Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   103061
Name   oriT_AC2901 in_silico
Organism   Citrobacter freundii strain AC2901
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_KU987452 (43234..43319 [-], 86 nt)
oriT length   86 nt
IRs (inverted repeats)      61..68, 73..80  (TTGGTGGT..ACCACCAA)
 27..34, 37..44  (GCAAAAAC..GTTTTTGC)
 8..14, 20..26  (TGATTTA..TAAATCA)
Location of nic site      53..54
Conserved sequence flanking the
  nic site    		  TGTGTGGTGC
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 86 nt

>oriT_AC2901
AATTACATGATTTAAAACGTAAATCAGCAAAAACTTGTTTTTGCGTAGTGTGTGGTGCTTTTGGTGGTGAGAACCACCAACCTGTT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2291 GenBank   WP_000948354
Name   traI_HTI52_RS00005_AC2901 insolico UniProt ID   A0AA36L3I8
Length   1756 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1756 a.a.        Molecular weight: 191683.22 Da        Isoelectric Point: 5.6912

>WP_000948354.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacteriaceae]
MLSFSVVKSAGSAGNYYTDKDNYYVLGSMGERWAGQGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQ
DGSNKHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQDPQLHTHVVVANVTQHNGEWKTLSSDKVGKTGFSENVLANRIAFGKIYQSELRQRVEA
LGYETEVVGKHGMWEMPGVPVEAFSSRSQAIREAVGEDASLKSRDVAALDTRKSKQHVDPEVRMAEWMQT
LKETGFDIRAYRDAADQRAEIRTQAPGPASQDGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE
NGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS
DAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMAREQGREVQIIAADRRSQMNLKQDERLSGELITGR
RQLQEGMVFTPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKDAGVNTYRW
QGGEQRPATIISEPDRNVRYDRLAGDFAASVKAGEESVAQVSGVREQAILTQAIRSELKTQGVLGHPEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDAQGETQVVRISSLDS
SWSLFRPEKMPVADGERLRVTGKIPGLRVSGGDRLQVASVSEDAMTVVVPGRAEPATLPVADSPFTALKL
ENGWVETPGHSVSDSATVFASVTQMAMDNATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI
KARAGETSLETAISLQKTGLHTPAQQAIHLALPVLESKNLAFSMVDLLTEAKSFAAEGTGFTELGGEINA
QIKRGDLLYVDVAKGYGTGLLVSRASYEAEKSILRHILEGKEAVTPLMERVPGELMETLTSGQRAATRMI
LETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPASERPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT
QLQQRSGETPDFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA
ADVVIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRQEGAWAPEHSVTEFSHSQEAKLAEA
QQKAMLKGETFPDVPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDAREKAGELGKEQVM
VPVLNTANIRDGELRRLSTWENNPDALALVDSVYHRIAGISKDDGLITLEDAEGNTRLISPREAVAEGVT
LYTPDKIRVGTGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGQQTRVIRPGQERAEQHIDLAYAI
TAHGAQGASETFAIALEGTEGNRKLMAGFESAYVALSRMKQHVQVYTDNRQGWTDAINNAVQKGTAHDVL
EPKPDREVMNAQRLFSTARELRDVAAGRAVLRQAGLAGGDSPARFIAPGRKYPQPYVALPAFDRNGKSAG
IWLNPLTTDDGNGLRGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGVVVRIAGE
GRPWNPGAITGGRVWGDIPDSSVQPGAGNGEPVTAEVLAQRQAEEAIRRETERRADEIVRKMAENKPDLP
DGKTEQAVREIAGQERDRADITEREAALPESVLRESQREQEAVREVARENLLQERLQQIERDMVRDLQKE
KTLGGD

  Protein domains


Predicted by InterproScan.

DNA helicase TraI (TraI_C)

(1434-1557)

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

(633-712)

TrwC relaxase (TrwC)

(10-283)

AAA domain (AAA_30)

(968-1156)

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

(575-626)


  Protein structure



No available structure.




Auxiliary protein

ID   950 GenBank   WP_001354030
Name   WP_001354030_AC2901 insolico UniProt ID   A0A734M5H3
Length   127 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 127 a.a.        Molecular weight: 14508.47 Da        Isoelectric Point: 4.7116

>WP_001354030.1 MULTISPECIES: conjugal transfer relaxosome DNA-binding protein TraM [Gammaproteobacteria]
MARVILYISNDVYDKVNAIVEQRRQEGARDKDISVSGTASMLLELGLRVYEAQMERKESAFNQTEFNKLL
LECVVKTQSSVAKILGIESLSPHVSGNPKFEYANMVEDIREKVSSEMERFFPKNDEE

  Protein domains


Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-126)


  Protein structure


Source ID Structure
AlphaFold DB A0A734M5H3

ID   951 GenBank   WP_000089263
Name   WP_000089263_AC2901 insolico UniProt ID   A0A3U3XJL9
Length   75 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 75 a.a.        Molecular weight: 8541.74 Da        Isoelectric Point: 8.6796

>WP_000089263.1 MULTISPECIES: conjugal transfer relaxosome protein TraY [Gammaproteobacteria]
MSRNIIRPAPGNKVLLVLDDATNHKLLGARERSGRTKTNEVLVRLRDHLNRFPDFYNLDAIKEGAEETDS
IIKDL

  Protein domains


Predicted by InterproScan.

