Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100106
Name   oriT_pKS208 in_silico
Organism   Uncultured bacterium
Sequence Completeness      core
NCBI accession of oriT (coordinates [strand])   JQ432564 (39342..39384 [+], 43 nt)
oriT length   43 nt
IRs (inverted repeats)      1..19, 22..40  (GTGAAGAAGGCCGACCCGC..GCGGGTGGGCCTACTTCAC)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   

  oriT sequence  


Download         Length: 43 nt

>oriT_pKS208
GTGAAGAAGGCCGACCCGCTTGCGGGTGGGCCTACTTCACCTG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   101 GenBank   AFS51557
Name   TraI_pKS208 insolico UniProt ID   J9Z856
Length   803 a.a. PDB ID   
Note   TraI relaxase

  Relaxase protein sequence


Download         Length: 803 a.a.        Molecular weight: 87470.13 Da        Isoelectric Point: 10.8015

>AFS51557.1 TraI relaxase (plasmid) [uncultured bacterium]
MISKRIPMTSAKKSSFAGLVNYITNSQGISERVGEVRITNCQSEDLRWAVGEVLSTQQQNTRAEGDKTYH
LLISFAPGEKPSAEVLRDVEDRICAAMGYGEHQRVSAVHNDTDVLHIHVAINKIHPVRHTMHEPYRDFKT
RSDICAKLEIEHGLERVNHAGKKPYSESRANDMERHAGVESLLSWVRKECLEQMQGASSWKQLHQVLHEH
GLELREKGNGFVIQSQDGTMVKASTVARELSKAKLEGRLGAYEVRPSVGVQSLPAGAVPKKPGIGRVGRK
PPPLSRNRLRSLGSLQSLELDSGKRYEKRPIGNSDTTELYARYRDDQAAVRHTRTKELALERERRDRALD
YAKKESALKRASIKLMVTPGITKKLLYASAHQTLQKQLAKIRADHRKAVERINTTQKARQWADWLQAKAK
DGDQEALAALRAREGARGLRGDAIAGKNKPKATTVVRAAQEHITKEGTVIYRAGASAIRDDGSKLQLSRG
TNFDGIETALRMAVARYGEQITVTGSQQFKEQVAQTAALRGLPIKFDDPALEQRRQVLQQAIEKERSNVG
TDRGRAAGAGPGSDGIDTARRGRSGAGRNTTGATSGRPDGVRGYATGTGVPGRAGAGLGADGGRIAVRAT
GGTAKPGIARVGRKPPPESQNRLRTLSQLGVVQLTNGGESLLPSHVPGRVEQQGAATDNGLRRNVSRGGI
EGLPPSIDGIKAARQYIAEREDKRAKGFDIPKHRLYNATDEGAAAFAGVRSVEGQSMALLKRGDEVLVLP
INEATARRMKRMKLGEPVTTTAKGAIKSKGRSR

  Protein domains


Predicted by InterproScan.

Relaxase/Mobilisation nuclease domain (Relaxase)

(12-251)

Large polyvalent protein-associated domain 7 (LPD7)

(459-547)


  Protein structure


Source ID Structure
AlphaFold DB J9Z856

  Reference


[1] Sen D et al. (2013) Inferring the evolutionary history of IncP-1 plasmids despite incongruence among backbone gene trees. Mol Biol Evol. 30(1):154-66. [PMID:22936717]


Auxiliary protein

ID   149 GenBank   AFS51579
Name   TraH_pKS208 insolico UniProt ID   J9Z6L8
Length   142 a.a. PDB ID   _
Note   TraH DNA transfer protein

  Auxiliary protein sequence


Download         Length: 142 a.a.        Molecular weight: 15706.51 Da        Isoelectric Point: 3.7496

>AFS51579.1 TraH DNA transfer protein (plasmid) [uncultured bacterium]
MSEPTEDELLAQALAAMESTPPVEVGAEPDETPPEPPVDDLTEFEGMPPEPEFLDELGPASAPMEDESPF
APRGEPQSLVLRELDESRRPKARTVCEHCPNSVWFSSPTEVKAYCRVMFLVVWSNKEPQQITGCDGMFLG
EE

  Protein domains



No domain identified.



  Protein structure


Source ID Structure
AlphaFold DB J9Z6L8

  Reference


[1] Sen D et al. (2013) Inferring the evolutionary history of IncP-1 plasmids despite incongruence among backbone gene trees. Mol Biol Evol. 30(1):154-66. [PMID:22936717]

ID   150 GenBank   AFS51558
Name   TraJ_pKS208 insolico UniProt ID   J9Z6S7
Length   124 a.a. PDB ID   _
Note   TraJ DNA transfer protein

  Auxiliary protein sequence


Download         Length: 124 a.a.        Molecular weight: 13255.23 Da        Isoelectric Point: 7.9911

>AFS51558.1 TraJ DNA transfer protein (plasmid) [uncultured bacterium]
MKKDQSEATRKSSPPIKVYCLPDEKAHIESGARNAGKSASAYLLALGMGYEVGSVIDAELVGGLAKVNAD
QGRLGGLLKLWLTNDERFAGFDEATMRATIKAVLSKIEATQDALLELATRGVKF

  Protein domains



No domain identified.



