Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilD   Type   Machinery gene
Locus tag   ABNK63_RS04380 Genome accession   NZ_CP157948
Coordinates   1006080..1006937 (-) Length   285 a.a.
NCBI ID   WP_007809538.1    Uniprot ID   I4VV21
Organism   Rhodanobacter sp. IGA1.0     
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)
Genomic island 1006953..1031066 1006080..1006937 flank 16


Gene organization within MGE regions


Location: 1006080..1031066
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  ABNK63_RS04380 (ABNK63_04375) pilD 1006080..1006937 (-) 858 WP_007809538.1 A24 family peptidase Machinery gene
  ABNK63_RS04385 (ABNK63_04380) - 1006953..1007345 (-) 393 WP_007809537.1 endonuclease domain-containing protein -
  ABNK63_RS04390 (ABNK63_04385) pilC 1007402..1008673 (-) 1272 WP_007809536.1 type II secretion system F family protein Machinery gene
  ABNK63_RS04395 (ABNK63_04390) pilB 1008816..1010540 (-) 1725 WP_350016799.1 type IV-A pilus assembly ATPase PilB Machinery gene
  ABNK63_RS04400 (ABNK63_04395) - 1010888..1011130 (+) 243 WP_007809534.1 AbrB/MazE/SpoVT family DNA-binding domain-containing protein -
  ABNK63_RS04405 (ABNK63_04400) - 1011127..1011522 (+) 396 WP_007809533.1 type II toxin-antitoxin system VapC family toxin -
  ABNK63_RS04410 (ABNK63_04405) - 1011854..1012708 (+) 855 WP_350016800.1 glycosyltransferase family 2 protein -
  ABNK63_RS04415 (ABNK63_04410) - 1012701..1013927 (+) 1227 WP_350016801.1 glycosyltransferase -
  ABNK63_RS04420 (ABNK63_04415) - 1014119..1014817 (+) 699 WP_350016802.1 class I SAM-dependent methyltransferase -
  ABNK63_RS04425 (ABNK63_04420) - 1014954..1015883 (-) 930 WP_350016803.1 glycosyltransferase -
  ABNK63_RS04430 (ABNK63_04425) - 1015889..1017034 (-) 1146 WP_350016804.1 glycosyltransferase family 4 protein -
  ABNK63_RS04435 (ABNK63_04430) asnB 1017034..1018971 (-) 1938 WP_350016805.1 asparagine synthase (glutamine-hydrolyzing) -
  ABNK63_RS04440 (ABNK63_04435) - 1018974..1020071 (-) 1098 WP_350016806.1 glycosyltransferase -
  ABNK63_RS04445 (ABNK63_04440) - 1020068..1020874 (-) 807 WP_350016807.1 methyltransferase domain-containing protein -
  ABNK63_RS04450 (ABNK63_04445) - 1020864..1022024 (-) 1161 WP_350016808.1 oligosaccharide flippase family protein -
  ABNK63_RS04455 (ABNK63_04450) - 1022311..1024419 (-) 2109 WP_350016809.1 hypothetical protein -
  ABNK63_RS04460 (ABNK63_04455) - 1024652..1026607 (-) 1956 WP_350016810.1 hypothetical protein -
  ABNK63_RS04465 (ABNK63_04460) pilA 1026708..1027133 (-) 426 WP_350016811.1 pilin Machinery gene
  ABNK63_RS04470 (ABNK63_04465) - 1027578..1028006 (-) 429 WP_350016812.1 pilin -
  ABNK63_RS04475 (ABNK63_04470) - 1028205..1030337 (+) 2133 WP_350016813.1 S9 family peptidase -
  ABNK63_RS04480 (ABNK63_04475) - 1030776..1031066 (+) 291 WP_350016814.1 nucleotidyltransferase domain-containing protein -

Sequence

Protein


Download         Length: 285 a.a.        Molecular weight: 30988.14 Da        Isoelectric Point: 8.1484

>NTDB_id=1009309 ABNK63_RS04380 WP_007809538.1 1006080..1006937(-) (pilD) [Rhodanobacter sp. IGA1.0]
MPDLPFALWIALAAVLGLLVGSFLNVVILRLPERMAAAWRHEARDVLKIEGDAEPMPPGIVREPSHCPHCKHPLSALDNI
PLFGWLLLRGRCRYCQTKISIQYPLVELLSGILSAVIVWKFGPSWAALAGLGFTWVLIAAAGIDFRTQLLPDQLTLPLLW
LGLLLSLLPMFVSAPSAILAAAIGYLSLWSVYWGFKLLTGKEGMGYGDFKLLAALGAWMGPVALLPIVLLSSLIGALVGG
SLIALRKHEREIPMPFGPFIAAAGWVWFVAGPDLLDGYLHLTGMR

Nucleotide


Download         Length: 858 bp        

>NTDB_id=1009309 ABNK63_RS04380 WP_007809538.1 1006080..1006937(-) (pilD) [Rhodanobacter sp. IGA1.0]
ATGCCCGATCTTCCGTTCGCCCTCTGGATTGCCCTGGCCGCCGTGCTCGGCCTGCTGGTGGGCAGCTTTCTCAACGTGGT
GATCCTGCGCCTGCCCGAGCGCATGGCTGCGGCCTGGCGCCACGAAGCCCGTGACGTGCTGAAGATCGAGGGCGACGCCG
AACCCATGCCCCCGGGCATCGTGCGCGAGCCGTCACACTGCCCGCACTGCAAGCATCCGCTGTCGGCGCTGGACAACATC
CCGCTGTTCGGCTGGCTGCTGCTGCGCGGACGCTGCCGCTATTGCCAGACGAAAATCTCGATCCAGTACCCGCTGGTGGA
ATTGCTCAGCGGCATCCTGAGCGCGGTGATCGTGTGGAAGTTCGGGCCCTCGTGGGCCGCGCTGGCGGGACTGGGGTTCA
CCTGGGTCTTGATCGCGGCAGCCGGCATCGACTTCCGCACTCAATTGCTGCCCGATCAGCTGACCTTGCCGCTGTTGTGG
CTTGGTCTGTTGCTGTCGTTGCTGCCGATGTTCGTCAGCGCACCCAGCGCGATTCTTGCCGCGGCGATCGGCTACCTCAG
CCTGTGGAGCGTGTACTGGGGATTCAAGCTGCTGACCGGCAAGGAAGGCATGGGTTACGGCGATTTCAAGCTGTTGGCGG
CCCTGGGCGCGTGGATGGGCCCGGTCGCGCTGCTGCCGATCGTGCTGCTGTCCTCGCTGATCGGCGCGCTGGTGGGCGGC
AGCCTGATCGCACTGCGCAAGCATGAGCGCGAGATCCCGATGCCGTTCGGCCCGTTCATCGCTGCCGCGGGCTGGGTCTG
GTTCGTGGCCGGCCCGGATCTGCTGGACGGCTATCTGCATCTGACCGGCATGCGATGA

Domains

Predicted by InterproScan.

Type IV leader peptidase family (Peptidase_A24)

(133-239)

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
  AlphaFold DB I4VV21

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

53.676

95.439

0.512
  pilD Acinetobacter nosocomialis M2

52.174

96.842

0.505
  pilD Acinetobacter baumannii D1279779

51.812

96.842

0.502
  pilD Vibrio campbellii strain DS40M4

50.362

96.842

0.488
  pilD Neisseria gonorrhoeae MS11

48.746

97.895

0.477

Multiple sequence alignment