Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   114577
Name   oriT_pCIT-a850 in_silico
Organism   Citrobacter sp. CFNIH10
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP026212 (32405..32453 [+], 49 nt)
oriT length   49 nt
IRs (inverted repeats)      6..13, 16..23  (GCAAAATT..AATTTTGC)
Location of nic site      32..33
Conserved sequence flanking the
  nic site    		  TGTGTGGTGA
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 49 nt

>oriT_pCIT-a850
AATCTGCAAAATTTTAATTTTGCGTAGTGTGTGGTGATTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Auxiliary protein

ID   5464 GenBank   WP_004197733
Name   WP_004197733_pCIT-a850 insolico UniProt ID   A0A0E3KB00
Length   129 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 129 a.a.        Molecular weight: 14835.90 Da        Isoelectric Point: 4.6012

>WP_004197733.1 MULTISPECIES: conjugal transfer relaxosome DNA-binding protein TraM [Bacteria]
MGKVQAYPSDEVCEKINAIVEKRRMEGAKDKDVSFSSISTMLLELGLRVYEAQMERKESGFNQMAFNRAL
LESVVKTQFSVNKILGIECLSPHVKDDPRWQWKSMVLNIQEDVQEAMRNFFPDEDAEGE

  Protein domains


Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-124)


  Protein structure


Source ID Structure
AlphaFold DB A0A0E3KB00


T4CP

ID   10837 GenBank   WP_042946329
Name   traD_C2U53_RS00855_pCIT-a850 insolico UniProt ID   _
Length   769 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 769 a.a.        Molecular weight: 85713.82 Da        Isoelectric Point: 5.3307

>WP_042946329.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIANMRFRMFGQIANIIFYVLFILFWVLCGLMLMYRLSWQTFVNGCVYWWCTTLGPMR
DIIRSQPVYTIQYYGQSLEYTSEQILADKYTIWCGEQLWTGFAFAAVVSLVICIVTFFIASWVLGRQGKQ
QSEDENTGGRQLSDKPKEVARQMKRDGVASDIKIGDLPILKNSEIQNFCLHGTVGSGKSEVIRRLLNYVR
ARGDMAIIYDRSCEFVKSYYDPSLDKILNPLDSRCAAWDLWKECLTLPDFDNISNTLIPMGTKEDPFWQG
SGRTIFAEGAYLMREDKDRSYEKLVDTMLSIKIDKLRAYLQNTPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEKNGEPFTIRDWMRGVREDRPNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGVKPAATLFDVMNTRAFFRSPSKEIA
EFAAGEIGEKEILKASEQYSYGADPVRDGVSTGKEKERETLVSYSDIQTLPDLSCYVTLPGPYPAVKLAL
KYKPRPKIAEGFIPRTLDARVDARLSALLEAREAEGSLARALFTPDAPASWPDDAGSHAGEQPEPVSQPA
PAVMTVTPAPVKSPPTTKRPAAEPSARTAEPPVLRVTTVPLIKPKAAAAAGTAATASSAGTPAAAAGGTE
QVLAQQSAEQGQAMLPAGMNEDGVIEDMQAYDAWADEQTQRDMQRREEVNINHSHRHDEQDDLEIGGNF

  Protein domains


Predicted by InterproScan.

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

(172-560)

F sex factor protein N terminal (TraD_N)

