Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   118693
Name   oriT_pFF1003_1 in_silico
Organism   Klebsiella africana strain FF1003
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP059392 (60416..60465 [-], 50 nt)
oriT length   50 nt
IRs (inverted repeats)      7..14, 17..24  (GCAAAATT..AATTTTGC)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 50 nt

>oriT_pFF1003_1
AAATCTGCAAAATTTTAATTTTGCGTAGTGTGTGGTCATTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   11858 GenBank   WP_203034335
Name   traI_H1X61_RS25775_pFF1003_1 insolico UniProt ID   _
Length   1752 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1752 a.a.        Molecular weight: 190625.34 Da        Isoelectric Point: 5.9980

>WP_203034335.1 conjugative transfer relaxase/helicase TraI [Klebsiella africana]
MLSFSQVKSAGSAGNYYTEKDNYYVIGSMEERWQGKGAELLGLEGKVDKQVFTELLQGKLPDGSDLTRIQ
DGVNKHRPGYDLTFSAPKSVSMLAMLGGDKRLIDAHNRAVTVALNQVESLASTRVKKDGVSETVLTGNLI
IARFNHDTSRAQDPQIHTHSLVINATQNGDKWQTLASDTVGKTGFSETILANRIAFGKIYQNSLRADVES
MGYKTVDAGRNGMWEMEGVPVESFSTRSQELREAAGPDASLKSRDVAALDTRKSKEAIDPAEKMVEWMNT
LKETGFDIRGYREAADARAAELARAPAAPVNTDGPDITDVVTKAIAGLSDRKVQFTYADLLARTVGQLEA
KDGVFELARKGIDAAIEREQLIPLDREKGLFTSNIHVLDELAVKALSQEVQRQNHVSVTPDASVVRQVPF
SDAVSVLAQDRPVMGIVSGQGGATGQRERVAELTLMAREQGRDVHILAADNRSRDFLAGDVRLAGETVTG
KSALQDGTAFIPGGTLIVDQAEKLSLKETISLLDGAMRHNVQVLLSDSGKRSGTGSALTVLKDSGVNTYR
WQGGHQTTADIISEPDKGARYSRLAQEFAVSVREGQESVAQISGTREQSVLNGLIRDSLRHEGVLGEKDT
TITALTPVWLDSKSRGVRDYYREGMVMERWDPENRTHDRFVIDRVTASSNMLTLKDRDGVRLDLKVSAVD
SQWTLFRAETLPVAEGERLAVLGKIPDTRLKGGESITVMKVEDGQLTVQRPGQKTTQTLAVGAGAFDGIK
IGHGWVESPGRSVSETATVFASVTQRELDNATLNQLAQSGSHLRLYSAQDAARTTEKLSRHTAFSVVSEQ
LKTRSGETDLDAAIAQQKAGLHTPAEQAIHLSIPLLESQDLTFTRPQLLATALETGGDKVPMWSIEMTIK
KQIKSGQLLNVGVSPGHGNDLLISRQTWDAEKSILTRVLEGKDAVAPLMDRVPASLMTDLTAGQRAATRM
ILETPDRFTVVQGYAGVGKTTQFRAVMSAISLLPEETRPHVIGLGPTHRAVGEMQSAGVDARTTASFLHD
TQLLQRNGQTPDFSNTLFLLDESSMVGLSDTAKALSLIAAGGGRAVLSGDTDQLQSISPGQPFRLMQQRS
AADVAIMKEIVRQVPELRPAVYSLIDRDIDRALATIEQVTPERVPRKEGAWVPGSSVVEFTPTQEEEIRK
ALSKGESLPAGQPATLYEALVKDYTGRTPEAQSQTLIITHLNNDRRALNGLIHDARRENGETGREEITLP
VLVTSNIRDGELRKLSTWTAHKGAVALVDNVYHRIDNVDKDNQLITLTDSEGKERYISPREASAEGVTLY
RQEEITVSQGDRMRFSKSDPERGYVANSVWEVQSVSGDSVTLSDGKTTRTLTPKADEAQQHIDLAYAITA
HGAQGASEPYAIALEGMVGARKLMASFESAYVGLSRMKQHVQVYTDRREGWIKAIQHSPEKATAHDILEP
RNDRAVKTADLLFGRARPLDETAAGRAALQQSGLAQGSSPGKFISPGKKYPQPHVALPAFDKNGKAAGIW
LSPLTDRDGRLEAIGGEGRIMGNEDARFVALQNSRNGESLLAGNIGEGVRMARDNPDTGVVVRLAGDDRP
WNPGAITGGRVWAEPAPVAPVPQAGADIILPPEVLAQRAAEEQQRREMEKQAEQTAREVAGEARKAGEPV
DRVKEVIGDVIRGLERDRPGTEKTTLPDDPQFRRQEAAIQQVASETLQRDRLQAVERDMVRDLNREKTLG
GD

  Protein domains


Predicted by InterproScan.

