Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   114017
Name   oriT_KHPS1|unnamed in_silico
Organism   Pseudomonas sp. KHPS1
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP100552 (48087..48194 [-], 108 nt)
oriT length   108 nt
IRs (inverted repeats)      70..75, 78..83  (ACCCGC..GCGGGT)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 108 nt

>oriT_KHPS1|unnamed
CCGGCGCCTCGCAGAGCAAGACACCCCCTTGAGCGCGTAGCGCGAATGTGGGGGAAGTGAAGAAGGCCGACCCGCTTGCGGGTGGGCCTACTTCACCTGTCTTGCCCG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   9006 GenBank   WP_254300308
Name   traI_NLY39_RS23760_KHPS1|unnamed insolico UniProt ID   _
Length   803 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 803 a.a.        Molecular weight: 87575.28 Da        Isoelectric Point: 10.7517

>WP_254300308.1 TraI/MobA(P) family conjugative relaxase [Pseudomonas sp. KHPS1]
MISKRIPMTSAKKSSFAGLVNYITNSQGISERVGEVRITNCQSEDLRWAVGEVLGTQQQNTRAEGDKTYH
LLISFAPGEKPSAEVLRDVEDRICAAMGYGEHQRVSAVHNDTDVLHIHVAINKIHPVRHTMHEPYRDFKT
RSDICAKLEIEHGLERVNHAGKKPYSESRANDMERHAGVESLLSWVRKECLEQMQGASSWKQLHQVLHEH
GLELREKGNGFVIQSQDGTMVKASTVARELSKAKLEGRLGAYEVRPSVGVQSLPAGAIPKKPGIGRVGRK
PPPLSRNRLRSLGSLQSLELDSGKRYEKRPIGNSDTTELYARYRDDQAAVRHTRTKELALERERRDRALD
YAKKESALKRASIKLMVTPGITKKLLYASAHQTLQKQLAKIRADHRKAVERINTTQKARQWADWLQAKAK
DGDQEALTALRAREGARGLRGDAIAGKNKPKATTVVRAAQEHITKEGTVIYRAGASAIRDDGSKLQLSRG
TDFDGIETALRMAVARYGEQITVTGSQQFKEQVAQTAALRGLPIKFDDPALEQRRQVLQQAIEKERSNVG
TDRGRAAGAGPGSDGIDTARRGRSGAGRNTTGATSGRPDGVRGYATGTGVPGRAGAGLGADGGRIAVRTT
GGTAKPGIARVGRKPPPESQNRLRTLSQLGVVQLTNGGESLLPSHVPGRVEQQGAATDNGLRWNVSRGGI
EGLPPSIDGIKAARQYIAEREDKRAKGFDIPKHRLYNAADEGMAAFAGVRSVEGQSMALLKRGDEVLVLP
INEATARRMKRMKLGEPVTTTAKGAIKSKGRSR

  Protein domains


Predicted by InterproScan.

Relaxase/Mobilisation nuclease domain (Relaxase)

(12-251)

Large polyvalent protein-associated domain 7 (LPD7)

(459-547)


  Protein structure



No available structure.




T4CP

ID   10438 GenBank   WP_254300388
Name   t4cp2_NLY39_RS23635_KHPS1|unnamed insolico UniProt ID   _
Length   852 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 852 a.a.        Molecular weight: 94657.92 Da        Isoelectric Point: 6.4722

>WP_254300388.1 VirB4 family type IV secretion/conjugal transfer ATPase [Pseudomonas sp. KHPS1]
MIEGIAYAIAALGIVLVLILVQRLMTVDAELKLKKRRAKDAGLADLLIHAAVVDDGVIVGKNGSLMASWL
YKGDDNASSTEEQRELVSHRINQAFVGLGNGWMIHVDAVRRAAPNYSERGVSRFPDPLTAAIDEERRRLF
EGLGTMFEGYFVLTLTYFPPMLAQQKFVELMFDDEATPPDHKARTRNLIDQFKRDCASIEGSLSSVLKMS
RLRGNKVTLEDGRTVTHDDMLRWLQFCITGVSHPVMLPSNPMYLDAVLGGKELWGGVVPKVGRNFIQAVA
IEGFPLESAPGVLSALAEQPCEYRWSSRYIFMDAHEATKHLEKFRKKWKQKVRGFFDQVFNTNSGAIDQD
AMSMVQDAADAIAEVNSGLVSQGYFTSVVILMDENRERLRESAIKLEKLLERLGFAARIESINTMEAYLG
SIPGHGVENVRRPLIHTMNLADLLPTSTIWTGSNAAPCPLYPPLSPALMHCVTNGATPFRLNLHVRDLGH
TFMFGPTGAGKSTHLAILAAQLRRYEGMSIFAFDKGMSMYPLAAGINAATRGTSGLHFTVAADDEQLAFC
PLQFLETKADRAWAMEWIDTILALNGLNTSTEQRNHIGEAILTMHKDKSRTLSEFSINVQDQAIRSALAQ
YTVDGSMGHLLDAEEDGLALSDFTVFEIEELMNLGDKYALPVLLYLFRRIERALKGQPAVIILDEAWLML
GHPVFREKIKEWLKVLRKANCLVLMATQSLSDAANSGILDVIVESTATKIFLPNVYARDEDTAALYRRMG
LNNRQIEILASAIPKRQYYYVSENGRRLYDLALGPLALAFVGSSDKESVAAIKTLQAKFGDRWVDEWLAA
RGLRINDYGVAA

  Protein domains


Predicted by InterproScan.