TraY domain (TraY)

(14-60)


  Protein structure


Source ID Structure
AlphaFold DB A0A3U3XJL9


T4CP

ID   1998 GenBank   WP_012917677
Name   traC_HTI52_RS00375_AC2901 insolico UniProt ID   _
Length   876 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 876 a.a.        Molecular weight: 99204.83 Da        Isoelectric Point: 6.0793

>WP_012917677.1 MULTISPECIES: type IV secretion system protein TraC [Enterobacteriaceae]
MSNNPLEAVTQAVNSLVTALKLPDESAKANEVLGEMSFPQFSRLLPYRDYNQESGLFMNDTTMGFMLEAI
PINGANKSIVEALDHMLRTKLPRGIPLCIHLMSSQLVGDRIEYGLREFSWSGEQAERFNAITRAYYMKAA
ATQFPLPEGMNLPLTLRHYRVFISYCSPSKKKSRADILEMENLVKIIRASLQGASIATQTVDAQAFIDIV
GEMINHNPDSLYPKRRQLDPYSDLNYQCVEDSFDLNVRADYLTLGLRENGRNSTARILNFHLARNPEIAF
LWNMADNYSNLLNPELSISCPFILTLTLVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWG
ELRQRLGSGQSSVVSYFLNITAFCKDNNETALEVEQDILNSFRKNGFELISPRFNHMRNFLTCLPFMAGK
GLFKQLKEAGVVQRAESFNVANLMPLVADNPLTPAGLLAPTYRNQLAFIDIFFRGMNNTNYNMAVCGTSG
AGKTGLIQPLIRSVLDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLRFNPFANITDIDQSAERVRDQLS
VMASPNGNLDEVHEGLLLQAVRASWLAKENRARIDDVVDFLKNASDSEQYAGSPTIRSRLDEMIVLLDQY
TANGTYGQYFNSDEPSLRDDAKMVVLELGGLEDRPSLLVAVMFSLIIYIENRMYRTPRNLKKLNVIDEGW
RLLDFKNHKVGEFIEKGYRTARRHTGAYITITQNIVDFDSDKASSAARAAWGNSSYKIILRQSAKEFAKY
NQLYPDQFQPLQRDMIGKFGAAKDQWFSSFLLQVENHSSWHRLFVDPLSRAMYSSDGPDFEFVQQKRKEG
LSIHEAVWQLAWKKSGPEMASLEAWLEEHEKYRSVA

  Protein domains


Predicted by InterproScan.

TraG P-loop domain (P-loop_TraG)

(469-764)

Family of unknown function (DUF5934) (DUF5934)

(290-447)

TraC protein (TraC_F_IV)

(39-277)

  Protein structure



No available structure.



ID   1999 GenBank   WP_125097878
Name   traD_HTI52_RS00470_AC2901 insolico UniProt ID   _
Length   762 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 762 a.a.        Molecular weight: 86727.59 Da        Isoelectric Point: 5.1644

>WP_125097878.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILIGLVLWVKISWQTFINGCIYWWCTSLEGMR
DLIKSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLASVVALVICLITFFVVSWILGRQGKQ
QSENEVTGGRQLTDNPKDVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
QRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGDPFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVMNTRAFFRSPSHKIA
EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQARPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFEPEVASGEDVTQAEQPQQPQQPQQPQQ
PQQPQQPQQPQQPQQPQQPQQPQQPQQPQQPQQPQQPQQPVSSVINDKKSDAGVSVPAGGIEQELKMKPE
EEMEQQLPPGISESGEVVDMAAYEAWQQENHPDIQQHMQRREEVNINVHRERGEDVEPGDDF

  Protein domains


Predicted by InterproScan.

