Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilD   Type   Machinery gene
Locus tag   EP379_RS11055 Genome accession   NZ_AP018724
Coordinates   2181837..2182709 (+) Length   290 a.a.
NCBI ID   WP_197722776.1    Uniprot ID   -
Organism   Sulfurivermis fontis strain JG42     
Function   type IV pilus biogenesis and function (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)
Genomic island 2183343..2205864 2181837..2182709 flank 634


Gene organization within MGE regions


Location: 2181837..2205864
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  EP379_RS11055 pilD 2181837..2182709 (+) 873 WP_197722776.1 prepilin peptidase Machinery gene
  EP379_RS11060 coaE 2182713..2183312 (+) 600 WP_127477863.1 dephospho-CoA kinase -
  EP379_RS11065 zapD 2183343..2184110 (+) 768 WP_127477864.1 cell division protein ZapD -
  EP379_RS11070 yacG 2184107..2184307 (+) 201 WP_127477865.1 DNA gyrase inhibitor YacG -
  EP379_RS11075 - 2184319..2185266 (-) 948 WP_127477866.1 Nudix family hydrolase -
  EP379_RS11080 argJ 2185263..2186477 (-) 1215 WP_127477867.1 bifunctional glutamate N-acetyltransferase/amino-acid acetyltransferase ArgJ -
  EP379_RS11085 secA 2186493..2189189 (-) 2697 WP_127477868.1 preprotein translocase subunit SecA -
  EP379_RS11090 - 2189350..2190327 (-) 978 WP_127477869.1 M23 family metallopeptidase -
  EP379_RS17025 - 2190346..2190714 (+) 369 WP_172600453.1 DUF721 domain-containing protein -
  EP379_RS11100 lpxC 2190787..2191698 (-) 912 WP_127477871.1 UDP-3-O-acyl-N-acetylglucosamine deacetylase -
  EP379_RS11105 ftsZ 2191834..2192985 (-) 1152 WP_127477872.1 cell division protein FtsZ -
  EP379_RS11110 ftsA 2193031..2194269 (-) 1239 WP_127477873.1 cell division protein FtsA -
  EP379_RS11115 - 2194288..2195028 (-) 741 WP_172600454.1 cell division protein FtsQ/DivIB -
  EP379_RS11120 - 2195025..2195942 (-) 918 WP_127478902.1 D-alanine--D-alanine ligase -
  EP379_RS11125 murB 2195944..2196849 (-) 906 WP_127477875.1 UDP-N-acetylmuramate dehydrogenase -
  EP379_RS11130 murC 2196846..2198285 (-) 1440 WP_172600455.1 UDP-N-acetylmuramate--L-alanine ligase -
  EP379_RS11135 murG 2198282..2199388 (-) 1107 WP_127477876.1 undecaprenyldiphospho-muramoylpentapeptide beta-N-acetylglucosaminyltransferase -
  EP379_RS11140 ftsW 2199385..2200497 (-) 1113 WP_127478904.1 putative lipid II flippase FtsW -
  EP379_RS11145 murD 2200566..2201903 (-) 1338 WP_127477877.1 UDP-N-acetylmuramoyl-L-alanine--D-glutamate ligase -
  EP379_RS11150 mraY 2201905..2202987 (-) 1083 WP_127477878.1 phospho-N-acetylmuramoyl-pentapeptide- transferase -
  EP379_RS11155 - 2202987..2204351 (-) 1365 WP_127477879.1 UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D- alanine ligase -
  EP379_RS11160 - 2204362..2205864 (-) 1503 WP_127477880.1 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--2, 6-diaminopimelate ligase -

Sequence

Protein


Download         Length: 290 a.a.        Molecular weight: 32023.21 Da        Isoelectric Point: 8.6126

>NTDB_id=70523 EP379_RS11055 WP_197722776.1 2181837..2182709(+) (pilD) [Sulfurivermis fontis strain JG42]
MSDPTALMLADPLFITLVAAIFGLVMGSFLNVVIYRLPIIMERNWRRDCAELAGEAPAPQERFDLVMPRSRCPHCGQMVT
ARDNIPVLSYLLLRGRCRACGARLSLRYPLVELLTAALTVVTALHFGLNMQGLFAVLLTWSLIALGFIDFDKQLLPDSIT
LPMLWLGLLLSLFGIYTDSQASIIGAAAGYLSLWSIYHLFRLLTGKEGMGYGDFKLFALFGAWLGWQSLPLIILLSSAVG
AVLGLTLIVFRGRNRHIPLPFGPFLAIAGWIALLWGEQLNAWYLKTALPA

Nucleotide


Download         Length: 873 bp        

>NTDB_id=70523 EP379_RS11055 WP_197722776.1 2181837..2182709(+) (pilD) [Sulfurivermis fontis strain JG42]
ATGAGCGATCCGACGGCACTCATGCTGGCCGATCCGCTGTTCATCACCCTGGTCGCCGCAATATTCGGCCTGGTAATGGG
CAGCTTTCTGAATGTGGTCATCTACCGGCTACCCATCATCATGGAGCGGAACTGGCGGCGTGACTGCGCCGAGCTGGCCG
GCGAGGCGCCTGCGCCTCAGGAGCGTTTCGATCTGGTGATGCCCCGCTCACGTTGTCCGCATTGCGGGCAGATGGTCACG
GCACGCGACAACATTCCTGTGCTCAGTTATCTGTTGCTGCGGGGCCGCTGCCGGGCCTGTGGGGCACGCCTCTCTCTCCG
TTATCCGCTGGTCGAGCTGCTGACCGCTGCGCTGACGGTGGTAACGGCCCTGCATTTTGGCCTGAACATGCAGGGGCTAT
TCGCCGTCCTGCTGACCTGGTCGCTCATCGCCCTCGGCTTCATCGATTTCGACAAGCAGCTGTTGCCCGACAGCATCACC
CTGCCCATGCTCTGGCTGGGTTTGCTGCTCAGCCTGTTTGGCATCTATACCGACAGTCAGGCCAGTATCATTGGTGCCGC
CGCCGGTTATCTGTCGCTCTGGTCCATCTACCATCTGTTCCGTCTGCTCACCGGCAAGGAGGGCATGGGTTATGGCGACT
TCAAGCTGTTCGCCTTGTTCGGTGCCTGGCTCGGCTGGCAAAGCCTGCCACTGATCATCCTGCTATCCTCCGCCGTCGGC
GCCGTACTCGGTCTCACCCTGATCGTCTTCCGCGGCCGCAACCGCCACATCCCCCTTCCCTTCGGTCCCTTTCTGGCCAT
CGCCGGCTGGATTGCCCTGCTCTGGGGTGAACAGTTGAACGCTTGGTACCTGAAAACCGCCCTTCCGGCCTAA

Domains

Predicted by InterproScan.

Bacterial Peptidase A24 N-terminal domain (A24_N_bact)

(21-126)

Type IV leader peptidase family (Peptidase_A24)

(137-245)


Secondary structure

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



3D structure

Source ID Structure

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 campbellii strain DS40M4

56.071

96.552

0.541
  pilD Vibrio cholerae strain A1552

54.317

95.862

0.521
  pilD Acinetobacter baumannii D1279779

49.301

98.621

0.486
  pilD Acinetobacter nosocomialis M2

48.601

98.621

0.479
  pilD Neisseria gonorrhoeae MS11

47.308

89.655

0.424

Multiple sequence alignment