Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilD   Type   Machinery gene
Locus tag   ACFYG5_RS11280 Genome accession   NZ_CP170721
Coordinates   2376013..2376870 (+) Length   285 a.a.
NCBI ID   WP_395117089.1    Uniprot ID   A0AB74ULG0
Organism   Rhodanobacter sp. FW102-FHT14D07     
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 2355745..2379291 2376013..2376870 within 0


Gene organization within MGE regions


Location: 2355745..2379291
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  ACFYG5_RS11190 (ACFYG5_11190) - 2355745..2357508 (+) 1764 WP_395117124.1 tetratricopeptide repeat protein -
  ACFYG5_RS11195 (ACFYG5_11195) - 2357505..2359502 (+) 1998 WP_395117122.1 hypothetical protein -
  ACFYG5_RS11200 (ACFYG5_11200) - 2359538..2360659 (+) 1122 WP_395117120.1 glycosyltransferase family 4 protein -
  ACFYG5_RS11205 (ACFYG5_11205) - 2360652..2361578 (+) 927 WP_395117118.1 NAD-dependent epimerase/dehydratase family protein -
  ACFYG5_RS11210 (ACFYG5_11210) - 2361548..2362594 (+) 1047 WP_395117116.1 glycosyltransferase family 2 protein -
  ACFYG5_RS11215 (ACFYG5_11215) - 2362680..2363834 (-) 1155 WP_395117114.1 glycoside hydrolase family 99-like domain-containing protein -
  ACFYG5_RS11220 (ACFYG5_11220) - 2363834..2365087 (-) 1254 WP_395117112.1 class I SAM-dependent methyltransferase -
  ACFYG5_RS11225 (ACFYG5_11225) - 2365084..2366043 (-) 960 WP_395117110.1 GDP-mannose 4,6-dehydratase -
  ACFYG5_RS11230 (ACFYG5_11230) - 2366043..2367068 (-) 1026 WP_395117109.1 glycosyltransferase family 2 protein -
  ACFYG5_RS11235 (ACFYG5_11235) - 2367068..2367919 (-) 852 WP_395117107.1 hypothetical protein -
  ACFYG5_RS11240 (ACFYG5_11240) - 2367938..2369446 (-) 1509 WP_395117105.1 lipopolysaccharide biosynthesis protein -
  ACFYG5_RS11245 (ACFYG5_11245) gmd 2369451..2370545 (-) 1095 WP_395117103.1 GDP-mannose 4,6-dehydratase -
  ACFYG5_RS11250 (ACFYG5_11250) - 2370589..2371446 (-) 858 WP_395117101.1 glycosyltransferase family 2 protein -
  ACFYG5_RS11255 (ACFYG5_11255) - 2371515..2371910 (-) 396 WP_395117099.1 PIN domain-containing protein -
  ACFYG5_RS11260 (ACFYG5_11260) - 2371907..2372146 (-) 240 WP_395117097.1 AbrB/MazE/SpoVT family DNA-binding domain-containing protein -
  ACFYG5_RS11265 (ACFYG5_11265) pilB 2372392..2374113 (+) 1722 WP_395117095.1 type IV-A pilus assembly ATPase PilB Machinery gene
  ACFYG5_RS11270 (ACFYG5_11270) pilC 2374255..2375523 (+) 1269 WP_395135987.1 type II secretion system F family protein Machinery gene
  ACFYG5_RS11275 (ACFYG5_11275) - 2375610..2376002 (+) 393 WP_395117091.1 endonuclease domain-containing protein -
  ACFYG5_RS11280 (ACFYG5_11280) pilD 2376013..2376870 (+) 858 WP_395117089.1 prepilin peptidase Machinery gene
  ACFYG5_RS11285 (ACFYG5_11285) coaE 2376867..2377478 (+) 612 WP_395117087.1 dephospho-CoA kinase -
  ACFYG5_RS11290 (ACFYG5_11290) - 2377498..2377896 (-) 399 WP_395117085.1 NUDIX domain-containing protein -
  ACFYG5_RS11295 (ACFYG5_11295) - 2377896..2378384 (-) 489 WP_395117083.1 dihydrofolate reductase -
  ACFYG5_RS11300 (ACFYG5_11300) - 2378476..2379291 (-) 816 WP_395117081.1 thymidylate synthase -

