148710 type IV secretion system protein VirB3 virB3
KHC17_RS28375 (KHC17_28375) 390850..393231 + 2382 WP_217006049 VirB4 family type IV secretion/conjugal transfer ATPase virb4
KHC17_RS28380 (KHC17_28380) 393231..393929 + 699 WP_217006051 P-type DNA transfer protein VirB5 virB5
KHC17_RS28385 (KHC17_28385) 393926..394159 + 234 WP_217006054 EexN family lipoprotein -
KHC17_RS28390 (KHC17_28390) 394164..395099 + 936 WP_217006056 type IV secretion system protein virB6
KHC17_RS28395 (KHC17_28395) 395135..395401 + 267 WP_217006058 hypothetical protein -
KHC17_RS28400 (KHC17_28400) 395405..396076 + 672 WP_217006060 virB8 family protein virB8
KHC17_RS28405 (KHC17_28405) 396073..396927 + 855 WP_217006062 P-type conjugative transfer protein VirB9 virB9
KHC17_RS28410 (KHC17_28410) 396942..398114 + 1173 WP_217006064 type IV secretion system protein VirB10 virB10
KHC17_RS28415 (KHC17_28415) 398123..399130 + 1008 WP_217006066 P-type DNA transfer ATPase VirB11 virB11
KHC17_RS28420 (KHC17_28420) 399055..399372 - 318 WP_333781944 leucine zipper domain-containing protein -
KHC17_RS28425 (KHC17_28425) 399441..400586 - 1146 WP_217006070 HlyD family secretion protein -
KHC17_RS28430 (KHC17_28430) 400723..401622 + 900 WP_217006072 LysR family transcriptional regulator -
KHC17_RS28435 (KHC17_28435) 401702..403327 - 1626 WP_217006074 MFS transporter -
KHC17_RS28440 (KHC17_28440) 403602..404048 - 447 WP_217006076 carboxymuconolactone decarboxylase family protein -

Host bacterium

ID   14461 GenBank   NZ_CP074400
Plasmid name   pDG3-1g Incompatibility group   -
Plasmid size   521982 bp Coordinate of oriT [Strand]   341001..341029 [+]
Host baterium   Agrobacterium salinitolerans strain DG3-1

Cargo genes

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