(32-128)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 1494..33011

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
C2U53_RS00855 (C2U53_00855) 1494..3803 - 2310 WP_042946329 type IV conjugative transfer system coupling protein TraD virb4
C2U53_RS29725 3929..4621 - 693 WP_009309879 hypothetical protein -
C2U53_RS00870 (C2U53_00870) 5356..8031 - 2676 Protein_3 conjugal transfer mating-pair stabilization protein TraG -
C2U53_RS00885 (C2U53_00885) 8313..9389 + 1077 WP_000227969 IS110 family transposase -
C2U53_RS00890 (C2U53_00890) 9421..9603 - 183 Protein_5 traG protein -
C2U53_RS00895 (C2U53_00895) 9603..10973 - 1371 WP_009309877 conjugal transfer pilus assembly protein TraH traH
C2U53_RS00900 (C2U53_00900) 10960..11388 - 429 WP_004152689 hypothetical protein -
C2U53_RS00905 (C2U53_00905) 11381..11953 - 573 WP_009309876 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
C2U53_RS00910 (C2U53_00910) 11925..12164 - 240 WP_009309875 type-F conjugative transfer system pilin chaperone TraQ -
C2U53_RS00915 (C2U53_00915) 12175..12927 - 753 WP_042946327 type-F conjugative transfer system pilin assembly protein TraF traF
C2U53_RS00920 (C2U53_00920) 12948..13274 - 327 WP_004194451 hypothetical protein -
C2U53_RS00925 (C2U53_00925) 13287..13535 - 249 WP_004152675 hypothetical protein -
C2U53_RS00930 (C2U53_00930) 13513..13767 - 255 WP_004195500 conjugal transfer protein TrbE -
C2U53_RS00935 (C2U53_00935) 13799..15754 - 1956 WP_049192820 type-F conjugative transfer system mating-pair stabilization protein TraN traN
C2U53_RS00940 (C2U53_00940) 15813..16460 - 648 WP_039698503 type-F conjugative transfer system pilin assembly protein TrbC trbC
C2U53_RS00945 (C2U53_00945) 16604..17206 - 603 WP_022631520 hypothetical protein -
C2U53_RS00955 (C2U53_00955) 17927..18475 - 549 WP_022631518 hypothetical protein -
C2U53_RS00960 (C2U53_00960) 18490..19449 - 960 WP_029497356 conjugal transfer pilus assembly protein TraU traU
C2U53_RS00965 (C2U53_00965) 19493..20119 - 627 WP_020314628 type-F conjugative transfer system protein TraW traW
C2U53_RS00970 (C2U53_00970) 20119..20511 - 393 WP_042946321 type-F conjugative transfer system protein TrbI -
C2U53_RS00975 (C2U53_00975) 20508..23147 - 2640 WP_042946320 type IV secretion system protein TraC virb4
C2U53_RS00980 (C2U53_00980) 23219..23617 - 399 WP_074186017 hypothetical protein -
C2U53_RS00985 (C2U53_00985) 23625..23915 - 291 WP_023340940 hypothetical protein -
C2U53_RS00990 (C2U53_00990) 23912..24316 - 405 WP_042939116 hypothetical protein -
C2U53_RS00995 (C2U53_00995) 24383..24694 - 312 WP_023316403 hypothetical protein -
C2U53_RS01000 (C2U53_01000) 24695..24913 - 219 WP_023316402 hypothetical protein -
C2U53_RS01005 (C2U53_01005) 24937..25221 - 285 WP_023316401 hypothetical protein -
C2U53_RS01010 (C2U53_01010) 25226..25636 - 411 WP_020805613 hypothetical protein -
C2U53_RS01015 (C2U53_01015) 25768..26337 - 570 WP_023340942 type IV conjugative transfer system lipoprotein TraV traV
C2U53_RS01020 (C2U53_01020) 26360..26956 - 597 WP_023340943 conjugal transfer pilus-stabilizing protein TraP -
C2U53_RS01025 (C2U53_01025) 26949..28373 - 1425 WP_042946342 F-type conjugal transfer pilus assembly protein TraB traB
C2U53_RS01030 (C2U53_01030) 28373..29113 - 741 WP_032738531 type-F conjugative transfer system secretin TraK traK
C2U53_RS01035 (C2U53_01035) 29100..29666 - 567 WP_020316627 type IV conjugative transfer system protein TraE traE
C2U53_RS01040 (C2U53_01040) 29686..29991 - 306 WP_004178059 type IV conjugative transfer system protein TraL traL
C2U53_RS01045 (C2U53_01045) 30005..30373 - 369 WP_042946346 type IV conjugative transfer system pilin TraA -
C2U53_RS01050 (C2U53_01050) 30423..30641 - 219 WP_172619300 TraY domain-containing protein -
C2U53_RS01055 (C2U53_01055) 30791..31465 - 675 WP_004197737 hypothetical protein -
C2U53_RS01060 (C2U53_01060) 31704..32093 - 390 WP_004197733 conjugal transfer relaxosome DNA-binding protein TraM -
C2U53_RS01065 (C2U53_01065) 32526..33011 + 486 WP_022631514 transglycosylase SLT domain-containing protein virB1
C2U53_RS01070 (C2U53_01070) 33044..33373 - 330 WP_011977736 DUF5983 family protein -
C2U53_RS01075 (C2U53_01075) 33406..34227 - 822 WP_004152492 DUF932 domain-containing protein -
C2U53_RS01085 (C2U53_01085) 35047..35880 - 834 WP_004152751 N-6 DNA methylase -
C2U53_RS01090 (C2U53_01090) 35931..36077 - 147 WP_004152750 hypothetical protein -
C2U53_RS01095 (C2U53_01095) 36172..36519 - 348 WP_004152749 hypothetical protein -
C2U53_RS01100 (C2U53_01100) 36576..36929 - 354 WP_004152748 hypothetical protein -
C2U53_RS01115 (C2U53_01115) 37559..37909 - 351 WP_004153414 hypothetical protein -

Host bacterium

ID   15012 GenBank   NZ_CP026212
Plasmid name   pCIT-a850 Incompatibility group   IncFII
Plasmid size   126940 bp Coordinate of oriT [Strand]   32405..32453 [+]
Host baterium   Citrobacter sp. CFNIH10

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   silE, arsR, arsD, arsA, arsB, arsC
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   AcrIE9