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

(634-713)

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

(576-628)

TrwC relaxase (TrwC)

(11-283)

AAA domain (AAA_30)

(970-1157)

DNA helicase TraI (TraI_C)

(1432-1554)


  Protein structure



No available structure.




T4CP

ID   13889 GenBank   WP_228290733
Name   traD_H1X61_RS25770_pFF1003_1 insolico UniProt ID   _
Length   760 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 760 a.a.        Molecular weight: 85013.94 Da        Isoelectric Point: 4.9596

>WP_228290733.1 type IV conjugative transfer system coupling protein TraD [Klebsiella africana]
MSFNAKDMTQGGQIANMRFRMFGQIANIIFYVLFILFWVLCGLMLMYRLSWQTFVNGCVYWWCTTLGPMR
DIIRSQPVYTIQYYGQSLEYTSEQILADKYTIWCGEQLWTSFVFAAVVSLVICIVTFFIASWVLGRQGKQ
QSEDENTGGRQLSDKPKEVARQMKRDGMASDIKIGDLPILKNSEIQNFCLHGTVGSGKSEVIRRLLNYVR
ARGDMAIIYDRSCEFVKSYYDQSLDKILNPLDSRCAAWDLWKECLTLPDFDNISNTLIPMGTKEDPFWQG
SGRTIFAEGAYLMREDKDRSYEKLVDTMLSIKIDKLRAYLQNTPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEKNGEPFTIRDWMRGVREDRPNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGVKPAATLFDVMNTRAFFRSPSREIA
EFAAGEIGEKEILKASEQYSYGADPVRDGVSTGKEKERETLVSYSDIQTLPDLSCYVTLPGPYPAVKLAL
KYKPRPKIAEGFIPRTLDARVDARLSALLEAREAEGSLARALFTPDAPEPGPADTESHASEQPESVSPPA
PAEMTVTPAPVKAPPTTKRPAAEPPVLPVTPVPLLNQKAAAAAATASSAGTPAAAAGGTEQELAQQSAEQ
GQDMLPAGMNEDGVIEDMQAYDAWLADEQTQRDMQRREEVNINHSHRHDEQDDVEIGGNI

