Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   102278
Name   oriT_DSM 25444|unnamed3 in_silico
Organism   Klebsiella michiganensis strain DSM 25444
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_PRDB01000032 (84817..84864 [-], 48 nt)
oriT length   48 nt
IRs (inverted repeats)      5..12, 15..22  (GCAAAATT..AATTTTGC)
Location of nic site      31..32
Conserved sequence flanking the
  nic site    		  GGTGTGGTGA
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 48 nt

>oriT_DSM 25444|unnamed3
ATCTGCAAAATTTTAATTTTGCGTGGGGTGTGGTGATTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1750 GenBank   WP_064362890
Name   traI_CDA56_RS30485_DSM 25444|unnamed3 insolico UniProt ID   A0A443W956
Length   1753 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1753 a.a.        Molecular weight: 190128.87 Da        Isoelectric Point: 6.1737

>WP_064362890.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Klebsiella]
MMSIGSVKSAGSASNYYTDKDNYYVIGSMEERWQGKGAEALGLDGKAVDKAVFTELLKGKLPDGSDLTRM
QDGANKHRPGYDLTFSAPKSVSVMAMLGGDKRLIDAHNQAVTVAVKQLETLAATRVMTDGKSETVLTGNL
IVAKFNHDTNRNQEPQLHTHAVVINATQNGDKWQSLGTDTVGKTGFIENVYANQTAFGKLYREALKPLVE
KLGYETKVVGKHGMWEMKDVPVEAFSTRSQELREAAGPDASLKSRDVAALDTRKSKEAIDPAEKMVEWMN
TLKETGFDIRGYREAADAHAAELARAPVAPEKTDGPDITDVVTRAIAGLSDRKVQFTYADVLARTVGQLE
AKPGVFELARTGIDAAIEREQLIPLDREKGLFTSNIHVLDELSVKALSQEIQRQNHVSVTPDAGVVREKP
FSDAVSVLAQDRPAMGIVAGQGGAAGQRERVAELTLMAREQGRDVHILAADNRSREFLAGDARLAGETVT
GKSALQDGTAFIPGGTLIVDQAEKLSLKETISLLDGAMRHNVQVLLSDSGKRSGTGSALTVLKDSGVNTY
RWQGGKQATADIISEPDKSARYSRLAQEFAASVREGQESVAQISGTREQNVLNNVIRDTLKNEGALGNRD
MAVTALTPVWLDSKSRGVRDFYREGMVMERWDPEARKHDRFVIDRVTASSNMLTLKDREGERLDLKVSAV
DSQWTLFRTDKLPVAEGERLAVLGKIPDTRLKGGESVTVLKAEAGQLTVQRPGQKTTQTLPVGSSPFDGI
KVGHGWVESPGRSVSETATVFASVTQRELDNATLNQLAQSGNHIRLYSAQDAARTTEKLARHTAFSVVSE
QLKARSGEADLEAAIAQQKAGLHTPAEQAVHLSIPLLESNSLTFTRPQLLAAALETGDGKVPMKDIEATI
QAQIKAGSLLNVPVASGHGNDLLISRQTWDAEKSVLTRVLEGKDAVAPLMGRVPGSLMTDLTAGQRAATR
MILETPDRFTVVQGYAGVGKTTQFKAVMSAISLLPEETRPRVIGLGPTHRAVGEMQSAGVDAQTTASFLH
DTQLQQRNGQTPDFSNTLFLLDESSMVGLADTAKALSLIAAGGGRAVLSGDTDQLQSIAPGQPFRLMQQR
SAADVAIMKEIVRQVPELRPAVYSLIDRDISRALSTIEQVTPEQVPRKDGAWVPENSVTEFTPAQEKAIQ
DALKEGKEIPPGTPVSLHDAIVKDYTGRTPAAQASTLIITHLNADRRALNGLIHDARVQNGEVSKEEVTL
PVLVTSNIRDGELRKLSTWSEHQGAVALLDNTYQRIESVDKENQLITLKDNEGNIRLLSPREASAEGVTL
YRPEHITVSQGDRMRFSKSDPERGYVANSVWEVKTVSGDSVTLSDGKTTRTLNPKADEAQRHIDLAYAIT
AHGAQGASEPFAIALEGVEGRRKALVSFESAYVALSRMKQHAQVYTDNREGWTTAVSRSQEKASAHDVLE
PQNARAVKNAGQLYGRAQPLDETAAGRAALQQSGLARGRSPGKFISPGKKYPQPHVALPAFDKNGKEAGI
WLSPLTDRDGRLEAIGGEGRIMGDETARFVALQSSRNGESLLAGNMGEGVRIARDNPDSGVVVRLAGDDR
PWNPEAITGGRIWADPLPNPPLPDTGTDIPLPPEVLAQRAAEEAQRREMEKQAEQATREVAGEEKKAGEP
GERIKEVIGDVIRGLERDRPGEEKTRLPDDPQTRRQEAAIQQVASESLQRERLQQMERDMVRDLNREKTL
GGD

  Protein domains


Predicted by InterproScan.

