Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilU   Type   Machinery gene
Locus tag   LDN68_RS02865 Genome accession   NZ_AP024948
Coordinates   570328..571437 (-) Length   369 a.a.
NCBI ID   WP_041214461.1    Uniprot ID   A0A839D3X0
Organism   Aeromonas caviae strain KAM345     
Function   type IV pilus retraction (predicted from homology)   
DNA binding and uptake

Related MGE

Note: This gene co-localizes with putative mobile genetic elements (MGEs) in the genome predicted by VRprofile2, as detailed below.

Gene-MGE association summary

MGE type MGE coordinates Gene coordinates Relative position Distance (bp)
ICE 530543..572495 570328..571437 within 0


Gene organization within MGE regions


Location: 530543..572495
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  LDN68_RS02645 (KAM345_004960) - 530543..531559 (+) 1017 WP_119197020.1 tyrosine-type recombinase/integrase -
  LDN68_RS02650 - 531816..531959 (+) 144 WP_162726529.1 hypothetical protein -
  LDN68_RS02655 (KAM345_004980) - 531956..532438 (+) 483 WP_223954832.1 hypothetical protein -
  LDN68_RS02660 (KAM345_004990) - 532541..532786 (+) 246 WP_119197017.1 hypothetical protein -
  LDN68_RS02665 (KAM345_005000) - 532952..534796 (+) 1845 WP_223954833.1 AAA family ATPase -
  LDN68_RS02670 (KAM345_005010) - 535146..535451 (+) 306 WP_223954834.1 DUF5681 domain-containing protein -
  LDN68_RS02675 (KAM345_005020) - 535448..535687 (+) 240 WP_223954835.1 hypothetical protein -
  LDN68_RS02680 (KAM345_005030) - 535687..535953 (+) 267 WP_223954836.1 hypothetical protein -
  LDN68_RS02685 (KAM345_005040) - 535966..536634 (+) 669 WP_223954837.1 hypothetical protein -
  LDN68_RS02690 (KAM345_005050) - 536690..537010 (+) 321 WP_223954838.1 hypothetical protein -
  LDN68_RS02695 (KAM345_005060) - 537052..538266 (-) 1215 WP_025711969.1 IS256 family transposase -
  LDN68_RS02700 (KAM345_005070) - 538387..538788 (-) 402 WP_201880070.1 hypothetical protein -
  LDN68_RS02705 (KAM345_005080) - 539291..539659 (-) 369 WP_049636484.1 VOC family protein -
  LDN68_RS02710 (KAM345_005090) amt 540193..541620 (+) 1428 WP_010673021.1 ammonium transporter -
  LDN68_RS02715 (KAM345_005100) rlmD 541852..543204 (+) 1353 WP_049636483.1 23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD -
  LDN68_RS02720 (KAM345_005110) - 543392..543901 (+) 510 WP_174217465.1 GNAT family N-acetyltransferase -
  LDN68_RS02725 (KAM345_005120) - 543983..544153 (+) 171 WP_174217464.1 DUF5363 family protein -
  LDN68_RS02730 (KAM345_005130) tppF 544122..544736 (-) 615 WP_029313748.1 type IVa pilus pseudopilin TppF -
  LDN68_RS02735 (KAM345_005140) - 544777..545565 (+) 789 WP_049636482.1 TatD family hydrolase -
  LDN68_RS02740 (KAM345_005150) - 545779..547053 (+) 1275 WP_010673026.1 NupC/NupG family nucleoside CNT transporter -
