Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   114673
Name   oriT_pDCA-1 in_silico
Organism   Achromobacter sp. strain ANB-1
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_MW679657 (45379..45475 [-], 97 nt)
oriT length   97 nt
IRs (inverted repeats)      24..31, 34..41  (TAACCGGC..GCCGGTTA)
Location of nic site      60..61
Conserved sequence flanking the
  nic site    		  TCCTGCCCGC
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 97 nt

>oriT_pDCA-1
GAATAAGGGACAGCGAAGATAGATAACCGGCCCGCCGGTTAGCTAACTTCGCACATCCTGCCCGCCTTACGGCGTTGATAACACCAAGGAAAGTCTA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   9412 GenBank   WP_012478238
Name   traI_KC533_RS00280_pDCA-1 insolico UniProt ID   A0A1H7CDK8
Length   752 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 752 a.a.        Molecular weight: 82867.55 Da        Isoelectric Point: 10.6815

>WP_012478238.1 MULTISPECIES: TraI/MobA(P) family conjugative relaxase [Pseudomonadota]
MIAKHVPMRSLGKSDFAGLVNYVTDAQSKDHRLGQVQITNCDAVSVQDAITEVLATQHTNTRAKGDKTYH
LIVSFRAGEQPSADTLRAIEERICAGLGYGEHQRVSAVHNDTDNLHIHIAINKIHPTRNTMHEPYYSHRA
LAELCTALERDYGLERDNHEPRQRGAEGRAADMEQHAGVESLVGWIKRECLDEIKGAQSWQELHQVMRDN
GLELRERANGLVIEAGDGTMVKASTLARDLSKPKLEARLGPFEASPERQTRTKAKRQYQKDPIRLRVNTV
ELYARYKAEQQTLTATRGQALEQARRRKDRLVEAAKRSGRLRRATIKVIGESGPNKKLLYAQASKALRDE
IQAINKQYQQDRQALYDSHSRRTWADWLKKEATHGNAEALTALRAREAAQGLKGNTIQGRGDPRPGHAPV
TDNITKKGTIIFRAGLTAVRDDGDKLQVSREATREGLQEALRLAMERYGSRITVNGTTQFQAQIIRAAVD
SQLPITFADPALESRRLALLKKENTHERPDRTERADQRPAEHRGRAGRGPGGPGQRAATHDDAARPIAVA
RAGFGRPGGGRAGTAGVHAGAVHRKPDIGRIGRVPPPQSQHRLRTLSQLGVVRIAGGSEVLLPRDVPRHL
EQQGTQPDHQLRRDISRPGSGVAAAPPGLAAADKYIAERESKRSKGFDIPKHARYTAGEGGLAFEGVRNI
EGQALALLKRGDEVMVMPIDQATARRMSRIAVGDAVTITPKGSIKTSKGRSR

  Protein domains


Predicted by InterproScan.

Relaxase/Mobilisation nuclease domain (Relaxase)

(12-251)

Large polyvalent protein-associated domain 7 (LPD7)

(420-507)


  Protein structure


Source ID Structure
AlphaFold DB A0A1H7CDK8


Auxiliary protein

ID   5519 GenBank   WP_011255188
Name   WP_011255188_pDCA-1 insolico UniProt ID   A0A1H7CD62
Length   123 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 123 a.a.        Molecular weight: 13964.97 Da        Isoelectric Point: 8.4531

>WP_011255188.1 MULTISPECIES: conjugal transfer transcriptional regulator TraJ [Pseudomonadota]
MEADEQPTAKRRQHLRVPVFPDEKEQIEANAKRAGVSVARYLRDVGQGYQIRGVMDYEYVRELVRVNGDL
GRLGGLLKLWLTDDPRTARFGDATILALLGRIEATQDEMSRLMKSVVQPRAEP

  Protein domains



No domain identified.



  Protein structure


Source ID Structure
AlphaFold DB A0A1H7CD62


T4CP

ID   10934 GenBank   WP_011013264
Name   t4cp2_KC533_RS00145_pDCA-1 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: 94125.12 Da        Isoelectric Point: 6.3997

>WP_011013264.1 MULTISPECIES: VirB4 family type IV secretion/conjugal transfer ATPase [Pseudomonadota]
MIEAIAIGIAVLGAVLLLILFARIRQVDAELKLKKHRSKDAGLADLLNYAAVVDDGVIVGKNGSFMAAWL
YQGDDNASSTEEQREMVSFRINQALAGLGSGWMVHVDAVRRPAPNYSERGVSTFTDPVSAAIDEERRRLF
EGLGTMYEGHFVFAVTWFPPVLAQRKFVELMFDDDAVTPDHTARTVGLIEQFKREIRSLESRMSSAVKLT
RLKGHKIATEEGREVTHDDFLSWLQFCVTGNYHPVQLPSNPMYLDAVIGGQELWGGVVPKIGRKFIQVVS
LEGFPLESTPGLLSALAELPSEYRWSSRFIFMDQHESLKHLDKFRKKWKQKIRGFFDQVFNTNTGSVNQD
AATMVADAEAAIAEVNSGLVAAGYFTSVVVLMDEDRERLAAAALSVEKAINRLAFAARIETINTMDAYLG
SLPGHGVENVRRPLINTMNLADLLPTSSIWTGSATAPCPMYPPLAPALMHCVTVGATPFRLNLHVRDLGH
TFMFGPTGAGKSTHLGIIAAQLRRYAGMSIYAFDKGMSMYPLAAAINAGSKGKTGLHFTVAADDDRLAFC
PLQFLETKADRAWAMEWIDTILALNGVDTTPGQRNEIGHAIMSMHASGARTLSEFSVTIQDEAIREAIKQ
YTVDGSMGHLLDAEEDGLSLSDFTVFEIEELMNLGEKFALPVLLYLFRRIERGLKGQPAVIILDEAWLML
GHPAFRAKIREWLKVLRKANCLVLMATQSLSDAANSGILDVIVESTATKIFLPNVYARDEDTAALYRRMG
LNKRQIEILATAVPKRQYYYVSENGRRLYDLALGPLALAFVGASDKESVAAIKSLQAKFGHEWVDHWLAG
RNLNLNDYLEAA

  Protein domains


Predicted by InterproScan.