TrwC relaxase (TrwC)

(10-284)

single-stranded DNA binding TraI N-terminal subdomain (ssDNA_TraI_N)

(577-629)

DNA helicase TraI (TraI_C)

(1433-1555)

DNA relaxase TraI 2B/2B-like domain (TraI_2B)

(635-714)

AAA domain (AAA_30)

(971-1157)


  Protein structure



No available structure.




T4CP

ID   1339 GenBank   WP_064174013
Name   traD_CDA56_RS30480_DSM 25444|unnamed3 insolico UniProt ID   _
Length   766 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 766 a.a.        Molecular weight: 85728.45 Da        Isoelectric Point: 4.8494

>WP_064174013.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Klebsiella]
MSFNAKDMTQGGQIANMRFRMFGQIANIIFYVLFILFWVLCGLMLMYRLSWQTFVNGCVYWWCTTLGPMR
DIIRSQPVYTIQYYGQSLEYTSEQILADKYTIWCGEQLWTSFVFAAVVSLVICIVTFFVASWVLGRQGKQ
QSEDENTGGRQLSDKPKEVARQMKRDGMASDIKIGDLPILLNSEIQNFCLHGTVGSGKSEVIRRLLNYVR
ARGDMAIIYDRSCEFVKSYYDPSLDKILNPLDSRCAAWDLWKECLTLPDFDNVSNTLIPMGTKEDPFWQG
SGRTIFAEGAYLMREDKDRSYEKLVDTMLSIKIDKLRAYLQNTPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEKNGEPFTIRDWMRGVREDRPNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGVKPAATLFDVMNTRAFFRSPSREIA
EFAAGEIGEKEILKASEQYSYGADPVRDGVSTGKEKERETLVSYSDIQTLPDLSCYVTLPGPYPAVKLAL
KYKPRPKIAEGFIQRTLDTRVDARLSALLEAREAEGSLARALFTPDAPEPEQSDADSRTSPGQPEPESAP
VSPAPVKSASTAETLAAQPSVKASEAPQAKVTTVPLTRPVPAATTTAAASATGSSAAATATTGGTEQELA
QQPAEQGQEMMPAGMNEDGEIEDMQAYDAWLADEQTQREMQRREEVNINHSHRRDEQDDIEIGGNF

  Protein domains


Predicted by InterproScan.

F sex factor protein N terminal (TraD_N)

(32-128)

Type IV secretion-system coupling protein DNA-binding domain (TrwB_AAD_bind)

(172-560)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 84259..110829

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
CDA56_RS30255 (CDA56_30250) 79287..79637 + 351 WP_004152758 hypothetical protein -
CDA56_RS30270 (CDA56_30265) 80266..80622 + 357 WP_019706019 hypothetical protein -
CDA56_RS30275 (CDA56_30270) 80683..80895 + 213 WP_019706020 hypothetical protein -
CDA56_RS30280 (CDA56_30275) 80906..81130 + 225 WP_014343499 hypothetical protein -
CDA56_RS30285 (CDA56_30280) 81211..81531 + 321 WP_004152720 type II toxin-antitoxin system RelE/ParE family toxin -
CDA56_RS30290 (CDA56_30285) 81521..81799 + 279 WP_032411288 helix-turn-helix transcriptional regulator -
CDA56_RS30295 (CDA56_30290) 81800..82213 + 414 WP_032411285 helix-turn-helix domain-containing protein -
CDA56_RS30310 (CDA56_30305) 83043..83864 + 822 WP_004182076 DUF932 domain-containing protein -
CDA56_RS30315 (CDA56_30310) 83897..84226 + 330 WP_032420969 DUF5983 family protein -
CDA56_RS30320 (CDA56_30315) 84259..84744 - 486 WP_001568108 transglycosylase SLT domain-containing protein virB1
CDA56_RS30325 (CDA56_30320) 85165..85560 + 396 WP_022644714 conjugal transfer relaxosome DNA-binding protein TraM -
CDA56_RS30330 (CDA56_30325) 85732..86418 + 687 WP_022644713 transcriptional regulator TraJ family protein -
CDA56_RS30335 (CDA56_30330) 86497..86877 + 381 WP_032409797 TraY domain-containing protein -
CDA56_RS30340 (CDA56_30335) 86936..87301 + 366 WP_020314752 type IV conjugative transfer system pilin TraA -
CDA56_RS30345 (CDA56_30340) 87315..87620 + 306 WP_020323523 type IV conjugative transfer system protein TraL traL
CDA56_RS30350 (CDA56_30345) 87640..88206 + 567 WP_064373744 type IV conjugative transfer system protein TraE traE
CDA56_RS30355 (CDA56_30350) 88193..88933 + 741 WP_064362918 type-F conjugative transfer system secretin TraK traK
CDA56_RS30360 (CDA56_30355) 88933..90348 + 1416 WP_064362917 F-type conjugal transfer pilus assembly protein TraB traB
CDA56_RS30815 90341..90943 + 603 WP_115723427 conjugal transfer protein TraP -
CDA56_RS31625 (CDA56_30365) 91011..91148 + 138 Protein_111 conjugal transfer protein TraP -
CDA56_RS30375 (CDA56_30370) 91171..91734 + 564 WP_064362913 type IV conjugative transfer system lipoprotein TraV traV
CDA56_RS30380 (CDA56_30375) 91881..92084 + 204 WP_064362911 hypothetical protein -
CDA56_RS31115 92325..92462 + 138 WP_164879260 hypothetical protein -
CDA56_RS31120 92497..92739 + 243 WP_074181267 hypothetical protein -
CDA56_RS30390 (CDA56_30385) 92768..93067 + 300 WP_020315144 hypothetical protein -
CDA56_RS30395 (CDA56_30390) 93084..93308 + 225 WP_022644711 hypothetical protein -
CDA56_RS30400 (CDA56_30395) 93305..93709 + 405 WP_064362909 hypothetical protein -
CDA56_RS30405 (CDA56_30400) 93842..96481 + 2640 WP_064362907 type IV secretion system protein TraC virb4
CDA56_RS30410 (CDA56_30405) 96514..96915 + 402 WP_064362936 type-F conjugative transfer system protein TrbI -
CDA56_RS30415 (CDA56_30410) 96912..97538 + 627 WP_064362905 type-F conjugative transfer system protein TraW traW
CDA56_RS30420 (CDA56_30415) 97558..98541 + 984 WP_155553410 conjugal transfer pilus assembly protein TraU traU
CDA56_RS30425 (CDA56_30420) 98554..99171 + 618 WP_064362903 type-F conjugative transfer system pilin assembly protein TrbC trbC
CDA56_RS30430 (CDA56_30425) 99168..101048 + 1881 WP_064362901 type-F conjugative transfer system mating-pair stabilization protein TraN traN
CDA56_RS30435 (CDA56_30430) 101086..101367 + 282 WP_064174416 hypothetical protein -
CDA56_RS30440 (CDA56_30435) 101357..101584 + 228 WP_064174417 conjugal transfer protein TrbE -
CDA56_RS30445 (CDA56_30440) 101595..101921 + 327 WP_064362899 hypothetical protein -
CDA56_RS30450 (CDA56_30445) 101940..102692 + 753 WP_040118488 type-F conjugative transfer system pilin assembly protein TraF traF
CDA56_RS30455 (CDA56_30450) 102703..102942 + 240 WP_047722563 type-F conjugative transfer system pilin chaperone TraQ -
CDA56_RS30460 (CDA56_30455) 102914..103492 + 579 WP_064362897 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
CDA56_RS30465 (CDA56_30460) 103479..104849 + 1371 WP_064362895 conjugal transfer pilus assembly protein TraH traH
CDA56_RS30470 (CDA56_30465) 104849..107719 + 2871 WP_064362893 conjugal transfer mating-pair stabilization protein TraG traG
CDA56_RS30475 (CDA56_30470) 107853..108293 + 441 WP_224313869 conjugal transfer protein TraS -
CDA56_RS30480 (CDA56_30475) 108529..110829 + 2301 WP_064174013 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   2722 GenBank   NZ_PRDB01000032
Plasmid name   DSM 25444|unnamed3 Incompatibility group   IncFII
Plasmid size   136210 bp Coordinate of oriT [Strand]   84817..84864 [-]
Host baterium   Klebsiella michiganensis strain DSM 25444

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   ncrY, ncrC, ncrB, ncrA, chrA
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   AcrIE9