Detailed information NTG0022753

Bioinformatically predicted

Overview

• Name: pilD
• Type: Machinery gene
• Locus tag: VP_RS12250
• Genome accession: NC_004603
• Coordinates: 2666661..2667530 (+)
• Length: 289 a.a.
• NCBI ID: WP_005490359.1
• Uniprot ID: Q87LT5
• Organism: Vibrio parahaemolyticus RIMD 2210633
• Function: type IV pilus biogenesis and function (predicted from homology) DNA binding and uptake

Genomic Context

Location: 2661661..2672530

Locus tag	Gene name	Coordinates (strand)	Size (bp)	Protein ID	Product	Description
VP_RS12230 (VP2522)	nadC	2662085..2662972 (+)	888	WP_005479699.1	carboxylating nicotinate-nucleotide diphosphorylase	-
VP_RS12235 (VP2523)	pilA	2663235..2663654 (+)	420	WP_005479693.1	pilin	Machinery gene
VP_RS12240 (VP2524)	pilB	2663664..2665349 (+)	1686	WP_005479695.1	type IV-A pilus assembly ATPase PilB	Machinery gene
VP_RS12245 (VP2525)	pilC	2665373..2666596 (+)	1224	WP_005479682.1	type II secretion system F family protein	Machinery gene
VP_RS12250 (VP2526)	pilD	2666661..2667530 (+)	870	WP_005490359.1	A24 family peptidase	Machinery gene
VP_RS12255 (VP2527)	coaE	2667531..2668145 (+)	615	WP_005480887.1	dephospho-CoA kinase	-
VP_RS12260 (VP2528)	zapD	2668173..2668913 (+)	741	WP_005480890.1	cell division protein ZapD	-
VP_RS12265 (VP2529)	yacG	2668982..2669176 (+)	195	WP_005462546.1	DNA gyrase inhibitor YacG	-
VP_RS12270 (VP2530)	rplS	2669585..2669938 (-)	354	WP_005462554.1	50S ribosomal protein L19	-
VP_RS12275 (VP2531)	trmD	2669980..2670723 (-)	744	WP_005462562.1	tRNA (guanosine(37)-N1)-methyltransferase TrmD	-
VP_RS12280 (VP2532)	rimM	2670751..2671299 (-)	549	WP_005462552.1	ribosome maturation factor RimM	-
VP_RS12285 (VP2533)	rpsP	2671328..2671576 (-)	249	WP_005379962.1	30S ribosomal protein S16	-

Sequence

Protein

• Length: 289 a.a.
• Molecular weight: 32453.53 Da
• Isoelectric Point: 7.1971

>NTDB_id=22753 VP_RS12250 WP_005490359.1 2666661..2667530(+) (pilD) [Vibrio parahaemolyticus RIMD 2210633]
MEVFQYYPWLFVVFASIFGLIVGSFLNVVIYRLPKIMELEWRRECAESFPEYKIKPPQEVLTLSVPRSSCQNCATPIRIR
DNIPVISWLLLKGKCHHCHTAISPRYPLIELLTAACAGFVAYHFGFSYFTVALIFFTFFLIAATFIDLDTMLLPDQLTLP
LTWAGIALALTEISPVSLQDAVIGAIAGYLCLWSVYWGFKLLTGKEGMGYGDFKLLAALGAWLGWQSLPMIILLSSVVGV
IFGLVQLRLQKQGIERAFPFGPYLAIAGWVSLIWGDQILSWYFTSILGV

Nucleotide

• Length: 870 bp

>NTDB_id=22753 VP_RS12250 WP_005490359.1 2666661..2667530(+) (pilD) [Vibrio parahaemolyticus RIMD 2210633]
ATGGAAGTGTTCCAGTACTACCCTTGGCTATTCGTGGTGTTTGCCAGTATCTTCGGTTTAATTGTGGGTAGTTTTCTTAA
TGTAGTCATTTATCGGCTACCTAAAATCATGGAATTAGAATGGCGCCGTGAATGCGCCGAATCATTCCCTGAATATAAGA
TTAAGCCACCTCAAGAAGTTTTGACATTAAGCGTGCCTCGCTCTTCGTGCCAAAACTGCGCGACGCCAATTCGTATTCGA
GACAATATTCCTGTAATCAGCTGGCTACTGTTAAAAGGAAAATGCCATCATTGTCATACCGCAATTAGTCCTCGATATCC
GCTGATAGAATTACTCACTGCAGCGTGCGCTGGTTTTGTGGCTTATCATTTCGGCTTTAGCTACTTTACGGTTGCGTTAA
TCTTTTTCACATTTTTCTTAATAGCCGCGACTTTTATCGATCTCGATACTATGCTGCTACCGGACCAATTAACATTACCA
TTAACTTGGGCTGGCATTGCGTTAGCATTAACAGAAATAAGCCCTGTTAGTCTACAAGACGCCGTAATTGGTGCGATTGC
CGGTTATTTGTGTCTTTGGTCAGTATATTGGGGGTTCAAACTGCTTACTGGTAAAGAAGGCATGGGTTACGGTGATTTTA
AATTGCTGGCTGCCCTTGGCGCTTGGCTAGGATGGCAATCATTACCAATGATCATCCTACTTTCTTCCGTCGTCGGTGTG
ATATTCGGGCTCGTTCAGTTACGACTACAAAAACAAGGTATAGAGAGAGCTTTCCCTTTCGGCCCATATTTAGCGATTGC
AGGATGGGTAAGCTTAATCTGGGGCGACCAAATTCTAAGTTGGTACTTCACGTCAATTTTAGGGGTGTAA

Domains

Predicted by InterproScan.

• Bacterial Peptidase A24 N-terminal domain (A24_N_bact) (17-124)

• Type IV leader peptidase family (Peptidase_A24) (135-244)

3D structure

• AlphaFold DB: Q87LT5

Similar proteins

Only experimentally validated proteins are listed.

Protein	Organism	Identities (%)	Coverage (%)	Ha-value
pilD	Vibrio campbellii strain DS40M4	88.927	100	0.889
pilD	Vibrio cholerae strain A1552	73.264	99.654	0.73
pilD	Acinetobacter baumannii D1279779	52.239	92.734	0.484
pilD	Acinetobacter nosocomialis M2	51.292	93.772	0.481
pilD	Neisseria gonorrhoeae MS11	47.464	95.502	0.453