Detailed information NTG0001293

Experimentally validated

Overview

• Name: pilB
• Type: Machinery gene
• Locus tag: VP_RS12240
• Genome accession: NC_004603
• Coordinates: 2663664..2665349 (+)
• Length: 561 a.a.
• NCBI ID: WP_005479695.1
• Uniprot ID: A0A0L8T4E0
• Organism: Vibrio parahaemolyticus RIMD 2210633
• Function: assembly of type IV pilus DNA binding and uptake

Function

The ΔtfoX or ΔcytR mutant showed significant downregulation in pilA, pilB, comEA, comEC, and qstR.

Genomic Context

Location: 2658664..2670349

Locus tag	Gene name	Coordinates (strand)	Size (bp)	Protein ID	Product	Description
VP_RS12220 (VP2520)	pdhR	2660268..2661035 (-)	768	WP_005462576.1	pyruvate dehydrogenase complex transcriptional repressor PdhR	-
VP_RS12225 (VP2521)	ampD	2661441..2661992 (-)	552	WP_005479703.1	1,6-anhydro-N-acetylmuramyl-L-alanine amidase AmpD	-
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	-

Regulatory network

Positive effect      

Negative effect

Regulator	Target	Regulation
tfoX	pilB	positive effect
tfoX	qstR	positive effect
cytR	qstR	positive effect
tfoX	comEC	positive effect
cytR	comEC	positive effect
cytR	pilB	positive effect
tfoX	comEA	positive effect
cytR	comEA	positive effect
tfoX	pilA	positive effect
cytR	pilA	positive effect

Sequence

Protein

• Length: 561 a.a.
• Molecular weight: 62392.18 Da
• Isoelectric Point: 5.6538

>NTDB_id=1293 VP_RS12240 WP_005479695.1 2663664..2665349(+) (pilB) [Vibrio parahaemolyticus RIMD 2210633]
MHSNLSTILRQKGLLTFSQEESLIEQVKASGISMPEALLSSGFFTSSELAEHLSSIFGLSQPELSQYEYASLCQQLGLRE
LITRHNALPLHRTPSTLLLAVADPTNQQAEDDFRFATGLQVELVLADFRELSTAIRRLYGRSLSHEKSGLKEINQEELAS
LVDVGADEIDNIEDLSQDESPVSRYINQILLDAVRKGASDIHFEPYEKMYRVRLRCDGILIETQQPPNHLSRRLSARIKI
LSKLDIAERRLPQDGRIKLKLNQDTAIDMRVSTLPTLFGEKIVLRLLDSSSASLDIDKLGYSEQQKQLYLEALRRPQGMI
LMTGPTGSGKTVSLYTGLNILNKPEINISTAEDPVEINLSGINQVQVQPKIGFGFAEALRSFLRQDPDVVMVGEIRDLDT
AEIAIKASQTGHLVLSTLHTNSAAETIIRLSNMGVESFNLASSLSLIIAQRLARKLCPYCKQPQEHTVQLQHLGIQTTDN
IFRANPDGCNECTHGYSGRTGIYEVMRFDESLSEALIKGASVHELEKLAIANGMSTLQMSGIEKLKQGITSFSELQRVLY
F

Nucleotide

• Length: 1686 bp

>NTDB_id=1293 VP_RS12240 WP_005479695.1 2663664..2665349(+) (pilB) [Vibrio parahaemolyticus RIMD 2210633]
ATGCACTCCAACCTCTCCACGATTCTTCGTCAAAAAGGATTACTGACGTTTTCCCAAGAAGAATCGTTAATAGAGCAAGT
TAAAGCTTCTGGCATCTCGATGCCGGAAGCTTTACTCAGTTCTGGATTCTTCACATCAAGCGAACTGGCCGAGCACTTAA
GTTCTATTTTTGGCCTAAGTCAGCCCGAGTTATCTCAATATGAATATGCTTCGCTTTGCCAACAGCTCGGCCTACGTGAA
TTAATCACACGACATAATGCACTCCCACTCCACCGTACTCCTTCAACTTTATTATTAGCGGTTGCCGACCCCACGAATCA
ACAAGCTGAAGATGATTTCCGCTTTGCCACTGGTTTACAGGTTGAGTTGGTGTTGGCGGATTTTCGCGAACTCAGTACAG
CAATTCGACGCTTATATGGTCGTTCATTGAGTCATGAAAAGTCTGGGTTAAAAGAGATCAACCAAGAAGAACTAGCGAGT
CTGGTGGATGTCGGTGCAGATGAAATCGACAATATCGAAGACTTGAGCCAAGACGAATCTCCTGTTAGCCGTTACATCAA
CCAAATTCTGTTGGACGCTGTACGCAAAGGCGCATCCGATATCCACTTTGAACCTTATGAAAAGATGTACCGAGTTCGTC
TACGTTGCGATGGCATTTTGATCGAAACTCAGCAACCGCCAAATCACTTGAGTCGTCGCTTATCAGCTCGTATAAAAATT
CTCTCTAAACTTGATATTGCCGAGCGACGTTTACCACAAGATGGGCGAATTAAACTCAAACTGAATCAAGACACCGCGAT
TGATATGCGGGTATCCACTCTACCTACCTTGTTTGGAGAGAAGATCGTACTACGACTGCTCGATAGCAGCTCTGCATCAC
TGGATATCGACAAGCTTGGTTATAGTGAGCAACAAAAACAGCTGTATTTAGAGGCTCTGCGTCGTCCACAAGGTATGATT
CTGATGACAGGTCCAACAGGAAGCGGCAAAACCGTTTCGTTGTACACTGGGCTAAATATTCTCAATAAACCAGAGATCAA
CATCTCCACAGCGGAAGACCCAGTAGAAATTAACTTATCGGGCATTAACCAAGTTCAAGTCCAACCTAAGATTGGTTTTG
GCTTTGCAGAAGCACTACGTTCTTTTCTGCGTCAAGATCCCGATGTGGTCATGGTGGGTGAAATTCGAGACCTAGATACT
GCGGAAATCGCCATCAAGGCTTCCCAAACCGGTCACTTAGTGCTCTCTACTTTGCATACCAACTCTGCGGCTGAAACCAT
CATTCGTTTATCAAACATGGGCGTAGAAAGTTTTAACCTCGCCTCTTCTCTTAGTTTGATTATTGCCCAACGCCTAGCTC
GCAAACTTTGTCCATATTGTAAACAACCGCAAGAGCATACCGTTCAACTTCAGCACCTCGGCATTCAAACAACTGACAAC
ATTTTTAGAGCCAATCCAGATGGTTGCAACGAATGCACCCATGGTTATTCTGGCCGAACAGGTATCTATGAAGTCATGCG
CTTTGATGAATCTCTATCCGAAGCTCTTATTAAAGGAGCCTCGGTACATGAACTGGAAAAGCTTGCCATTGCGAACGGCA
TGAGCACCTTGCAAATGTCCGGAATAGAAAAACTCAAACAAGGCATCACAAGCTTTAGTGAGTTACAACGAGTGCTCTAT
TTCTAA

Domains

Predicted by InterproScan.

• Type II secretion system (T2SS), protein E, N-terminal domain (MshEN) (38-144)

• Type II/IV secretion system protein (T2SSE) (188-455)

3D structure

• AlphaFold DB: A0A0L8T4E0

Similar proteins

Only experimentally validated proteins are listed.

Protein	Organism	Identities (%)	Coverage (%)	Ha-value
pilB	Vibrio campbellii strain DS40M4	90.374	100	0.904
pilB	Vibrio cholerae strain A1552	73.665	100	0.738
pilB	Acinetobacter baumannii D1279779	51.698	94.474	0.488
pilB	Acinetobacter baylyi ADP1	48.115	99.287	0.478
pilB	Legionella pneumophila strain ERS1305867	48.98	96.078	0.471
pilF	Neisseria gonorrhoeae MS11	45.567	100	0.461
pilB	Haemophilus influenzae Rd KW20	40.373	100	0.42
pilB	Haemophilus influenzae 86-028NP	39.959	100	0.416
pilB	Glaesserella parasuis strain SC1401	39.13	100	0.41
pilB/pilB1	Synechocystis sp. PCC 6803	37.099	100	0.392
pilB	Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539	36.861	100	0.373
pilF	Thermus thermophilus HB27	36.396	100	0.367

References

• [1]: Anusuya Debnath et al. (2022) Regulators of natural competence in Vibrio parahaemolyticus. Brazilian Journal of Microbiology : [publication of The Brazilian Society For Microbiology] 53(3):1491-1499. [PMID: 35761009]