Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilD   Type   Machinery gene
Locus tag   AXG53_RS04885 Genome accession   NZ_CP014274
Coordinates   1139016..1139882 (+) Length   288 a.a.
NCBI ID   WP_062166723.1    Uniprot ID   A0A126NKI7
Organism   Stenotrophomonas sp. KCTC 12332 strain YM1     
Function   assembly of type IV pilus (predicted from homology)   
DNA binding and uptake

Genomic Context

Location: 1134016..1144882
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  AXG53_RS04870 (AXG53_04870) pilB 1134241..1135971 (-) 1731 WP_062166720.1 type IV-A pilus assembly ATPase PilB Machinery gene
  AXG53_RS04875 (AXG53_04875) pilA/pilAI 1136806..1137219 (-) 414 WP_062166721.1 pilin Machinery gene
  AXG53_RS04880 (AXG53_04880) pilC 1137756..1139012 (+) 1257 WP_062166722.1 type II secretion system F family protein Machinery gene
  AXG53_RS04885 (AXG53_04885) pilD 1139016..1139882 (+) 867 WP_062166723.1 A24 family peptidase Machinery gene
  AXG53_RS04890 (AXG53_04890) coaE 1139938..1140555 (+) 618 WP_062166724.1 dephospho-CoA kinase -
  AXG53_RS04895 (AXG53_04895) - 1140718..1142058 (-) 1341 WP_062166725.1 HAMP domain-containing sensor histidine kinase -
  AXG53_RS04900 (AXG53_04900) - 1142051..1142728 (-) 678 WP_057629745.1 response regulator transcription factor -
  AXG53_RS04905 (AXG53_04905) rimK 1143091..1143966 (-) 876 WP_062166726.1 30S ribosomal protein S6--L-glutamate ligase -

Sequence

Protein


Download         Length: 288 a.a.        Molecular weight: 32034.06 Da        Isoelectric Point: 8.2359

>NTDB_id=170137 AXG53_RS04885 WP_062166723.1 1139016..1139882(+) (pilD) [Stenotrophomonas sp. KCTC 12332 strain YM1]
MAFLDQHPGLGYPAAAGLGLLIGSFLNVVILRLPKRMEWQWKRDAREILEEPDIYEPPPPGIVVEPSHCPHCKHKLSWYE
NIPLFSWLFLRGKCRHCQASISIQYPIVELVTSLMVLASVWQFGFGWQGFGAIVLSCFLVALSGIDLRTQLLPDQLTLPL
MWLGLIGSMDNLYMPAKPALIGAAVGYLSLWTVWWLFKQITGKEGMGHGDFKLLAALGAWCGLKGILPIILLSSLVGAII
GSIWLYSRGRDRATPIPFGPYLAIAGWLVFMWGDQMIGGYMRLAGLQQ

Nucleotide


Download         Length: 867 bp        

>NTDB_id=170137 AXG53_RS04885 WP_062166723.1 1139016..1139882(+) (pilD) [Stenotrophomonas sp. KCTC 12332 strain YM1]
ATGGCATTTCTCGACCAGCATCCCGGTCTCGGCTATCCCGCCGCGGCCGGACTGGGACTGCTGATCGGCAGCTTCCTCAA
CGTGGTGATCCTGCGCTTGCCCAAGCGCATGGAGTGGCAGTGGAAGCGCGATGCGCGCGAAATCCTCGAAGAGCCCGATA
TCTATGAGCCGCCGCCGCCGGGCATCGTGGTGGAGCCTTCGCACTGCCCGCACTGCAAGCACAAGCTGAGCTGGTACGAG
AACATTCCGCTGTTCAGCTGGCTGTTCCTGCGTGGCAAGTGCCGCCATTGCCAAGCTTCGATCTCCATCCAGTACCCAAT
CGTGGAACTGGTCACCAGCCTGATGGTGCTGGCCAGCGTCTGGCAATTCGGCTTCGGCTGGCAGGGCTTTGGCGCCATCG
TGCTGAGCTGCTTCCTGGTTGCGCTGTCCGGCATCGACCTGCGCACCCAGCTGCTGCCCGACCAGCTCACCCTGCCACTG
ATGTGGCTGGGCCTGATAGGCAGCATGGACAATCTCTACATGCCGGCCAAGCCGGCGCTGATTGGTGCCGCCGTCGGCTA
CCTGTCGCTATGGACGGTGTGGTGGCTGTTCAAGCAGATCACCGGCAAGGAAGGCATGGGCCACGGCGACTTCAAGTTGC
TGGCCGCGTTGGGTGCTTGGTGCGGACTGAAGGGCATCCTGCCGATCATCCTGCTGTCCTCCCTGGTCGGCGCCATCATC
GGCTCGATCTGGCTGTACTCGCGCGGGCGCGACCGCGCCACGCCGATTCCATTCGGTCCGTACCTGGCTATCGCCGGCTG
GCTGGTCTTCATGTGGGGCGACCAGATGATAGGCGGCTACATGCGATTGGCAGGGCTACAGCAATAA

Domains

Predicted by InterproScan.

Bacterial Peptidase A24 N-terminal domain (A24_N_bact)

(18-123)

Type IV leader peptidase family (Peptidase_A24)

(133-241)


Secondary structure

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



3D structure

Source ID Structure
  AlphaFold DB A0A126NKI7

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 Acinetobacter baumannii D1279779

50

97.917

0.49
  pilD Acinetobacter nosocomialis M2

50

97.917

0.49
  pilD Vibrio cholerae strain A1552

49.275

95.833

0.472
  pilD Vibrio campbellii strain DS40M4

47.183

98.611

0.465
  pilD Neisseria gonorrhoeae MS11

43.682

96.181

0.42

Multiple sequence alignment