NTDB

Overview

Name	ssb	Type	Machinery gene
Locus tag	JYR06_RS17375	Genome accession	NZ_CP071062
Coordinates	3963298..3963849 (+)	Length	183 a.a.
NCBI ID	WP_022634792.1	Uniprot ID	-
Organism	Dickeya solani strain IPO2019
Function	ssDNA binding (predicted from homology) DNA processing

Related MGE

Note: This gene co-localizes with putative mobile genetic elements (MGEs) in the genome predicted by VRprofile2, as detailed below.

Gene-MGE association summary

MGE type	MGE coordinates	Gene coordinates	Relative position	Distance (bp)
Prophage	3963298..3977358	3963298..3963849	within	0

Gene organization within MGE regions

Location: 3963298..3977358

Locus tag	Gene name	Coordinates (strand)	Size (bp)	Protein ID	Product	Description
JYR06_RS17375 (JYR06_17375)	ssb	3963298..3963849 (+)	552	WP_022634792.1	single-stranded DNA-binding protein	Machinery gene
JYR06_RS17380 (JYR06_17380)	-	3964134..3964319 (-)	186	WP_022634794.1	hypothetical protein	-
JYR06_RS17385 (JYR06_17385)	-	3964498..3964986 (+)	489	WP_022634795.1	hypothetical protein	-
JYR06_RS17390 (JYR06_17390)	-	3965249..3965821 (+)	573	WP_022634796.1	DUF4255 domain-containing protein	-
JYR06_RS17395 (JYR06_17395)	-	3965827..3966624 (+)	798	WP_022634797.1	hypothetical protein	-
JYR06_RS17400 (JYR06_17400)	-	3966769..3968322 (+)	1554	WP_022634798.1	phage tail sheath family protein	-
JYR06_RS17405 (JYR06_17405)	-	3968374..3968844 (+)	471	WP_022634799.1	phage tail protein	-
JYR06_RS17410 (JYR06_17410)	-	3968931..3969389 (+)	459	WP_023637986.1	phage tail protein	-
JYR06_RS17415 (JYR06_17415)	-	3969410..3969592 (+)	183	WP_022634801.1	hypothetical protein	-
JYR06_RS17420 (JYR06_17420)	-	3969608..3970255 (+)	648	WP_022634802.1	hypothetical protein	-
JYR06_RS17425 (JYR06_17425)	vgrG	3970267..3972057 (+)	1791	WP_022634803.1	type VI secretion system tip protein VgrG	-
JYR06_RS17430 (JYR06_17430)	-	3972516..3972815 (+)	300	WP_022634804.1	PAAR domain-containing protein	-
JYR06_RS17435 (JYR06_17435)	-	3972818..3973237 (+)	420	WP_022634805.1	GPW/gp25 family protein	-
JYR06_RS17440 (JYR06_17440)	-	3973234..3977358 (+)	4125	WP_022634806.1	baseplate J/gp47 family protein	-

Sequence

Protein

Download Length: 183 a.a. Molecular weight: 19717.72 Da Isoelectric Point: 4.9658

                                >NTDB_id=542611 JYR06_RS17375 WP_022634792.1 3963298..3963849(+) (ssb) [Dickeya solani strain IPO2019]

MASRGVNKVILIGNLGQDPEVRYMPNGGAVANLTLATSDSWRDKQTGEQKERTEWHRVALYGKLAEIAGEYLRKGSQVYI

EGQLRTRKWQDQGGQDRYTTEVVVDISGSMQMLGGRTGGGAPAGGGMGNNAGGNPQQGGWGQPQQPQQENQFSGGGQPQS

RPQQSAPMPGNEPPMDFDDDIPF

Nucleotide

Download Length: 552 bp

                                >NTDB_id=542611 JYR06_RS17375 WP_022634792.1 3963298..3963849(+) (ssb) [Dickeya solani strain IPO2019]

ATGGCCAGCAGAGGCGTTAATAAAGTGATTCTTATCGGGAATCTGGGTCAGGACCCGGAAGTCCGTTACATGCCGAACGG

CGGCGCAGTCGCTAACCTGACTCTGGCCACGTCGGACAGCTGGCGCGACAAGCAGACCGGCGAGCAGAAAGAACGCACCG

AGTGGCACCGCGTCGCGCTGTACGGCAAGCTGGCGGAAATCGCCGGTGAATACCTGCGCAAAGGCTCTCAGGTATATATC

GAAGGCCAGCTGCGCACCCGCAAATGGCAGGACCAGGGCGGCCAGGACCGCTACACCACCGAAGTGGTAGTCGATATCTC

CGGCAGCATGCAGATGCTGGGCGGCCGCACAGGCGGCGGCGCTCCGGCCGGTGGCGGCATGGGCAACAATGCGGGCGGCA

ATCCGCAGCAAGGCGGTTGGGGTCAGCCGCAACAGCCGCAGCAAGAGAACCAGTTCAGCGGCGGCGGTCAGCCCCAGTCC

CGTCCGCAGCAAAGCGCGCCGATGCCGGGCAACGAGCCGCCGATGGATTTTGATGACGATATTCCGTTCTGA

Domains

Predicted by InterproScan.

Single-strand binding protein family (SSB)

(6-112)

Secondary structure

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

3D structure

Source	ID	Structure

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
ssb	Vibrio cholerae strain A1552	74.054	100	0.749
ssb	Glaesserella parasuis strain SC1401	54.645	100	0.546
ssb	Neisseria meningitidis MC58	45.503	100	0.47
ssb	Neisseria gonorrhoeae MS11	45.503	100	0.47

Detailed information NTG0542611