  Protein structure


Source ID Structure
AlphaFold DB J9Z6S7

  Reference


[1] Sen D et al. (2013) Inferring the evolutionary history of IncP-1 plasmids despite incongruence among backbone gene trees. Mol Biol Evol. 30(1):154-66. [PMID:22936717]

ID   151 GenBank   AFS51559
Name   TraK_pKS208 insolico UniProt ID   J9Z6K2
Length   150 a.a. PDB ID   _
Note   TraK oriT-binding protein

  Auxiliary protein sequence


Download         Length: 150 a.a.        Molecular weight: 16736.11 Da        Isoelectric Point: 10.7112

>AFS51559.1 TraK oriT-binding protein (plasmid) [uncultured bacterium]
MAKKAGMSLSERIAERAKRKQKQARGGANRAEFLAVKDEVAKALEHQWPVKEIWETLREEGAISFSYDAF
IGYVRRLITAPKADKPSPLPSRPSQLPQPAKEPEPVSSKSPILAAKENDQRPAPEPRPAPVTKGFQFNPK
PKNRRETDNG

  Protein domains


Predicted by InterproScan.

Family of unknown function (DUF5338) (DUF5338)

(8-77)


  Protein structure


Source ID Structure
AlphaFold DB J9Z6K2

  Reference


[1] Sen D et al. (2013) Inferring the evolutionary history of IncP-1 plasmids despite incongruence among backbone gene trees. Mol Biol Evol. 30(1):154-66. [PMID:22936717]


T4CP

ID   101 GenBank   AFS51556
Name   TraG_pKS208 insolico UniProt ID   J9Z8Q9
Length   638 a.a. PDB ID   _
Note   TraG coupling protein

  T4CP protein sequence


Download         Length: 638 a.a.        Molecular weight: 70240.55 Da        Isoelectric Point: 8.7813

>AFS51556.1 TraG coupling protein (plasmid) [uncultured bacterium]
MISKDKFNNAVGPQVRAKKPGVGKLIPALSLLSIGVGLAASTQYFAYDFKYQDVLGPHYNHIYAPWSILT
WANKWYGTYPDAFMRAGSIGVLATGVGLLGLVITKMIQANSSKANEYLHGSARWASKKDIQASGLLPRSR
TLLEVVTGKEAPSSTGVYVGAWVDDQGVQQYLRHSGPEHVLTYAPTRSGKGVGLVVPTLLSWGASTVVTD
LKGELWALTSGWRQKHARNKVLRFEPATTAGSVRWNPLDEIRIGTEYEVGDVQNLATLIVDPDGKGLDSH
WQKTSQALLVGLIMHVLYKSKNEGTPATLPEVDRILADPDRDLGELWMEMTTYSHSDGRNHPVVGSAARD
MMDRPEEEAGSVLSTAKSYLALYRDPVVARNVSASEFKVKDLMNHDNPVSLFIVTQPNDKARLRPLVRVL
INMIVRLLADKMDFDKGRPVAHYKHRLLMMLDEFPSLGKLEILQESLAFVAGYGIKCYLICQDINQLKSR
ETGYGPDETITSNCHVQNAYPPNRVETAEHLSKLTGQTTVVKEQITTSGRRTSAMLGQVSRTMQEVQRPL
LTPDECLRMPGPIKTASGDIAEAGDMVVYVAGYPAIYGKQPLYFKDPVFQARAAIPAPKVSDKLRVVQEQ
AEAEAITL

  Protein domains


Predicted by InterproScan.

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

(123-623)

  Protein structure


Source ID Structure
AlphaFold DB J9Z8Q9

  Reference


[1] Sen D et al. (2013) Inferring the evolutionary history of IncP-1 plasmids despite incongruence among backbone gene trees. Mol Biol Evol. 30(1):154-66. [PMID:22936717]


T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 2220..12821

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
Locus_0 1..1089 - 1089 AFS51515 TrfA replication initiation protein -
Locus_1 1134..1496 - 363 AFS51516 single strand DNA-binding protein -
Locus_2 1604..1975 + 372 AFS51517 TrbA transcriptional repressor -
Locus_3 2220..3197 + 978 AFS51518 TrbB mating pair formation protein virB11
Locus_4 3229..3636 + 408 AFS51519 TrbC mating pair formation protein virB2
Locus_5 3639..3950 + 312 AFS51520 TrbD mating pair formation protein virB3
Locus_6 3947..6505 + 2559 AFS51521 TrbE mating pair formation protein virb4
Locus_7 6502..7227 + 726 AFS51522 TrbF mating pair formation protein virB8
Locus_8 7239..8129 + 891 AFS51523 TrbG mating pair formation protein virB9
Locus_9 8133..8600 + 468 AFS51524 TrbH mating pair formation protein -
Locus_10 8605..10029 + 1425 AFS51575 TrbI mating pair formation protein virB10
Locus_11 10052..10831 + 780 AFS51525 TrbJ plasmid entry exclusion protein virB5
Locus_12 10831..11067 + 237 AFS51526 TrbK plasmid entry exclusion protein -
Locus_13 11082..12821 + 1740 AFS51527 TrbL mating pair formation protein virB6
Locus_14 12847..13149 + 303 AFS51528 TrbM mating pair formation protein -
Locus_15 13159..13788 + 630 AFS51529 TrbN mating pair formation protein -
Locus_16 13788..14258 + 471 AFS51530 TrbO mating pair formation protein -
Locus_17 14262..15017 + 756 AFS51531 TrbP mating pair formation protein -
Locus_18 15031..15264 + 234 AFS51532 TrbS mating pair formation protein -
Locus_19 15274..15936 + 663 AFS51533 hypothetical protein -
Locus_20 15945..16274 + 330 AFS51534 TrbU mating pair formation protein -
Locus_21 16291..16548 + 258 AFS51535 hypothetical protein -
Locus_22 16642..16887 + 246 AFS51536 hypothetical protein -
Locus_23 17030..17734 - 705 AFS51537 transposase -

Host bacterium

ID   101 GenBank   JQ432564
Plasmid name   pKS208 Incompatibility group   IncP1
Plasmid size   50604 bp Coordinate of oriT [Strand]   39342..39384 [+]
Host baterium   Uncultured bacterium

Cargo genes

Drug resistance gene   blaIMP-8
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -