NTDB

Overview

Name	pilD	Type	Machinery gene
Locus tag	RO838_RS10825	Genome accession	NZ_CP135134
Coordinates	2367497..2368360 (-)	Length	287 a.a.
NCBI ID	WP_004084594.1	Uniprot ID	B2I9Q6
Organism	Xylella fastidiosa strain CFBP8478
Function	type IV pilus biogenesis and function (predicted from homology) DNA binding and uptake

Genomic Context

Location: 2362497..2373360

Locus tag	Gene name	Coordinates (strand)	Size (bp)	Protein ID	Product	Description
RO838_RS10805 (RO838_10805)	rimK	2363026..2363931 (+)	906	WP_057682390.1	30S ribosomal protein S6--L-glutamate ligase	-
RO838_RS10810 (RO838_10810)	-	2364588..2365265 (+)	678	WP_010894955.1	response regulator transcription factor	-
RO838_RS10815 (RO838_10815)	-	2365258..2366595 (+)	1338	WP_057682389.1	HAMP domain-containing sensor histidine kinase	-
RO838_RS10820 (RO838_10820)	coaE	2366862..2367485 (-)	624	WP_020851236.1	dephospho-CoA kinase	-
RO838_RS10825 (RO838_10825)	pilD	2367497..2368360 (-)	864	WP_004084594.1	A24 family peptidase	Machinery gene
RO838_RS10830 (RO838_10830)	pilC	2368367..2369569 (-)	1203	WP_010894959.1	type II secretion system F family protein	Machinery gene
RO838_RS10835 (RO838_10835)	pilA	2370010..2370456 (+)	447	WP_057682388.1	pilin	Machinery gene
RO838_RS10840 (RO838_10840)	-	2370702..2370929 (-)	228	WP_057682387.1	hypothetical protein	-
RO838_RS10845 (RO838_10845)	-	2371317..2371619 (-)	303	WP_128734940.1	hypothetical protein	-
RO838_RS10850 (RO838_10850)	pilA/pilAI	2371763..2372197 (+)	435	WP_004084597.1	pilin	Machinery gene

Sequence

Protein

Download Length: 287 a.a. Molecular weight: 31704.79 Da Isoelectric Point: 8.6709

                                >NTDB_id=810205 RO838_RS10825 WP_004084594.1 2367497..2368360(-) (pilD) [Xylella fastidiosa strain CFBP8478]

MAFLDQHPGLGYPLASGLGLLLGSFLNVVILRLPRRLEWQWKRDAREILEMPDIYDPPPPGIVVEPSHDPVTGDRLKWWE

NIPVLSWLLLRGRSRYSGKSISLQYPLVELLTCLLVLASVWRFGFGWHGFGAIVFSCFLVALAGIDLRTRLLPDQLTLML

MWLGLIGSADNLFMAAKPALLGAAVGYLSLWIVAALFKLIFNKEGMGHGDFKMLGALGAWCGLKGILPIILISSLAGVVL

GSVWLVVRGHNRTTMIPFGPYLAVGGWIVFFFGDQIIHAYLELLSIG

Nucleotide

Download Length: 864 bp

                                >NTDB_id=810205 RO838_RS10825 WP_004084594.1 2367497..2368360(-) (pilD) [Xylella fastidiosa strain CFBP8478]

ATGGCATTTCTTGATCAGCACCCCGGACTCGGCTATCCCCTTGCGTCCGGTTTGGGGTTGTTGCTTGGTAGTTTTCTCAA

TGTGGTGATCCTGCGTTTGCCGCGCCGTTTGGAATGGCAATGGAAGCGCGATGCGCGCGAAATCCTGGAGATGCCGGACA

TTTATGATCCGCCACCGCCGGGAATTGTGGTCGAGCCTTCCCACGATCCAGTGACTGGTGATCGGTTGAAGTGGTGGGAA

AACATTCCGGTGCTTAGCTGGTTGTTGCTACGTGGACGTTCGCGTTACAGCGGCAAGTCAATCTCGTTGCAGTATCCGTT

GGTCGAATTGCTGACTTGCCTGCTGGTGCTGGCCAGTGTTTGGCGTTTTGGATTCGGTTGGCATGGTTTTGGGGCAATTG

TGTTCAGTTGTTTCCTGGTTGCGTTGGCTGGGATTGATTTGCGTACTCGGCTCTTACCTGACCAGTTAACTTTAATGCTC

ATGTGGCTGGGTTTGATTGGATCGGCGGATAACTTGTTTATGGCAGCCAAACCTGCGTTATTGGGGGCTGCAGTTGGTTA

TTTATCTCTGTGGATTGTGGCGGCGTTGTTCAAACTGATCTTTAACAAGGAAGGGATGGGCCATGGTGACTTCAAAATGC

TGGGCGCGCTTGGGGCATGGTGTGGGTTAAAGGGTATTCTCCCGATCATTTTGATTTCATCACTGGCTGGAGTGGTATTG

GGCTCCGTTTGGCTTGTTGTGCGTGGTCATAACCGTACGACGATGATTCCGTTTGGACCTTATCTGGCAGTTGGTGGATG

GATCGTGTTCTTTTTCGGCGATCAGATCATCCATGCTTATCTGGAGCTATTAAGTATCGGGTGA

Domains

Predicted by InterProScan.

Type IV leader peptidase family (Peptidase_A24)

(133-241)

Bacterial Peptidase A24 N-terminal domain (A24_N_bact)

(18-123)

Secondary structure

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

3D structure

Source	ID	Structure
AlphaFold DB	B2I9Q6

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 campbellii strain DS40M4	41.754	99.303	0.415
pilD	Vibrio cholerae strain A1552	42.049	98.606	0.415
pilD	Acinetobacter nosocomialis M2	41.343	98.606	0.408
pilD	Acinetobacter baumannii D1279779	41.343	98.606	0.408
pilD	Neisseria gonorrhoeae MS11	43.284	93.38	0.404

Detailed information NTG0810205