Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilD   Type   Machinery gene
Locus tag   UNDYM_RS04030 Genome accession   NZ_AP018441
Coordinates   877116..877940 (-) Length   274 a.a.
NCBI ID   WP_370529436.1    Uniprot ID   -
Organism   Undibacterium sp. YM2     
Function   assembly of type IV pilus (predicted from homology)   
DNA binding and uptake

Genomic Context

Location: 872116..882940
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  UNDYM_RS04005 (UNDYM_0809) - 873175..873738 (+) 564 WP_162039880.1 hypothetical protein -
  UNDYM_RS04010 (UNDYM_0810) - 873782..875338 (+) 1557 WP_162039881.1 sigma-54-dependent transcriptional regulator -
  UNDYM_RS04015 (UNDYM_0811) - 875369..875548 (-) 180 WP_162039882.1 DNA gyrase inhibitor YacG -
  UNDYM_RS04020 (UNDYM_0812) zapD 875551..876306 (-) 756 WP_162039883.1 cell division protein ZapD -
  UNDYM_RS04025 coaE 876481..877107 (-) 627 WP_162044436.1 dephospho-CoA kinase -
  UNDYM_RS04030 (UNDYM_0813) pilD 877116..877940 (-) 825 WP_370529436.1 A24 family peptidase Machinery gene
  UNDYM_RS04035 (UNDYM_0814) pilC 877976..879211 (-) 1236 WP_162039885.1 type II secretion system F family protein Machinery gene
  UNDYM_RS04040 (UNDYM_0815) pilF 879227..880954 (-) 1728 WP_162039886.1 type IV-A pilus assembly ATPase PilB Machinery gene
  UNDYM_RS04045 (UNDYM_0816) ispB 881279..882208 (-) 930 WP_162044437.1 octaprenyl diphosphate synthase -
  UNDYM_RS04050 (UNDYM_0817) rplU 882523..882834 (+) 312 WP_162020347.1 50S ribosomal protein L21 -

Sequence

Protein


Download         Length: 274 a.a.        Molecular weight: 30265.05 Da        Isoelectric Point: 7.7381

>NTDB_id=69624 UNDYM_RS04030 WP_370529436.1 877116..877940(-) (pilD) [Undibacterium sp. YM2]
MSTIAFGLLGLLIGSFLNVVIYRLPKMYLREVDNFVAEQRQEPLPHQDRFDLMLPRSACPHCGHKITELENIPIISYLVI
GGKCTGCKAKISVRYPLIEALTGLLTAGMIWHFGSGVVGMSAVVFVWFLIAMTFIDIDHKLLLDDLTLSLMWLGLLLNAY
GGFATLKDAVLGAAIGYMSLWSINWIYEKLRGRPGFGYGDLKLLAAFGAWMGWSMLPVIVLLSTLVGSVIGIGQIISKKF
GWETEIPFGPYLTGAGLIALIWGRQIVDFYLSTL

Nucleotide


Download         Length: 825 bp        

>NTDB_id=69624 UNDYM_RS04030 WP_370529436.1 877116..877940(-) (pilD) [Undibacterium sp. YM2]
TTGTCCACAATAGCCTTCGGGCTATTGGGGCTACTGATAGGCAGTTTTTTGAACGTGGTGATTTATCGCCTGCCTAAAAT
GTATCTGCGTGAAGTGGATAATTTTGTCGCAGAGCAAAGGCAGGAGCCATTGCCGCACCAGGACAGGTTTGACCTGATGC
TGCCTCGATCTGCCTGCCCGCATTGCGGGCACAAGATCACTGAACTGGAAAATATACCCATCATCAGCTACCTCGTCATT
GGTGGCAAATGCACGGGCTGCAAAGCCAAAATTTCCGTACGCTATCCATTGATAGAAGCCCTGACGGGCCTGCTCACTGC
TGGCATGATCTGGCATTTTGGCAGCGGCGTGGTGGGCATGAGTGCGGTGGTCTTTGTCTGGTTTCTGATCGCCATGACCT
TCATCGACATAGACCATAAATTGCTGCTGGATGACCTGACCCTGAGTTTGATGTGGCTGGGCCTGCTGCTGAATGCCTAC
GGCGGCTTCGCCACTTTGAAAGACGCAGTACTGGGAGCCGCCATCGGCTACATGTCACTATGGTCAATCAACTGGATTTA
TGAAAAACTGCGTGGCAGACCTGGCTTTGGCTACGGTGATCTCAAGTTACTGGCAGCCTTTGGGGCCTGGATGGGCTGGA
GCATGTTGCCAGTTATTGTTTTATTATCGACCCTGGTAGGCTCGGTCATAGGTATAGGACAAATTATCTCCAAGAAATTT
GGCTGGGAAACAGAAATACCCTTTGGACCCTACCTGACTGGCGCAGGTTTGATAGCACTGATCTGGGGCCGACAAATTGT
CGATTTCTATCTGAGCACCTTGTGA

Domains

Predicted by InterproScan.

Type IV leader peptidase family (Peptidase_A24)

(124-232)

Bacterial Peptidase A24 N-terminal domain (A24_N_bact)

(8-113)


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

51.111

98.54

0.504
  pilD Vibrio campbellii strain DS40M4

47.059

99.27

0.467
  pilD Neisseria gonorrhoeae MS11

47.244

92.701

0.438
  pilD Acinetobacter baumannii D1279779

44.444

98.54

0.438
  pilD Acinetobacter nosocomialis M2

43.704

98.54

0.431

Multiple sequence alignment