Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilD   Type   Machinery gene
Locus tag   ABFG87_RS20005 Genome accession   NZ_CP156074
Coordinates   4321052..4321924 (+) Length   290 a.a.
NCBI ID   WP_308418438.1    Uniprot ID   -
Organism   Chitiniphilus eburneus strain YS-30     
Function   type IV pilus biogenesis and function (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)
ICE 4309597..4327758 4321052..4321924 within 0


Gene organization within MGE regions


Location: 4309597..4327758
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  ABFG87_RS19950 - 4311109..4311951 (-) 843 WP_136773661.1 mechanosensitive ion channel family protein -
  ABFG87_RS19955 xerD 4312023..4312931 (-) 909 WP_136773660.1 site-specific tyrosine recombinase XerD -
  ABFG87_RS19960 - 4312928..4313422 (-) 495 WP_246038617.1 methylated-DNA--[protein]-cysteine S-methyltransferase -
  ABFG87_RS19965 rplS 4313508..4313888 (-) 381 WP_136773659.1 50S ribosomal protein L19 -
  ABFG87_RS19970 trmD 4313894..4314709 (-) 816 WP_373279535.1 tRNA (guanosine(37)-N1)-methyltransferase TrmD -
  ABFG87_RS19975 rimM 4314709..4315191 (-) 483 WP_136773675.1 ribosome maturation factor RimM -
  ABFG87_RS19980 rpsP 4315258..4315506 (-) 249 WP_136773658.1 30S ribosomal protein S16 -
  ABFG87_RS19985 ffh 4315611..4316960 (-) 1350 WP_136773657.1 signal recognition particle protein -
  ABFG87_RS19990 - 4317044..4317847 (+) 804 WP_169307375.1 inner membrane protein YpjD -
  ABFG87_RS19995 pilB 4318097..4319803 (+) 1707 WP_136773655.1 type IV-A pilus assembly ATPase PilB Machinery gene
  ABFG87_RS20000 pilC 4319820..4321055 (+) 1236 WP_136773654.1 type II secretion system F family protein Machinery gene
  ABFG87_RS20005 pilD 4321052..4321924 (+) 873 WP_308418438.1 A24 family peptidase Machinery gene
  ABFG87_RS20010 coaE 4321932..4322537 (+) 606 WP_136773653.1 dephospho-CoA kinase -
  ABFG87_RS20015 zapD 4322614..4323372 (+) 759 WP_136773652.1 cell division protein ZapD -
  ABFG87_RS20020 - 4323369..4323551 (+) 183 WP_211243442.1 DNA gyrase inhibitor YacG -
  ABFG87_RS20025 - 4323712..4324461 (+) 750 WP_136773650.1 GNAT family N-acetyltransferase -
  ABFG87_RS20030 - 4324655..4325335 (+) 681 WP_375591878.1 lysophospholipid acyltransferase family protein -
  ABFG87_RS20035 - 4325314..4326138 (-) 825 WP_136773648.1 symmetrical bis(5'-nucleosyl)-tetraphosphatase -
  ABFG87_RS20040 - 4326186..4327070 (+) 885 WP_136773647.1 HDOD domain-containing protein -
  ABFG87_RS20045 rplQ 4327147..4327539 (-) 393 WP_136773646.1 50S ribosomal protein L17 -

Sequence

Protein


Download         Length: 290 a.a.        Molecular weight: 31703.92 Da        Isoelectric Point: 8.4719

>NTDB_id=1001648 ABFG87_RS20005 WP_308418438.1 4321052..4321924(+) (pilD) [Chitiniphilus eburneus strain YS-30]
MMPFWQLLGENPLFYSGFLFVLGLLIGSFLNVVIHRLPKMIEAEFRHECNTLDLPSEAPLPAKPAYNLMVPRSACPQCGR
PISALENIPVLSYLALRGRCRGCGARISIRYPAVELICAVLTAAVGWHLGLTLPGLGAVALTWALIALFFIDADTYLLPD
SITLPLLWLGMLVNLAGGLVPLQDAVLGAVFGYLSLWSIYWLFKLATGKEGMGYGDFKLLAALGAWFGWQALPLIILLSS
VAGALIGIVLAWSARRGFSKPMPFGPYLAVAGWLTLIWGPQLQRLIFPHW

Nucleotide


Download         Length: 873 bp        

>NTDB_id=1001648 ABFG87_RS20005 WP_308418438.1 4321052..4321924(+) (pilD) [Chitiniphilus eburneus strain YS-30]
ATGATGCCATTCTGGCAATTGCTGGGTGAAAACCCGCTGTTCTACAGCGGGTTTTTATTCGTACTGGGCTTGCTCATCGG
CAGCTTTCTCAATGTGGTCATTCATCGTCTGCCCAAGATGATCGAAGCCGAATTCCGCCACGAATGCAACACGCTGGATT
TGCCCAGCGAGGCGCCGCTACCCGCCAAGCCCGCCTACAACCTGATGGTTCCACGGTCAGCCTGCCCACAATGCGGCAGG
CCGATCAGCGCCCTGGAGAACATCCCCGTACTCAGTTACCTCGCGCTGCGGGGACGCTGCCGTGGATGTGGCGCACGCAT
CAGTATTCGCTATCCCGCGGTAGAGTTGATCTGCGCCGTACTGACAGCCGCGGTCGGCTGGCATCTCGGCCTTACCCTGC
CCGGCCTGGGGGCGGTCGCGTTGACCTGGGCGCTTATCGCCCTCTTCTTCATTGACGCCGATACGTACCTGCTTCCCGAT
TCGATTACCTTGCCCTTGTTATGGCTGGGGATGCTGGTCAATCTGGCCGGTGGTCTGGTGCCGTTGCAGGATGCCGTTCT
GGGTGCCGTGTTCGGCTATCTGTCGCTCTGGAGCATTTATTGGCTCTTCAAGCTCGCGACAGGAAAGGAGGGAATGGGTT
ATGGCGACTTCAAGCTGCTGGCGGCGCTGGGGGCCTGGTTTGGCTGGCAGGCTTTACCCCTGATCATCCTGCTGTCATCG
GTTGCCGGTGCCCTGATCGGCATTGTGCTGGCCTGGAGCGCGCGCAGGGGCTTCTCCAAGCCCATGCCCTTCGGCCCCTA
TCTGGCGGTGGCCGGCTGGTTGACCTTGATCTGGGGGCCGCAATTGCAGCGGCTAATTTTCCCGCATTGGTAA

Domains

Predicted by InterproScan.

Type IV leader peptidase family (Peptidase_A24)

(140-248)

Bacterial Peptidase A24 N-terminal domain (A24_N_bact)

(21-128)


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 campbellii strain DS40M4

54.044

93.793

0.507
  pilD Vibrio cholerae strain A1552

52.768

93.448

0.493
  pilD Neisseria gonorrhoeae MS11

51.301

92.759

0.476
  pilD Acinetobacter baumannii D1279779

50.566

91.379

0.462
  pilD Acinetobacter nosocomialis M2

49.811

91.379

0.455

Multiple sequence alignment