oriTDB

The information of the oriT region

oriTDB accession number	100213
Name	oriT_pAKD33
Sequence Completeness	intact
oriT length	304 nt
oriT sequence	TGCCTCGCAGAGCAGGATGACCCGTTGAGCGCCCCCGGCGCGAATAAGGGACAGTGAAGA TAGATAACCGGCTCGCCGGTTAGCTAACTTCACACATCCTGCCCGCCTTACGGCGTTAAT AACACCAAGGAAAGTCTACACCAGCCATTACGATTTATCCGCAACTATCGCGCTATCAGG CCGCAAAAGCAGCAACGGATATAGCGAAAACCGCCACAATGGCCCATAATGCCGCTATCG AAGCGTGCCAATGCACGCCGATAGCGGACTTTTTGCGTTTCCGTAGCGCCGCTTAGTAGC GTTA
IR (inverted repeat)	[55-72] [75-92] nt (TGAAGATAGATAACCGGC..GCCGGTTAGCTAACTTCA)
Location of nic site	[101-102] nt
Conserved sequence flanking the nic site	CATCCTG\|C
Note	similar to oriT of the IncP-1beta multiresistance plasmid pB10
	L:55-72;R:75-92;D:101-102

Visualization of oriT structure

1...5....10....15....20....25....30....35....40....45....50....55....60

1

TGCCTCGCAGAGCAGGATGACCCGTTGAGCGCCCCCGGCGCGAATAAGGGACAGTGAAGA

61

TAGATAACCGGCTCGCCGGTTAGCTAACTTCACACATCCTGCCCGCCTTACGGCGTTAAT

121

AACACCAAGGAAAGTCTACACCAGCCATTACGATTTATCCGCAACTATCGCGCTATCAGG

181

CCGCAAAAGCAGCAACGGATATAGCGAAAACCGCCACAATGGCCCATAATGCCGCTATCG

241

AAGCGTGCCAATGCACGCCGATAGCGGACTTTTTGCGTTTCCGTAGCGCCGCTTAGTAGC

301

GTTA

Reference

[1] Sen D et al (2011) Broad-host-range plasmids from agricultural soils have IncP-1 backbones with diverse accessory genes. Appl Environ Microbiol. 77(22):7975-83. [PMID:21948829]

I. Information of Relaxase

ID	206
Name	TraI_pAKD33
GenBank accession number	AEV57343
Family	MOB_P
Length	746 aa
UniProt ID	Q7X3D1
PDB ID	_
Pfam	Relaxase [PF03432.13], Evalue: 9.90E-64, Aligned region: 12..252
Note	conjugal transfer relaxase TraI; Provisional
Protein sequence [Download]	MIAKHVPMRSLGKSDFAGLANYITDAQSKDHRLGHVQATNCEAGSIQDAITEVLATQHTN TRAKGDKTYHLIVSFRAGEQPSADTLRAIEERICVGLGYGEHQRISAVHNDTDNLHIHIA INKIHPTRHTMHEPYYPHRALAELCTALERDYGLERDNHEPRKRGAEGRAADMERHAGVE SLVGWIKRECLDEIKGAQSWQELHQVMRDNGMELRVRANGLVFEAGDGTMVKASTVARDL SKPSLEARLGPFEASPERQAQTTAKRQYRKDPIRLRVNTVELYAKYKAEQQSLTTARAQA LERARHRKDRLIEAAKRSNRLRRATIKVVGEGRANKKLLYAQASKALRSELQAINKQFQQ ERTALYAEHSRRTWADWLKKEAQHGGADALAALRAREAAQGLKGNTIRGEGQAKPGHAPA VDNITKKGTIIFRAGMSAVRDDGDRLQVSREATREGLQEALRLAMQRYGNRITVNGTVEF KAQMIRAAVDSQLPITFTDPALESRRQALLNKENTHERTERPEHRGRTGRGAGGPGQRPA ADQHATGAAAVARAGDGRPAAGRGDRADAGLHAATVHRKPDVGRLGRKPPPQSQHRLRAL SELGVVRIAGGSEVLLPRDVPRHVEQQGTQPDHALRRGISRPGTGVGQTPPGVAAADKYI AEREAKRLKGFDIPKHSRYTAGDGALTFQGTRTIEGQALALLKRGDEVMVMPIDQATARR LTRIAVGDAVSITAKGSIKTSKGRSR

Reference
N/A

II. Auxiliary DNA-binding protein(s) of the relaxosome

#	ID	Name	GenBank	Length	Note
1	288	TraH_pAKD33	AEV57344	130 aa	DNA-processing protein; relaxosome stabilisation
2	289	TraJ_pAKD33	AEV57345	124 aa	conjugal transfer relaxosome component TraJ
3	290	TraK_pAKD33	AEV57346	132 aa	DNA-processing protein; oriT-binding protein

Information of T4CP

ID	206
Name	TraG_pAKD33
SecReT4 accesion number	_
GenBank accession number	AEV57342
Family	VirD4/TraG
Length	637
UniProt ID	Q7X3D2
PDB ID	_
Pfam	T4SS-DNA_transf [PF02534.13], Evalue: 2.70E-162, Aligned region: 121..624 TraG-D_C [PF12696.6], Evalue: 5.50E-32, Aligned region: 444..569 TrwB_AAD_bind [PF10412.8], Evalue: 5.10E-22, Aligned region: 187..586
Note	conjugal transfer coupling protein TraG
Protein sequence [Download]	MKIKMNNAVGPQVRTAKPKPSKLLPVLGAASMVGGLQAATQFFAHTFAYHATLGPNVGHV YAPWSILHWTYKWYSQYPDEIMKAGSMGMLVSTVGLLGVAVAKVVTSNSSKANEYLHGSA RWAEKKDIQAAGLLPRERNVLEIVTGKAAPTATGVYVGGWQDKDGNFFYLRHSGPEHVLT YAPTRSGKGVGLVVPTLLSWGASSVITDLKGELWALTAGWRQKHAKNKVLRFEPASTSGG VCWNPLDEIRLGTEYEVGDVQNLATLIVDPDGKGLDSHWQKTAFALLVGVILHALYKAKD DGGTATLPSVDAMLADPNRDIGELWMEMATYGHVDGQNHHAIGSAARDMMDRPEEEAGSV LSTAKSYLALYRDPVVARNVSRSDFRIKQLMHEDDPVSLYIVTQPNDKARLRPLVRVMVN MIVRLLADKMDFEGGRPVAHYKHRLLMMLDEFPSLGKLEIMQESLAFVAGYGIKCYLICQ DINQLKSRETGYGHDESITSNCHVQNAYPPNRVETAEHLSRLTGQTTVVKEQITTSGRRT AAMLGQVSRTYQEVQRPLLTPDECLRMPGPKKNAQGEIEEAGDMVIYVAGYPAIYGKQPL YFKDPVFSARAAIPAPKVSDRLRAVAQAETEGEGITI

Reference
N/A

Information of plasmid

ID	206
Plasmid name	pAKD33
GenBank accession number	JN106174.1
Incompatibility group	IncP1
Genome size	57974 bp
Coordinate of oriT [Strand]	29904..30207 [+]
Drug resistance	_
Heavy-metal resistance	mercury resistance
Virulence factor	_
Xenobiotic degradation	_
Host bacterium [NCBI Taxonomy ID]	Uncultured bacterium [77133]

Reference

[1] Sen D et al (2011) Broad-host-range plasmids from agricultural soils have IncP-1 backbones with diverse accessory genes. Appl Environ Microbiol. 77(22):7975-83. [PMID:21948829]