Detailed information NTG0062562

Bioinformatically predicted

Overview

• Name: pilD
• Type: Machinery gene
• Locus tag: VIBNI_RS00870
• Genome accession: NC_022528
• Coordinates: 172363..173232 (-)
• Length: 289 a.a.
• NCBI ID: WP_022549575.1
• Uniprot ID: U4JU51
• Organism: Vibrio nigripulchritudo
• Function: type IV pilus biogenesis and function (predicted from homology) DNA binding and uptake

Genomic Context

Location: 167363..178232

Locus tag	Gene name	Coordinates (strand)	Size (bp)	Protein ID	Product	Description
VIBNI_RS00830 (VIBNI_A0165)	rpsP	168012..168260 (+)	249	WP_004408887.1	30S ribosomal protein S16	-
VIBNI_RS00835 (VIBNI_A0166)	rimM	168287..168841 (+)	555	WP_022599632.1	ribosome maturation factor RimM	-
VIBNI_RS00840 (VIBNI_A0167)	trmD	168869..169612 (+)	744	WP_022549571.1	tRNA (guanosine(37)-N1)-methyltransferase TrmD	-
VIBNI_RS00845 (VIBNI_A0168)	rplS	169654..170007 (+)	354	WP_004408890.1	50S ribosomal protein L19	-
VIBNI_RS00850 (VIBNI_A0169)	mutT	170195..170596 (+)	402	WP_004408891.1	8-oxo-dGTP diphosphatase MutT	-
VIBNI_RS00855 (VIBNI_A0170)	yacG	170683..170877 (-)	195	WP_022549572.1	DNA gyrase inhibitor YacG	-
VIBNI_RS00860 (VIBNI_A0171)	zapD	170934..171674 (-)	741	WP_022549573.1	cell division protein ZapD	-
VIBNI_RS00865 (VIBNI_A0172)	coaE	171708..172313 (-)	606	WP_022549574.1	dephospho-CoA kinase	-
VIBNI_RS00870 (VIBNI_A0173)	pilD	172363..173232 (-)	870	WP_022549575.1	A24 family peptidase	Machinery gene
VIBNI_RS00875 (VIBNI_A0174)	pilC	173273..174505 (-)	1233	WP_022549576.1	type II secretion system F family protein	Machinery gene
VIBNI_RS00880 (VIBNI_A0175)	pilB	174515..176203 (-)	1689	WP_022549577.1	type IV-A pilus assembly ATPase PilB	Machinery gene
VIBNI_RS00885 (VIBNI_A0176)	pilA	176203..176661 (-)	459	WP_022601072.1	prepilin-type N-terminal cleavage/methylation domain-containing protein	Machinery gene
VIBNI_RS00890 (VIBNI_A0177)	nadC	176939..177826 (-)	888	WP_022549579.1	carboxylating nicotinate-nucleotide diphosphorylase	-

Sequence

Protein

• Length: 289 a.a.
• Molecular weight: 32524.70 Da
• Isoelectric Point: 7.1423

>NTDB_id=62562 VIBNI_RS00870 WP_022549575.1 172363..173232(-) (pilD) [Vibrio nigripulchritudo]
MEVFHYYPWLFPVMAAIFGLVIGSFLNVVIYRLPKMMENEWRQECAESFPEYKIAPPKEKLTLSVPRSSCQSCKTPIRIR
DNIPVLSWLLLKGKCHACDDSIKVRYPLIELLTAGLSFAVAWQFGFSYFSVALLFFTFVLVAATFIDLDTLLLPDQLTLP
LMWAGIALSLFEINPISLTDAVIGAMVGYLCLWSVYQLFKLATGKEGMGYGDFKLLAALGAWLGWQSLPIVILMSSLVGV
VFGVIQLRLQKKGIEQAFPFGPYLAIAGWITLMFGQDITNWYFSHFLGI

Nucleotide

• Length: 870 bp

>NTDB_id=62562 VIBNI_RS00870 WP_022549575.1 172363..173232(-) (pilD) [Vibrio nigripulchritudo]
ATGGAAGTTTTTCACTACTACCCATGGTTATTCCCTGTGATGGCCGCAATCTTTGGATTGGTCATTGGCAGTTTCTTAAA
TGTAGTGATCTATCGGTTGCCTAAAATGATGGAAAACGAATGGAGGCAGGAGTGCGCAGAATCGTTTCCTGAGTACAAGA
TTGCCCCTCCAAAGGAGAAGCTGACACTTAGCGTTCCGCGTTCCAGTTGCCAAAGTTGTAAAACGCCAATTCGTATTCGA
GATAACATCCCTGTATTGAGTTGGCTGCTTTTAAAAGGGAAATGCCATGCATGCGACGATAGCATCAAGGTTCGATACCC
TTTAATCGAGTTACTTACGGCAGGGCTAAGCTTCGCGGTAGCCTGGCAATTTGGATTCAGTTACTTTTCTGTTGCTCTGC
TTTTCTTCACCTTCGTACTGGTTGCAGCCACGTTTATTGACCTTGATACGCTACTGTTACCCGATCAATTGACACTACCC
TTAATGTGGGCAGGTATTGCGTTATCTCTTTTTGAAATTAACCCAATCTCTCTTACCGACGCCGTCATTGGTGCCATGGT
TGGCTACCTCTGCTTATGGAGTGTCTACCAGTTGTTTAAGCTCGCAACTGGCAAAGAAGGGATGGGTTATGGTGACTTTA
AGTTGCTGGCTGCGCTCGGAGCATGGTTAGGCTGGCAAAGCCTCCCTATTGTCATCCTGATGTCCTCTCTGGTTGGCGTA
GTCTTTGGCGTTATTCAGCTCCGTCTGCAAAAGAAAGGCATCGAACAAGCTTTTCCTTTTGGTCCTTACCTTGCGATTGC
TGGGTGGATTACTCTGATGTTTGGACAAGACATCACTAACTGGTATTTCTCACATTTTCTTGGCATTTAA

Domains

Predicted by InterproScan.

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

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

3D structure

• AlphaFold DB: U4JU51

Similar proteins

Only experimentally validated proteins are listed.

Protein	Organism	Identities (%)	Coverage (%)	Ha-value
pilD	Vibrio campbellii strain DS40M4	77.855	100	0.779
pilD	Vibrio cholerae strain A1552	69.792	99.654	0.696
pilD	Acinetobacter baumannii D1279779	51.471	94.118	0.484
pilD	Acinetobacter nosocomialis M2	51.471	94.118	0.484
pilD	Neisseria gonorrhoeae MS11	45.818	95.156	0.436