Sequence

Protein


Download         Length: 285 a.a.        Molecular weight: 31000.16 Da        Isoelectric Point: 9.5080

>NTDB_id=1058864 ACFYG5_RS11280 WP_395117089.1 2376013..2376870(+) (pilD) [Rhodanobacter sp. FW102-FHT14D07]
MPELPLSVWIALAAVLGLLVGSFLNVVILRLPERMTASWRREAREVLELPADDAPLPPGIVREPSHCPHCKHPLSAADNI
PLFGWLLLRGRCRYCKAKISIQYPLVELFSGVLSALVVWKFGPSWTALAGLVFTWVLIAAAGIDFRTQLLPDQLTLPLLW
LGMVLSLIPLFASAPSAIIGAAIGYLSLWSVYWAFKLLTGKEGMGHGDFKLLAALGAWMGPVALLPVILLSSLIGALVGG
SLIALRRHGREIPMPFGPFLAAAGWVWFMAGPQLLQGYMHFTGLR

Nucleotide


Download         Length: 858 bp        

>NTDB_id=1058864 ACFYG5_RS11280 WP_395117089.1 2376013..2376870(+) (pilD) [Rhodanobacter sp. FW102-FHT14D07]
ATGCCCGAACTTCCGCTGTCCGTCTGGATCGCCCTCGCCGCCGTGCTCGGCCTGCTGGTGGGCAGTTTCCTCAACGTGGT
GATCCTGCGCCTGCCCGAGCGCATGACCGCAAGCTGGCGCCGGGAGGCGCGCGAGGTGCTGGAGTTGCCGGCGGATGACG
CGCCGCTGCCGCCGGGTATCGTGCGCGAGCCTTCGCACTGCCCGCATTGCAAGCATCCGTTGTCGGCGGCCGACAACATT
CCGCTGTTCGGCTGGCTGCTGCTGCGCGGACGCTGCCGCTATTGCAAGGCGAAGATCTCGATCCAGTATCCGCTGGTGGA
ACTGTTCAGCGGCGTGCTGAGCGCGCTGGTGGTCTGGAAATTCGGACCGTCCTGGACCGCGCTGGCAGGATTGGTGTTCA
CTTGGGTGCTGATCGCCGCGGCCGGCATCGACTTCCGCACGCAGTTGCTGCCGGACCAGTTGACCCTGCCGCTGCTGTGG
CTGGGCATGGTGCTGTCGCTGATCCCGCTGTTCGCCAGCGCGCCTTCGGCGATCATCGGTGCGGCGATCGGCTACCTGAG
CCTGTGGAGCGTCTACTGGGCGTTCAAGCTGCTCACCGGCAAGGAAGGCATGGGCCACGGCGACTTCAAGTTGCTGGCGG
CGCTGGGCGCGTGGATGGGGCCGGTGGCCCTGCTGCCGGTGATCCTGCTGTCGTCGCTGATCGGCGCCCTGGTGGGCGGC
AGCCTGATCGCGTTGCGCAGGCACGGGCGCGAGATCCCGATGCCGTTCGGACCGTTCCTGGCCGCCGCCGGCTGGGTGTG
GTTCATGGCCGGTCCCCAGTTGCTGCAGGGCTACATGCACTTCACCGGCCTGCGATGA

Domains

Predicted by InterproScan.

Type IV leader peptidase family (Peptidase_A24)

(131-239)

Bacterial Peptidase A24 N-terminal domain (A24_N_bact)

(15-121)


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 cholerae strain A1552

51.825

96.14

0.498
  pilD Vibrio campbellii strain DS40M4

50

96.14

0.481
  pilD Acinetobacter nosocomialis M2

49.818

96.491

0.481
  pilD Acinetobacter baumannii D1279779

49.455

96.491

0.477
  pilD Neisseria gonorrhoeae MS11

49.624

93.333

0.463

Multiple sequence alignment