Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilD   Type   Machinery gene
Locus tag   ALIDE_RS04550 Genome accession   NC_014910
Coordinates   971083..971961 (-) Length   292 a.a.
NCBI ID   WP_013517807.1    Uniprot ID   A0A858ZQU3
Organism   Alicycliphilus denitrificans BC     
Function   assembly of type IV pilus (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)
Prophage 971083..1004120 971083..971961 within 0


Gene organization within MGE regions


Location: 971083..1004120
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  ALIDE_RS04550 (Alide_0916) pilD 971083..971961 (-) 879 WP_013517807.1 prepilin peptidase Machinery gene
  ALIDE_RS04555 (Alide_0917) pilC 971961..973178 (-) 1218 WP_013517808.1 type II secretion system F family protein Machinery gene
  ALIDE_RS04560 (Alide_0918) pilB 973200..974939 (-) 1740 WP_013517809.1 type IV-A pilus assembly ATPase PilB Machinery gene
  ALIDE_RS04565 (Alide_0919) - 975890..977584 (+) 1695 WP_013517810.1 hypothetical protein -
  ALIDE_RS04570 (Alide_0920) - 977965..978954 (-) 990 WP_041715885.1 hypothetical protein -
  ALIDE_RS23980 (Alide_0923) - 980568..980915 (-) 348 WP_148237961.1 helix-turn-helix transcriptional regulator -
  ALIDE_RS04585 (Alide_0924) - 981016..982605 (-) 1590 WP_013517813.1 site-specific integrase -
  ALIDE_RS04595 (Alide_0925) - 982877..983860 (-) 984 WP_041700640.1 polyprenyl synthetase family protein -
  ALIDE_RS04600 (Alide_0926) rplU 984033..984344 (+) 312 WP_011804285.1 50S ribosomal protein L21 -
  ALIDE_RS04605 (Alide_0927) rpmA 984360..984617 (+) 258 WP_011804286.1 50S ribosomal protein L27 -
  ALIDE_RS04610 (Alide_0928) cgtA 984743..985816 (+) 1074 WP_013517815.1 Obg family GTPase CgtA -
  ALIDE_RS04615 (Alide_0929) proB 985881..987020 (+) 1140 WP_013517816.1 glutamate 5-kinase -
  ALIDE_RS04620 (Alide_0930) - 987044..987718 (-) 675 WP_013517817.1 RNA pyrophosphohydrolase -
  ALIDE_RS04625 (Alide_0931) - 987820..989565 (+) 1746 WP_013517818.1 proline--tRNA ligase -
  ALIDE_RS04630 (Alide_0932) - 989562..990206 (+) 645 WP_013517819.1 lytic transglycosylase domain-containing protein -
  ALIDE_RS04635 (Alide_0933) - 990182..991516 (-) 1335 WP_013517820.1 hemolysin family protein -
  ALIDE_RS04640 (Alide_0934) - 991560..992567 (-) 1008 WP_013517821.1 AAA family ATPase -
  ALIDE_RS04645 (Alide_0935) grxD 992708..993040 (-) 333 WP_013517822.1 Grx4 family monothiol glutaredoxin -
  ALIDE_RS04650 (Alide_0936) prmC 993097..993942 (-) 846 WP_013517823.1 peptide chain release factor N(5)-glutamine methyltransferase -
  ALIDE_RS04655 (Alide_0937) prfA 993985..995067 (-) 1083 WP_013517824.1 peptide chain release factor 1 -
  ALIDE_RS04660 (Alide_0938) hemA 995168..996481 (-) 1314 WP_013517825.1 glutamyl-tRNA reductase -
  ALIDE_RS04665 (Alide_0939) - 996556..996831 (+) 276 WP_013517826.1 hypothetical protein -
  ALIDE_RS04670 (Alide_0940) - 996948..997841 (-) 894 WP_013517827.1 LysR substrate-binding domain-containing protein -
  ALIDE_RS04675 (Alide_0941) - 997967..998950 (+) 984 WP_013517828.1 tripartite tricarboxylate transporter substrate binding protein BugE -
  ALIDE_RS04680 (Alide_0942) - 998950..999852 (+) 903 WP_013517829.1 N-formylglutamate amidohydrolase -
  ALIDE_RS04685 (Alide_0943) - 999896..1002328 (-) 2433 WP_013517830.1 DUF3772 domain-containing protein -
  ALIDE_RS04690 (Alide_0944) ugpQ 1002357..1003106 (-) 750 WP_013517831.1 glycerophosphodiester phosphodiesterase -
  ALIDE_RS04695 (Alide_0945) ugpC 1003113..1004120 (-) 1008 WP_013517832.1 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC -

Sequence

Protein


Download         Length: 292 a.a.        Molecular weight: 31415.02 Da        Isoelectric Point: 7.8150

>NTDB_id=39336 ALIDE_RS04550 WP_013517807.1 971083..971961(-) (pilD) [Alicycliphilus denitrificans BC]
MTGSAFADAVLVGVLGLLIGSFLNVVIHRLPRMMERQWAAECAQYAEDAGLPTQGGAAPTEQPFNLLTPRSRCPSCGHEV
RWYENIPVLSYLALRGRCSGCGTRIGVRYPLVELATAALFYACALRWGWSFTTLAWCGFCAALVALALIDWDTTLLPDDI
TLPLLWAGLLASVLRWIDVQPVDAVIGAAAGYVSLWLVYWGFKLATGKEGMGYGDFKLFAALGAWFGWQALVPIVLMASV
IGALVGIAMKFASSLREGKYVPFGPFLAGGGLAAMLWGPARIMRAIFSTLGL

Nucleotide


Download         Length: 879 bp        

>NTDB_id=39336 ALIDE_RS04550 WP_013517807.1 971083..971961(-) (pilD) [Alicycliphilus denitrificans BC]
ATGACGGGTTCCGCGTTTGCGGATGCCGTGCTCGTCGGCGTCCTGGGCCTGCTGATCGGCAGCTTTCTGAACGTGGTGAT
CCACCGCCTGCCGCGCATGATGGAACGGCAGTGGGCCGCGGAATGCGCGCAGTACGCCGAGGATGCGGGCTTGCCGACAC
AGGGCGGCGCCGCGCCGACCGAGCAGCCCTTCAACCTGCTGACGCCACGCTCGCGCTGTCCCTCCTGCGGGCACGAGGTG
CGCTGGTACGAGAACATTCCCGTGCTCAGCTATCTCGCACTGCGCGGCCGCTGCTCGGGCTGCGGCACGCGCATCGGCGT
GCGCTACCCGCTGGTCGAACTGGCCACCGCCGCCCTGTTCTATGCCTGCGCCCTGCGCTGGGGCTGGTCCTTCACGACGC
TGGCCTGGTGCGGCTTTTGCGCAGCCCTGGTGGCGCTGGCCCTCATCGACTGGGACACGACCCTGCTGCCCGACGACATC
ACCCTGCCCCTGCTGTGGGCCGGGCTGCTGGCCTCCGTGCTGCGCTGGATAGATGTGCAGCCGGTGGACGCGGTGATCGG
CGCGGCCGCGGGCTATGTATCGCTGTGGCTCGTCTACTGGGGCTTCAAGCTCGCCACGGGCAAGGAGGGCATGGGCTATG
GCGACTTCAAGCTGTTCGCGGCCCTGGGCGCGTGGTTCGGCTGGCAGGCCCTGGTGCCCATCGTCCTCATGGCGTCGGTC
ATCGGCGCCCTGGTAGGCATCGCCATGAAGTTCGCCAGCAGCCTGCGCGAGGGCAAGTACGTGCCCTTTGGCCCGTTCCT
GGCGGGAGGCGGGCTGGCCGCCATGCTGTGGGGGCCGGCGCGTATCATGCGTGCCATTTTCTCCACCCTGGGGCTGTAG

Domains

Predicted by InterproScan.

Type IV leader peptidase family (Peptidase_A24)

(139-247)

Bacterial Peptidase A24 N-terminal domain (A24_N_bact)

(14-126)


Secondary structure

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



3D structure

Source ID Structure
  AlphaFold DB A0A858ZQU3

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
  pilD Vibrio cholerae strain A1552

50.175

97.603

0.49
  pilD Vibrio campbellii strain DS40M4

45.39

96.575

0.438
  pilD Neisseria gonorrhoeae MS11

47.71

89.726

0.428
  pilD Acinetobacter nosocomialis M2

43.223

93.493

0.404
  pilD Acinetobacter baumannii D1279779

43.223

93.493

0.404

Multiple sequence alignment