TraG P-loop domain (P-loop_TraG)

(623-779)

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

(221-431)

  Protein structure



No available structure.



ID   10439 GenBank   WP_254300310
Name   t4cp2_NLY39_RS23765_KHPS1|unnamed insolico UniProt ID   _
Length   638 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 638 a.a.        Molecular weight: 70246.51 Da        Isoelectric Point: 8.5951

>WP_254300310.1 type IV secretory system conjugative DNA transfer family protein [Pseudomonas sp. KHPS1]
MISKDKFNNAVGPQVRAKKPGVGKIIPALSLLSIGVGLAASTQYFAYDFKYQDVLGPHYNHIYAPWSILT
WANKWYGTYPDAFMRAGSIGVLATGVGLLGLVITKMIQANSAKANEYLHGSARWANKKDIQASGLLPRSR
TLLEVVTGKEAPSSTGVYVGAWVDDQGVQHYLRHSGPEHVLTYAPTRSGKGVGLVVPTLLSWGASTVVTD
LKGELWALTSGWRQKHARNKVLRFEPATTAGSVRWNPLDEIRIGTEYEVGDVQNLATLIVDPDGKGLDSH
WQKTSQALLVGLIMHVLYKSKNEGTPATLPEVDRILADPDRDLGELWMEMTTYSHSDGRNHPVVGSAARD
MMDRPEEEAGSVLSTAKSYLALYRDPVVARNVSASEFKVKDLMNHDNPVSLFIVTQPNDKARLRPLVRVL
INMIVRLLADKMDFDKGRPVAHYNHRLLMMLDEFPSLGKLEILQESLAFVAGYGIKCYLICQDINQLKSR
ETGYGPDETITSNCHVQNAYPPNRVETAEHLSKLTGQTTVVKEQITTSGRRTSAMLGQVSRTMQEVQRPL
LTPDECLRMPGPIKTASGDIAEAGDMVVYVAGYPAIYGKQPLYFKDPVFQARAAIPAPKVSDKLRVVQEQ
AEAEAITL

  Protein domains


Predicted by InterproScan.

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

(123-623)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 23744..34370

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
NLY39_RS23560 (NLY39_23560) 18951..19889 + 939 WP_254300365 LysR family transcriptional regulator -
NLY39_RS23565 (NLY39_23565) 19987..20652 + 666 WP_254300366 lipopolysaccharide assembly protein LapB -
NLY39_RS23570 (NLY39_23570) 21097..21246 + 150 Protein_27 AAA family ATPase -
NLY39_RS23575 (NLY39_23575) 21233..21475 + 243 WP_254300368 hypothetical protein -
NLY39_RS23580 (NLY39_23580) 21578..22303 - 726 WP_254300370 TraX family protein -
NLY39_RS23585 (NLY39_23585) 22307..22777 - 471 WP_254300372 hypothetical protein -
NLY39_RS23590 (NLY39_23590) 22777..23406 - 630 WP_254300374 muramidase -
NLY39_RS23595 (NLY39_23595) 23416..23718 - 303 WP_254300376 TrbM/KikA/MpfK family conjugal transfer protein -
NLY39_RS23600 (NLY39_23600) 23744..25489 - 1746 WP_254300379 P-type conjugative transfer protein TrbL virB6
NLY39_RS23605 (NLY39_23605) 25511..25747 - 237 WP_254300381 entry exclusion lipoprotein TrbK -
NLY39_RS23610 (NLY39_23610) 25762..26553 - 792 WP_254300382 P-type conjugative transfer protein TrbJ virB5
NLY39_RS23615 (NLY39_23615) 26576..27970 - 1395 WP_254300404 TrbI/VirB10 family protein virB10
NLY39_RS23620 (NLY39_23620) 27999..28466 - 468 WP_254300384 conjugal transfer protein TrbH -
NLY39_RS23625 (NLY39_23625) 28470..29360 - 891 WP_031943183 P-type conjugative transfer protein TrbG virB9
NLY39_RS23630 (NLY39_23630) 29372..30097 - 726 WP_254300386 conjugal transfer protein TrbF virB8
NLY39_RS23635 (NLY39_23635) 30094..32652 - 2559 WP_254300388 VirB4 family type IV secretion/conjugal transfer ATPase virb4
NLY39_RS23640 (NLY39_23640) 32649..32960 - 312 WP_254300390 conjugal transfer protein TrbD virB3
NLY39_RS23645 (NLY39_23645) 32963..33370 - 408 WP_031943179 conjugal transfer system pilin TrbC virB2
NLY39_RS23650 (NLY39_23650) 33402..34370 - 969 WP_254300392 P-type conjugative transfer ATPase TrbB virB11
NLY39_RS23655 (NLY39_23655) 34625..34996 - 372 WP_046935729 transcriptional regulator -
NLY39_RS23660 (NLY39_23660) 35106..35465 + 360 WP_254300395 single-stranded DNA-binding protein -
NLY39_RS23665 (NLY39_23665) 35510..36598 + 1089 WP_254300397 plasmid replication initiator TrfA -
NLY39_RS23670 (NLY39_23670) 36602..36814 + 213 WP_073624929 hypothetical protein -
NLY39_RS23675 (NLY39_23675) 38515..38937 + 423 WP_254300399 antirestriction protein -

Host bacterium

ID   14452 GenBank   NZ_CP100552
Plasmid name   KHPS1|unnamed Incompatibility group   -
Plasmid size   79836 bp Coordinate of oriT [Strand]   48087..48194 [-]
Host baterium   Pseudomonas sp. KHPS1

Cargo genes

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