Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilD   Type   Machinery gene
Locus tag   OUY36_RS05065 Genome accession   NZ_CP113258
Coordinates   1086175..1087041 (+) Length   288 a.a.
NCBI ID   WP_267937010.1    Uniprot ID   -
Organism   Stutzerimonas sp. R40042     
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 1080139..1094997 1086175..1087041 within 0


Gene organization within MGE regions


Location: 1080139..1094997
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  OUY36_RS05035 (OUY36_05035) - 1080139..1080975 (-) 837 WP_267937006.1 hypothetical protein -
  OUY36_RS05040 (OUY36_05040) - 1080977..1081786 (-) 810 WP_267937007.1 ABC transporter permease subunit -
  OUY36_RS05045 (OUY36_05045) - 1082207..1082662 (-) 456 WP_267937008.1 hypothetical protein -
  OUY36_RS21985 - 1082692..1082877 (-) 186 WP_272890827.1 prepilin-type N-terminal cleavage/methylation domain-containing protein -
  OUY36_RS05055 (OUY36_05055) pilB 1083245..1084948 (+) 1704 WP_267937009.1 type IV-A pilus assembly ATPase PilB Machinery gene
  OUY36_RS05060 (OUY36_05060) pilC 1084951..1086171 (+) 1221 WP_063544459.1 type II secretion system F family protein Machinery gene
  OUY36_RS05065 (OUY36_05065) pilD 1086175..1087041 (+) 867 WP_267937010.1 A24 family peptidase Machinery gene
  OUY36_RS05070 (OUY36_05070) coaE 1087174..1087782 (+) 609 WP_267937011.1 dephospho-CoA kinase -
  OUY36_RS05075 (OUY36_05075) yacG 1087779..1087976 (+) 198 WP_102840588.1 DNA gyrase inhibitor YacG -
  OUY36_RS05080 (OUY36_05080) - 1088001..1088681 (-) 681 WP_102840589.1 energy-coupling factor ABC transporter permease -
  OUY36_RS05085 (OUY36_05085) - 1088720..1089757 (-) 1038 WP_267937013.1 NADP(H)-dependent aldo-keto reductase -
  OUY36_RS05090 (OUY36_05090) rplM 1090199..1090627 (+) 429 WP_063544471.1 50S ribosomal protein L13 -
  OUY36_RS05095 (OUY36_05095) rpsI 1090642..1091034 (+) 393 WP_013981948.1 30S ribosomal protein S9 -
  OUY36_RS05100 (OUY36_05100) petA 1091289..1091882 (+) 594 WP_156244357.1 ubiquinol-cytochrome c reductase iron-sulfur subunit -
  OUY36_RS05105 (OUY36_05105) - 1091882..1093093 (+) 1212 WP_110777978.1 cytochrome bc complex cytochrome b subunit -
  OUY36_RS05110 (OUY36_05110) - 1093093..1093872 (+) 780 WP_267937018.1 cytochrome c1 -
  OUY36_RS05115 (OUY36_05115) - 1093961..1094578 (+) 618 WP_110777975.1 glutathione S-transferase N-terminal domain-containing protein -
  OUY36_RS05120 (OUY36_05120) - 1094593..1094997 (+) 405 WP_267937020.1 ClpXP protease specificity-enhancing factor -

Sequence

Protein


Download         Length: 288 a.a.        Molecular weight: 32193.30 Da        Isoelectric Point: 7.6233

>NTDB_id=761338 OUY36_RS05065 WP_267937010.1 1086175..1087041(+) (pilD) [Stutzerimonas sp. R40042]
MIYELMASHVLAFVLSAAVLGLLVGSFLNVLIYRLPVMMQREWRVQAREFLELPCEPVGERFNLLLPNSRCPHCAHRIRA
WENVPLISWLLLRGKCSSCQAPISCRYPFVELACGVLSGYVAWHFGFSWQAAMMLLLTWGLLAMSMIDVDHQLLPDSLVL
PLLWLGLIVNHFGLFTSLESALWGAVTGYLSLWSVYWLFKLATGKEGMGYGDFKLLAMLGAWGGWQVLPLTILLSSVVGA
VLGSILLKVQRAESGTPIPFGPYLAIAGWIALLWGDRITESYLQFARF

Nucleotide


Download         Length: 867 bp        

>NTDB_id=761338 OUY36_RS05065 WP_267937010.1 1086175..1087041(+) (pilD) [Stutzerimonas sp. R40042]
ATGATCTACGAACTTATGGCCAGCCATGTGCTGGCCTTTGTTTTGTCTGCAGCAGTGCTCGGTCTGCTGGTTGGCAGTTT
CCTAAACGTCCTCATCTACCGGTTGCCGGTGATGATGCAGCGCGAATGGCGGGTGCAGGCGAGAGAATTTCTTGAGCTGC
CATGCGAACCGGTCGGTGAACGATTCAACCTGTTGCTACCGAATTCACGCTGTCCGCATTGCGCTCATCGAATCCGCGCA
TGGGAAAACGTTCCGCTGATCAGTTGGCTGTTGTTGCGTGGCAAGTGTTCATCCTGCCAGGCGCCGATCAGTTGTCGTTA
CCCGTTCGTGGAGCTGGCATGCGGTGTGCTCTCCGGGTATGTGGCATGGCATTTCGGCTTTTCCTGGCAGGCCGCCATGA
TGCTTTTGCTGACCTGGGGTCTGTTGGCGATGAGCATGATCGATGTCGATCATCAGTTGTTGCCTGACTCGCTCGTACTG
CCCTTGTTGTGGTTGGGGTTGATCGTTAACCACTTCGGCTTGTTCACTTCGCTGGAAAGTGCGCTGTGGGGGGCGGTGAC
GGGTTATCTGAGTCTTTGGTCGGTGTACTGGCTTTTCAAGCTCGCCACCGGCAAAGAGGGCATGGGCTACGGCGATTTCA
AGCTGTTGGCGATGCTTGGGGCCTGGGGTGGCTGGCAGGTATTGCCGCTTACCATCCTGTTGTCGTCAGTGGTCGGAGCG
GTGCTGGGTTCCATTCTTTTGAAGGTTCAGCGTGCAGAAAGCGGCACGCCCATTCCCTTTGGCCCTTATCTGGCGATCGC
TGGGTGGATCGCGCTTCTCTGGGGTGACAGGATCACCGAGAGCTATCTGCAATTCGCCCGCTTCTGA

Domains

Predicted by InterproScan.

Bacterial Peptidase A24 N-terminal domain (A24_N_bact)

(19-125)

Type IV leader peptidase family (Peptidase_A24)

(136-243)


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

54.064

98.264

0.531
  pilD Vibrio campbellii strain DS40M4

54.945

94.792

0.521
  pilD Acinetobacter baumannii D1279779

51.799

96.528

0.5
  pilD Acinetobacter nosocomialis M2

51.799

96.528

0.5
  pilD Neisseria gonorrhoeae MS11

53.992

91.319

0.493