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

(220-431)

TraG P-loop domain (P-loop_TraG)

(626-754)

  Protein structure



No available structure.



ID   10935 GenBank   WP_012478237
Name   t4cp2_KC533_RS00285_pDCA-1 insolico UniProt ID   _
Length   634 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 634 a.a.        Molecular weight: 69616.60 Da        Isoelectric Point: 8.4953

>WP_012478237.1 MULTISPECIES: type IV secretory system conjugative DNA transfer family protein [Pseudomonadota]
MKIKMNNAVGPQVRSAKPKPSKLLPILGGVSLVGGLQAATQFFAYTFQYHASLGANLGHVYAPWSILNWS
AKWYSQYPDEIMRAGSIGMVTATVGLLGVAVAKVVTSNSSKANEYLHGSARWAEKKDIQAAGLLPRERNV
LEIVTGKDAPTATGVYVGGWQDKDGNFYYLRHSGPEHVLTYAPTRSGKGVGLVVPTLLSWGASSVITDLK
GELWALTAGWRQKHAKNKVLRFEPASSSGGVCWNPLDEIRVGTEAEVGDVQNLATLIVDPDGKGLDSHWQ
KTAFALLVGVILHALYKARNDGGTATLPSVDAMLADPNRDIGELWMEMTTYGHVDGQNHHAIGSAARDMM
DRPEEEAGSVLSTAKSYLALYRDPVVARSVSRSDFRIKDLMHSDDPVSLYIVTQPNDKARLRPLVRVMVN
MIVRLLADKMDFENGRPVAHYKHRLLMMLDEFPSLGKLEIMQESLAFVAGYGIKCYLICQDINQLRSRET
GYGHDESITSNCHVQNAYPPNRVETAEHLSRLTGQTTVVKEQITTSGRRTAAMLGQVSRTYQEVQRPLLT
PDECLRMPGPKKNDKGEIEEAGDMVIYVAGYPAIYGKQPLYFKDPVFQARASIPAPKATDRLRQVVEAGE
GITI

  Protein domains


Predicted by InterproScan.

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

(121-618)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 20207..30830

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
KC533_RS00080 17001..17417 - 417 WP_012478195 hypothetical protein -
KC533_RS00085 17520..17963 - 444 WP_011255142 OmpA family protein -
KC533_RS00090 17979..18677 - 699 WP_012478194 TraX family protein -
KC533_RS00095 18674..18943 - 270 WP_011255140 hypothetical protein -
KC533_RS00100 18973..19608 - 636 WP_011255139 transglycosylase SLT domain-containing protein -
KC533_RS00105 19610..20188 - 579 WP_011255138 TrbM/KikA/MpfK family conjugal transfer protein -
KC533_RS00110 20207..21925 - 1719 WP_012478193 P-type conjugative transfer protein TrbL virB6
KC533_RS00115 21937..22158 - 222 WP_011255136 entry exclusion lipoprotein TrbK -
KC533_RS00120 22168..22941 - 774 WP_011255135 P-type conjugative transfer protein TrbJ virB5
KC533_RS00125 22958..24337 - 1380 WP_012478192 TrbI/VirB10 family protein virB10
KC533_RS00130 24341..24802 - 462 WP_011013267 lipoprotein -
KC533_RS00135 24805..25698 - 894 WP_014386236 P-type conjugative transfer protein TrbG virB9
KC533_RS00140 25716..26504 - 789 WP_011013265 conjugal transfer protein TrbF virB8
KC533_RS00145 26501..29059 - 2559 WP_011013264 VirB4 family type IV secretion/conjugal transfer ATPase virb4
KC533_RS00150 29056..29367 - 312 WP_011013263 conjugal transfer protein TrbD virB3
KC533_RS00155 29371..29835 - 465 WP_011013262 conjugal transfer system pilin TrbC virB2
KC533_RS00160 29865..30830 - 966 WP_011013261 P-type conjugative transfer ATPase TrbB virB11
KC533_RS00165 31145..31504 - 360 WP_011013260 transcriptional regulator -
KC533_RS00170 31614..31952 + 339 WP_011013259 single-stranded DNA-binding protein -
KC533_RS00175 32001..33224 + 1224 WP_011013257 plasmid replication initiator TrfA -
KC533_RS00180 34610..34891 - 282 WP_011114071 type II toxin-antitoxin system YafQ family toxin -
KC533_RS00185 34878..35141 - 264 WP_011114070 type II toxin-antitoxin system RelB/DinJ family antitoxin -
KC533_RS00190 35314..35742 + 429 WP_011114069 antirestriction protein -

Host bacterium

ID   15108 GenBank   NZ_MW679657
Plasmid name   pDCA-1 Incompatibility group   -
Plasmid size   87305 bp Coordinate of oriT [Strand]   45379..45475 [-]
Host baterium   Achromobacter sp. strain ANB-1

Cargo genes

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