  LDN68_RS02745 (KAM345_005160) - 547177..547347 (+) 171 WP_010673027.1 XapX domain-containing protein -
  LDN68_RS02750 (KAM345_005170) deoC 547735..548508 (+) 774 WP_039039946.1 deoxyribose-phosphate aldolase -
  LDN68_RS02755 (KAM345_005180) deoA 548591..549922 (+) 1332 WP_043153005.1 thymidine phosphorylase -
  LDN68_RS02760 (KAM345_005190) - 549937..551145 (+) 1209 WP_039039948.1 phosphopentomutase -
  LDN68_RS02765 (KAM345_005200) deoD 551279..551995 (+) 717 WP_005341325.1 purine-nucleoside phosphorylase -
  LDN68_RS02770 (KAM345_005210) - 552060..554306 (-) 2247 WP_049636481.1 PAS domain S-box protein -
  LDN68_RS02775 (KAM345_005220) - 554373..554981 (-) 609 WP_049636480.1 AhpA/YtjB family protein -
  LDN68_RS02780 (KAM345_005230) serB 555175..556179 (+) 1005 WP_049636479.1 phosphoserine phosphatase SerB -
  LDN68_RS02785 (KAM345_005240) - 556208..557113 (+) 906 WP_049636478.1 alpha/beta fold hydrolase -
  LDN68_RS02790 (KAM345_005250) - 557171..559546 (-) 2376 WP_049636477.1 PilZ domain-containing protein -
  LDN68_RS02795 (KAM345_005260) radA 559647..561011 (+) 1365 WP_010673036.1 DNA repair protein RadA -
  LDN68_RS02800 (KAM345_005270) - 561065..561451 (-) 387 WP_029313755.1 PilZ domain-containing protein -
  LDN68_RS02805 (KAM345_005280) - 561554..562036 (-) 483 WP_049636476.1 Rsd/AlgQ family anti-sigma factor -
  LDN68_RS02810 (KAM345_005290) hupA 562375..562647 (+) 273 WP_005305063.1 nucleoid-associated protein HU-alpha -
  LDN68_RS02815 (KAM345_005300) - 562761..563186 (+) 426 WP_029313758.1 hypothetical protein -
  LDN68_RS02820 (KAM345_005310) - 563270..563419 (-) 150 WP_080944170.1 hypothetical protein -
  LDN68_RS02825 (KAM345_005320) dusA 563422..564408 (-) 987 WP_049636475.1 tRNA dihydrouridine(20/20a) synthase DusA -
  LDN68_RS02830 (KAM345_005330) zur 564545..565003 (+) 459 WP_049636537.1 zinc uptake transcriptional repressor Zur -
  LDN68_RS02835 (KAM345_005340) - 564993..565454 (+) 462 WP_010673043.1 chemotaxis protein CheX -
  LDN68_RS02840 (KAM345_005350) - 565460..565687 (+) 228 WP_049636474.1 hypothetical protein -
  LDN68_RS02845 (KAM345_005360) brnQ 565778..567040 (-) 1263 WP_049636536.1 branched-chain amino acid transport system II carrier protein -
  LDN68_RS02850 (KAM345_005370) - 567276..567986 (-) 711 WP_049636473.1 tRNA1(Val) (adenine(37)-N6)-methyltransferase -
  LDN68_RS02855 (KAM345_005380) srmB 568114..569334 (+) 1221 WP_041210934.1 ATP-dependent RNA helicase SrmB -
  LDN68_RS02860 (KAM345_005390) yaaA 569522..570295 (-) 774 WP_049636472.1 peroxide stress protein YaaA -
  LDN68_RS02865 (KAM345_005400) pilU 570328..571437 (-) 1110 WP_041214461.1 PilT/PilU family type 4a pilus ATPase Machinery gene
  LDN68_RS02870 (KAM345_005410) pilT 571461..572495 (-) 1035 WP_010673050.1 type IVa pilus ATPase TapT Machinery gene