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

(173-560)

F sex factor protein N terminal (TraD_N)

(32-128)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 42666..71239

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HTI52_RS00270 38296..39965 - 1670 Protein_52 group II intron reverse transcriptase/maturase -
HTI52_RS00495 40539..40751 - 213 Protein_53 hypothetical protein -
HTI52_RS00500 40707..40844 - 138 Protein_54 hypothetical protein -
HTI52_RS00280 41144..41440 + 297 WP_001272251 hypothetical protein -
HTI52_RS00285 41550..42371 + 822 WP_001234437 DUF932 domain-containing protein -
HTI52_RS00290 42666..43268 - 603 WP_000243715 transglycosylase SLT domain-containing protein virB1
HTI52_RS00295 43591..43974 + 384 WP_001354030 conjugal transfer relaxosome DNA-binding protein TraM -
HTI52_RS00300 44168..44839 + 672 WP_000283561 conjugal transfer transcriptional regulator TraJ -
HTI52_RS00305 44976..45203 + 228 WP_000089263 conjugal transfer relaxosome protein TraY -
HTI52_RS00310 45236..45595 + 360 WP_001098992 type IV conjugative transfer system pilin TraA -
HTI52_RS00315 45610..45921 + 312 WP_000012113 type IV conjugative transfer system protein TraL traL
HTI52_RS00320 45943..46509 + 567 WP_000399780 type IV conjugative transfer system protein TraE traE
HTI52_RS00325 46496..47224 + 729 WP_001230772 type-F conjugative transfer system secretin TraK traK
HTI52_RS00330 47224..48675 + 1452 WP_000146675 F-type conjugal transfer pilus assembly protein TraB traB
HTI52_RS00335 48665..49231 + 567 WP_000896599 conjugal transfer pilus-stabilizing protein TraP -
HTI52_RS00340 49218..49538 + 321 WP_001057307 conjugal transfer protein TrbD -
HTI52_RS00345 49535..50050 + 516 WP_000809881 type IV conjugative transfer system lipoprotein TraV traV
HTI52_RS00350 50185..50406 + 222 WP_001278683 conjugal transfer protein TraR -
HTI52_RS00355 50399..50812 + 414 WP_000549589 hypothetical protein -
HTI52_RS00360 50805..51278 + 474 WP_000549568 hypothetical protein -
HTI52_RS00365 51358..51576 + 219 WP_000556745 hypothetical protein -
HTI52_RS00370 51604..51951 + 348 WP_000836682 hypothetical protein -
HTI52_RS00375 52077..54707 + 2631 WP_012917677 type IV secretion system protein TraC virb4
HTI52_RS00380 54704..55090 + 387 WP_000214084 type-F conjugative transfer system protein TrbI -
HTI52_RS00385 55087..55719 + 633 WP_001203728 type-F conjugative transfer system protein TraW traW
HTI52_RS00390 55716..56708 + 993 WP_000830838 conjugal transfer pilus assembly protein TraU traU
HTI52_RS00395 56738..57043 + 306 WP_000224416 hypothetical protein -
HTI52_RS00400 57052..57690 + 639 WP_001080256 type-F conjugative transfer system pilin assembly protein TrbC trbC
HTI52_RS00405 57687..59537 + 1851 WP_000821856 type-F conjugative transfer system mating-pair stabilization protein TraN traN
HTI52_RS00410 59564..59821 + 258 WP_000864353 conjugal transfer protein TrbE -
HTI52_RS00415 59814..60557 + 744 WP_001030371 type-F conjugative transfer system pilin assembly protein TraF traF
HTI52_RS00420 60571..60915 + 345 WP_000556796 conjugal transfer protein TrbA -
HTI52_RS00425 61034..61318 + 285 WP_000624194 type-F conjugative transfer system pilin chaperone TraQ -
HTI52_RS00430 61305..61850 + 546 WP_000059831 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
HTI52_RS00435 61780..62127 + 348 WP_001309242 P-type conjugative transfer protein TrbJ -
HTI52_RS00440 62108..62500 + 393 WP_000660699 F-type conjugal transfer protein TrbF -
HTI52_RS00445 62487..63860 + 1374 WP_000944331 conjugal transfer pilus assembly protein TraH traH
HTI52_RS00450 63857..66679 + 2823 WP_001007039 conjugal transfer mating-pair stabilization protein TraG traG
HTI52_RS00455 66695..67180 + 486 WP_000605870 hypothetical protein -
HTI52_RS00460 67229..67960 + 732 WP_000782451 conjugal transfer complement resistance protein TraT -
HTI52_RS00465 68163..68900 + 738 WP_000199905 hypothetical protein -
HTI52_RS00470 68951..71239 + 2289 WP_125097878 type IV conjugative transfer system coupling protein TraD prgC

Host bacterium

ID   3504 GenBank   NZ_KU987452
Plasmid name   AC2901 Incompatibility group   IncFII
Plasmid size   74385 bp Coordinate of oriT [Strand]   43234..43319 [-]
Host baterium   Citrobacter freundii strain AC2901

Cargo genes

Drug resistance gene   blaCTX-M-14
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -