NTDB

Overview

Name	pilD	Type	Machinery gene
Locus tag	LPB04_RS00985	Genome accession	NZ_CP062941
Coordinates	246387..247250 (+)	Length	287 a.a.
NCBI ID	WP_193686966.1	Uniprot ID	A0A7L9U6T1
Organism	Massilia litorea strain LPB0304
Function	assembly of type IV pilus (predicted from homology) DNA binding and uptake

Genomic Context

Location: 241387..252250

Locus tag	Gene name	Coordinates (strand)	Size (bp)	Protein ID	Product	Description
LPB04_RS00970 (LPB04_00970)	pilC	242924..244159 (+)	1236	WP_193688810.1	type II secretion system F family protein	Machinery gene
LPB04_RS00975 (LPB04_00975)	-	244228..244926 (+)	699	WP_193686964.1	hypothetical protein	-
LPB04_RS00980 (LPB04_00980)	-	244990..246168 (-)	1179	WP_193686965.1	pyridoxal phosphate-dependent aminotransferase	-
LPB04_RS00985 (LPB04_00985)	pilD	246387..247250 (+)	864	WP_193686966.1	A24 family peptidase	Machinery gene
LPB04_RS00990 (LPB04_00990)	coaE	247254..247901 (+)	648	WP_193686967.1	dephospho-CoA kinase	-
LPB04_RS00995 (LPB04_00995)	zapD	247966..248721 (+)	756	WP_193686968.1	cell division protein ZapD	-
LPB04_RS01000 (LPB04_01000)	-	248739..248927 (+)	189	WP_193686969.1	DNA gyrase inhibitor YacG	-
LPB04_RS01005 (LPB04_01005)	-	249084..250385 (-)	1302	WP_193686970.1	D-amino acid dehydrogenase	-
LPB04_RS01010 (LPB04_01010)	-	250419..250829 (-)	411	WP_193686971.1	NUDIX domain-containing protein	-
LPB04_RS01015 (LPB04_01015)	-	251013..251891 (-)	879	WP_193686972.1	ATP-binding protein	-

Sequence

Protein

Download Length: 287 a.a. Molecular weight: 30888.86 Da Isoelectric Point: 8.4678

                                >NTDB_id=492030 LPB04_RS00985 WP_193686966.1 246387..247250(+) (pilD) [Massilia litorea strain LPB0304]

METLLFAAPGSLGPTLVAGLLGLLIGSFLNVVIHRIPKMMQRESDNYVAHESGKELPHTDRYNLMVPRSACPHCGHQITA

LENIPVISWLALRGKCRKCKAPISARYPAVELLTGVLSALLVWTFGSGVAGMATLVFAWLLVAMTFIDVDTQLLPDDLTF

PLLWMGLLVNLNGTFVPLRDAVIGAAAGYLVLWAVYWLFKLVTGKEGMGYGDFKLLAALGAWLGWAMLPTIILLSSVVGA

IVGISLIVFARRGRDKPIPFGPYLAAAGMIALLYGEQIGGLFQGLLA

Nucleotide

Download Length: 864 bp

                                >NTDB_id=492030 LPB04_RS00985 WP_193686966.1 246387..247250(+) (pilD) [Massilia litorea strain LPB0304]

TTGGAAACTCTTCTCTTCGCCGCCCCGGGCTCGCTCGGTCCTACCCTGGTTGCCGGCCTGCTGGGCCTCCTGATCGGCAG

TTTCCTGAACGTGGTGATCCACCGCATTCCGAAGATGATGCAGCGCGAGTCCGACAATTACGTGGCCCACGAAAGCGGCA

AGGAGCTTCCGCATACCGACCGCTACAACCTGATGGTGCCGCGCTCCGCCTGTCCCCACTGCGGGCACCAGATCACGGCG

CTGGAAAACATTCCCGTGATCAGCTGGCTGGCGCTGCGCGGCAAGTGCCGCAAGTGCAAGGCCCCGATCTCGGCGCGTTA

CCCGGCCGTCGAACTGCTGACCGGCGTCCTGTCGGCCCTGCTGGTCTGGACTTTCGGATCCGGCGTGGCCGGCATGGCGA

CCCTGGTGTTCGCCTGGTTGCTGGTCGCGATGACCTTCATCGACGTGGACACCCAGCTGCTGCCGGACGACCTGACCTTC

CCGCTGCTGTGGATGGGTCTGCTGGTCAACCTGAACGGCACCTTCGTGCCGCTGCGTGACGCCGTGATTGGCGCCGCAGC

CGGCTACCTGGTGCTGTGGGCGGTGTACTGGCTGTTCAAACTGGTGACCGGCAAGGAAGGCATGGGCTATGGCGACTTCA

AGCTGCTCGCCGCGCTCGGCGCCTGGCTGGGCTGGGCGATGCTGCCGACCATTATCCTGCTATCCTCGGTGGTGGGCGCG

ATCGTCGGCATCAGCCTGATCGTGTTCGCGCGCCGCGGCCGCGACAAGCCGATCCCGTTCGGACCGTATCTGGCCGCCGC

CGGCATGATCGCCCTGCTCTACGGCGAGCAGATCGGCGGACTCTTCCAGGGCCTCCTTGCGTAA

Domains

Predicted by InterproScan.

Type IV leader peptidase family (Peptidase_A24)

(135-244)

Bacterial Peptidase A24 N-terminal domain (A24_N_bact)

(20-125)

Secondary structure

Protein secondary structures were predicted by S4PRED and visualized by seqviz.

3D structure

Source	ID	Structure
AlphaFold DB	A0A7L9U6T1

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 (%)	H_a-value
pilD	Vibrio cholerae strain A1552	56.767	92.683	0.526
pilD	Vibrio campbellii strain DS40M4	56.439	91.986	0.519
pilD	Acinetobacter baumannii D1279779	51.292	94.425	0.484
pilD	Acinetobacter nosocomialis M2	50.185	94.425	0.474
pilD	Neisseria gonorrhoeae MS11	47.744	92.683	0.443

Detailed information NTG0492030