Sequence

Protein


Download         Length: 369 a.a.        Molecular weight: 40856.99 Da        Isoelectric Point: 6.3155

>NTDB_id=89608 LDN68_RS02865 WP_041214461.1 570328..571437(-) (pilU) [Aeromonas caviae strain KAM345]
MNMDVLLAALVEQKGSDLFITVDAPPTLKVNGRLVSLGPAPLDKTTALALIRESLDETHFERFLHTREANYAIQRGSLGR
FRVSAFWQQDMPGMVLRRIETRIPTFDELVLPPILQEVAMAKRGLVLFVGATGAGKSTTQAAMIGFRNQHGDGHILTVED
PVEFVHQHDRCLVTQREVGIDTASFDVALKNSLRQAPDVILIGEIRSQETMEFAIQFAETGHLCLATLHANNANQALDRI
LHLVPQEKHRQFLFDLSFNLRAIVAQQLLPSAHGQRRVAAFEILLNTPLVTDIIRKGEMHRLKEVMTKSGELGMQTFDQA
LFGLFCAGQIGYSEALAHADSANDLRLLIKLSGREQLGAGTLDNVTLDE

Nucleotide


Download         Length: 1110 bp        

>NTDB_id=89608 LDN68_RS02865 WP_041214461.1 570328..571437(-) (pilU) [Aeromonas caviae strain KAM345]
ATGAACATGGATGTTCTGCTCGCCGCACTGGTTGAACAAAAGGGCTCGGATCTCTTCATCACGGTCGATGCCCCCCCGAC
CCTCAAGGTCAACGGGCGTCTGGTGTCGCTCGGGCCGGCTCCCCTCGACAAGACGACGGCGCTGGCGTTGATCAGGGAGA
GCCTGGACGAGACCCACTTCGAGCGCTTCCTGCACACCCGCGAGGCCAACTACGCCATCCAGCGGGGCTCGCTGGGGCGC
TTTCGGGTCAGCGCCTTCTGGCAACAGGATATGCCGGGCATGGTGCTGCGCCGCATCGAGACCCGCATCCCCACCTTTGA
CGAGCTGGTGCTGCCTCCCATCCTGCAGGAGGTCGCCATGGCCAAACGCGGGCTGGTGCTCTTCGTCGGCGCCACTGGCG
CCGGCAAGTCCACCACCCAGGCGGCCATGATCGGCTTTCGCAACCAGCACGGTGACGGCCACATCCTGACGGTGGAGGAT
CCGGTGGAGTTCGTCCATCAGCACGATCGCTGTCTGGTGACCCAGCGGGAGGTGGGGATCGACACCGCATCCTTCGATGT
CGCCCTCAAAAACTCCCTGCGCCAGGCCCCGGATGTCATCCTCATCGGTGAAATCCGCTCCCAGGAGACCATGGAATTCG
CCATCCAGTTCGCCGAGACGGGGCACCTCTGCCTCGCCACCTTGCACGCCAACAATGCCAACCAGGCGCTGGATCGCATC
CTGCATCTGGTCCCCCAGGAGAAGCACCGCCAGTTCCTGTTCGATCTCTCCTTCAACCTGCGCGCCATCGTCGCCCAGCA
GCTGCTCCCCTCCGCTCACGGGCAGCGCCGGGTCGCCGCCTTCGAGATCCTGCTCAACACCCCGCTCGTCACCGACATCA
TCCGCAAGGGAGAGATGCACAGACTCAAGGAGGTGATGACCAAATCCGGCGAGCTCGGCATGCAGACCTTCGATCAGGCG
CTGTTCGGCCTGTTCTGCGCCGGCCAAATTGGCTACAGTGAGGCCCTTGCCCATGCCGACTCCGCCAACGACCTGCGACT
GCTCATCAAGCTGTCGGGTCGCGAGCAGCTGGGCGCAGGCACTCTCGACAACGTGACCCTGGATGAATGA

Domains

Predicted by InterproScan.

Type II/IV secretion system protein (T2SSE)

(115-270)


Secondary structure

Protein secondary structures were predicted by S4PRED and visualized by seqviz.



3D structure

Source ID Structure
  AlphaFold DB A0A839D3X0

Transmembrane helices

Transmembrane helices of protein were predicted by TMHMM 2.0 and visualized by seqviz and ECharts.


Visualization of predicted probability:


Similar proteins

Only experimentally validated proteins are listed.

Protein Organism Identities (%) Coverage (%) Ha-value
  pilU Vibrio cholerae strain A1552

60.598

99.729

0.604
  pilU Pseudomonas stutzeri DSM 10701

58.974

95.122

0.561
  pilU Acinetobacter baylyi ADP1

57.79

95.664

0.553
  pilT Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539

43.155

91.057

0.393
  pilT Legionella pneumophila strain Lp02

40.816

92.954

0.379
  pilT Legionella pneumophila strain ERS1305867

40.816

92.954

0.379

Multiple sequence alignment