  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: 59858..88507

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
H1X61_RS25555 (H1X61_25545) 54875..55225 + 351 WP_023320095 hypothetical protein -
H1X61_RS25560 (H1X61_25550) 55861..56217 + 357 WP_004152717 hypothetical protein -
H1X61_RS25565 (H1X61_25555) 56278..56490 + 213 WP_004182070 hypothetical protein -
H1X61_RS25570 (H1X61_25560) 56501..56725 + 225 WP_023320096 hypothetical protein -
H1X61_RS25575 (H1X61_25565) 56806..57126 + 321 WP_004152720 type II toxin-antitoxin system RelE/ParE family toxin -
H1X61_RS25580 (H1X61_25570) 57116..57394 + 279 WP_203034326 helix-turn-helix transcriptional regulator -
H1X61_RS25585 (H1X61_25575) 57395..57808 + 414 WP_004182074 type II toxin-antitoxin system HigA family antitoxin -
H1X61_RS25590 (H1X61_25580) 58642..59463 + 822 WP_203034327 DUF932 domain-containing protein -
H1X61_RS25595 (H1X61_25585) 59496..59825 + 330 WP_011977736 DUF5983 family protein -
H1X61_RS25600 (H1X61_25590) 59858..60343 - 486 WP_004178063 transglycosylase SLT domain-containing protein virB1
H1X61_RS25605 (H1X61_25595) 60734..61150 + 417 WP_074181767 conjugal transfer relaxosome DNA-binding protein TraM -
H1X61_RS25610 (H1X61_25600) 61350..62069 + 720 WP_203034328 conjugal transfer protein TrbJ -
H1X61_RS25615 (H1X61_25605) 62202..62408 + 207 WP_172412524 TraY domain-containing protein -
H1X61_RS25620 (H1X61_25610) 62470..62838 + 369 WP_064147976 type IV conjugative transfer system pilin TraA -
H1X61_RS25625 (H1X61_25615) 62852..63157 + 306 WP_004178059 type IV conjugative transfer system protein TraL traL
H1X61_RS25630 (H1X61_25620) 63177..63743 + 567 WP_004152602 type IV conjugative transfer system protein TraE traE
H1X61_RS25635 (H1X61_25625) 63730..64470 + 741 WP_203034329 type-F conjugative transfer system secretin TraK traK
H1X61_RS25640 (H1X61_25630) 64470..65894 + 1425 WP_016529134 F-type conjugal transfer pilus assembly protein TraB traB
H1X61_RS25645 (H1X61_25635) 65887..66300 + 414 Protein_78 conjugal transfer pilus-stabilizing protein TraP -
H1X61_RS25650 (H1X61_25640) 66512..67081 + 570 WP_015065628 type IV conjugative transfer system lipoprotein TraV traV
H1X61_RS26240 67237..67635 + 399 WP_223177007 hypothetical protein -
H1X61_RS25660 (H1X61_25650) 67664..67954 + 291 WP_032426790 hypothetical protein -
H1X61_RS25665 (H1X61_25655) 67978..68196 + 219 WP_004171484 hypothetical protein -
H1X61_RS25670 (H1X61_25660) 68197..68514 + 318 WP_016530481 hypothetical protein -
H1X61_RS25675 (H1X61_25665) 68581..68985 + 405 WP_023320104 hypothetical protein -
H1X61_RS25680 (H1X61_25670) 69010..69408 + 399 WP_015065631 hypothetical protein -
H1X61_RS25685 (H1X61_25675) 69480..72119 + 2640 WP_203034330 type IV secretion system protein TraC virb4
H1X61_RS25690 (H1X61_25680) 72119..72508 + 390 WP_203034331 type-F conjugative transfer system protein TrbI -
H1X61_RS25695 (H1X61_25685) 72508..73134 + 627 WP_009309871 type-F conjugative transfer system protein TraW traW
H1X61_RS25700 (H1X61_25690) 73176..73565 + 390 WP_004194992 hypothetical protein -
H1X61_RS25705 (H1X61_25695) 73562..74551 + 990 WP_009309872 conjugal transfer pilus assembly protein TraU traU
H1X61_RS25710 (H1X61_25700) 74564..75202 + 639 WP_015065635 type-F conjugative transfer system pilin assembly protein TrbC trbC
H1X61_RS25715 (H1X61_25705) 75261..77216 + 1956 WP_203034332 type-F conjugative transfer system mating-pair stabilization protein TraN traN
H1X61_RS25720 (H1X61_25710) 77248..77484 + 237 WP_203034333 conjugal transfer protein TrbE -
H1X61_RS26355 77481..77666 + 186 WP_032446653 hypothetical protein -
H1X61_RS25725 (H1X61_25715) 77712..78038 + 327 WP_016529362 hypothetical protein -
H1X61_RS25730 (H1X61_25720) 78059..78811 + 753 WP_203034334 type-F conjugative transfer system pilin assembly protein TraF traF
H1X61_RS25735 (H1X61_25725) 78822..79061 + 240 WP_004144400 type-F conjugative transfer system pilin chaperone TraQ -
H1X61_RS25740 (H1X61_25730) 79033..79590 + 558 WP_004152678 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
H1X61_RS25745 (H1X61_25735) 79635..80078 + 444 WP_015065638 F-type conjugal transfer protein TrbF -
H1X61_RS25750 (H1X61_25740) 80056..81435 + 1380 WP_011977731 conjugal transfer pilus assembly protein TraH traH
H1X61_RS25755 (H1X61_25745) 81435..84257 + 2823 WP_023320108 conjugal transfer mating-pair stabilization protein TraG traG
H1X61_RS25760 (H1X61_25750) 84281..84883 + 603 WP_023280878 hypothetical protein -
H1X61_RS25765 (H1X61_25755) 85134..85865 + 732 WP_032415736 conjugal transfer complement resistance protein TraT -
H1X61_RS25770 (H1X61_25760) 86225..88507 + 2283 WP_228290733 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   19125 GenBank   NZ_CP059392
Plasmid name   pFF1003_1 Incompatibility group   IncFIA
Plasmid size   97925 bp Coordinate of oriT [Strand]   60416..60465 [-]
Host baterium   Klebsiella africana strain FF1003

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   AcrIE9