Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilD   Type   Machinery gene
Locus tag   LTQ54_RS11440 Genome accession   NZ_CP089203
Coordinates   2459691..2460560 (-) Length   289 a.a.
NCBI ID   WP_004735439.1    Uniprot ID   -
Organism   Vibrio splendidus strain 2_C04b     
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)
Genomic island 2455939..2473350 2459691..2460560 within 0


Gene organization within MGE regions


Location: 2455939..2473350
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  LTQ54_RS11410 (LTQ54_11410) rimM 2455939..2456493 (+) 555 WP_004735510.1 ribosome maturation factor RimM -
  LTQ54_RS11415 (LTQ54_11415) trmD 2456520..2457260 (+) 741 WP_004735512.1 tRNA (guanosine(37)-N1)-methyltransferase TrmD -
  LTQ54_RS11420 (LTQ54_11420) rplS 2457320..2457673 (+) 354 WP_004735514.1 50S ribosomal protein L19 -
  LTQ54_RS11425 (LTQ54_11425) yacG 2458028..2458225 (-) 198 WP_004735515.1 DNA gyrase inhibitor YacG -
  LTQ54_RS11430 (LTQ54_11430) zapD 2458307..2459047 (-) 741 WP_017087400.1 cell division protein ZapD -
  LTQ54_RS11435 (LTQ54_11435) coaE 2459074..2459688 (-) 615 WP_017088713.1 dephospho-CoA kinase -
  LTQ54_RS11440 (LTQ54_11440) pilD 2459691..2460560 (-) 870 WP_004735439.1 A24 family peptidase Machinery gene
  LTQ54_RS11445 (LTQ54_11445) pilC 2460628..2461857 (-) 1230 WP_243578787.1 type II secretion system F family protein Machinery gene
  LTQ54_RS11450 (LTQ54_11450) pilB 2461872..2463557 (-) 1686 WP_243578788.1 type IV-A pilus assembly ATPase PilB Machinery gene
  LTQ54_RS11455 (LTQ54_11455) pilA 2463557..2463985 (-) 429 WP_243578789.1 pilin Machinery gene
  LTQ54_RS11460 (LTQ54_11460) nadC 2464241..2465131 (-) 891 WP_017079961.1 carboxylating nicotinate-nucleotide diphosphorylase -
  LTQ54_RS11465 (LTQ54_11465) ampD 2465215..2465814 (+) 600 WP_054541864.1 1,6-anhydro-N-acetylmuramyl-L-alanine amidase AmpD -
  LTQ54_RS11470 (LTQ54_11470) pdhR 2466295..2467056 (+) 762 WP_004735446.1 pyruvate dehydrogenase complex transcriptional repressor PdhR -
  LTQ54_RS11475 (LTQ54_11475) aceE 2467119..2469782 (+) 2664 WP_004735447.1 pyruvate dehydrogenase (acetyl-transferring), homodimeric type -
  LTQ54_RS11480 (LTQ54_11480) aceF 2469809..2471680 (+) 1872 WP_243578790.1 pyruvate dehydrogenase complex dihydrolipoyllysine-residue acetyltransferase -
  LTQ54_RS11485 (LTQ54_11485) lpdA 2471923..2473350 (+) 1428 WP_004735450.1 dihydrolipoyl dehydrogenase -

Sequence

Protein


Download         Length: 289 a.a.        Molecular weight: 32585.83 Da        Isoelectric Point: 7.6347

>NTDB_id=635714 LTQ54_RS11440 WP_004735439.1 2459691..2460560(-) (pilD) [Vibrio splendidus strain 2_C04b]
MEVFHYYPWLFPVLAFIFSLLIGSFLNVVIHRLPIMMEREWQQECSEYFSQYKIPAPEGKFNLSIPRSTCPKCKTQLRII
DNIPVLSWLFLKGKCHSCANPISARYPLVELLTAILCTVVASHFGFSYYAIALIFFTFALITATFIDLDTMLLPDQITLP
LVWSGIALALFNISPVSLQDSVIGAMAGYLALWSVYWLFKLLTGKEGMGYGDFKLLAALGAWLGWQHLPMIILLSSLVGL
VFGLIQLRLKQQGIDKAFPFGPYLAIAGWVSLMWGNDIMGWYFTSVLGI

Nucleotide


Download         Length: 870 bp        

>NTDB_id=635714 LTQ54_RS11440 WP_004735439.1 2459691..2460560(-) (pilD) [Vibrio splendidus strain 2_C04b]
ATGGAAGTATTTCACTACTATCCTTGGCTATTCCCCGTATTAGCTTTCATTTTTAGCCTTCTTATCGGCAGCTTCCTCAA
CGTAGTCATACACCGTTTACCGATAATGATGGAACGAGAGTGGCAACAAGAGTGCTCGGAGTATTTCTCTCAATATAAAA
TTCCAGCACCAGAGGGAAAGTTCAATCTCAGTATCCCTCGTTCTACCTGCCCGAAATGTAAAACCCAATTAAGAATCATC
GACAATATTCCAGTATTAAGTTGGTTGTTCTTAAAGGGCAAGTGCCATAGCTGTGCTAACCCAATCAGCGCTCGTTACCC
ATTGGTCGAGTTACTTACGGCAATACTTTGTACCGTAGTCGCGAGCCACTTTGGTTTCAGTTACTACGCCATTGCTTTGA
TTTTTTTCACGTTTGCATTGATTACCGCAACCTTTATCGATCTCGATACTATGCTGTTGCCTGATCAAATTACCTTGCCT
TTAGTTTGGTCTGGTATCGCGTTAGCTCTGTTTAATATCAGCCCTGTATCGCTTCAAGATTCAGTGATTGGCGCAATGGC
AGGCTACCTAGCACTTTGGTCGGTTTATTGGCTGTTCAAGCTGTTAACAGGCAAAGAAGGCATGGGTTACGGCGACTTCA
AACTTCTGGCTGCGCTTGGCGCCTGGCTTGGCTGGCAGCACCTACCAATGATCATTCTTTTGTCGTCGCTGGTCGGCTTA
GTTTTCGGATTGATTCAACTTCGCTTGAAACAACAAGGCATAGATAAAGCCTTTCCATTTGGACCTTACCTTGCGATTGC
GGGTTGGGTGAGTTTGATGTGGGGCAACGACATCATGGGCTGGTATTTCACTTCTGTACTAGGAATTTAA

Domains

Predicted by InterproScan.

Bacterial Peptidase A24 N-terminal domain (A24_N_bact)

(17-124)

Type IV leader peptidase family (Peptidase_A24)

(135-244)


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

74.74

100

0.747
  pilD Vibrio cholerae strain A1552

69.444

99.654

0.692
  pilD Acinetobacter nosocomialis M2

51.311

92.388

0.474
  pilD Acinetobacter baumannii D1279779

50.936

92.388

0.471
  pilD Neisseria gonorrhoeae MS11

46.377

95.502

0.443