Detailed information NTG0000241

Experimentally validated

Overview

• Name: clpE
• Type: Regulator
• Locus tag: SP_RS04015
• Genome accession: NC_003028
• Coordinates: 770258..772516 (-)
• Length: 752 a.a.
• NCBI ID: WP_000882523.1
• Uniprot ID: A0A4J1WRX6
• Organism: Streptococcus pneumoniae TIGR4
• Function: degradation of ComX Competence regulation

Function

Degradation of the ComX protein depends largely on a ClpEP protease complex.

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)
IScluster/Tn	765229..770051	770258..772516	flank	207

Gene organization within MGE regions

Location: 765229..772516

Locus tag	Gene name	Coordinates (strand)	Size (bp)	Protein ID	Product	Description
SP_RS03970	tnpB	766227..766514 (-)	288	WP_000586646.1	IS66 family insertion sequence element accessory protein TnpB	-
SP_RS13145	-	766755..768092 (+)	1338	Protein_763	IS3 family transposase	-
SP_RS03995 (SP_0816)	-	768201..768500 (-)	300	WP_000767193.1	DUF1827 family protein	-
SP_RS04000 (SP_0817)	-	768665..769087 (-)	423	WP_001849729.1	NUDIX hydrolase	-
SP_RS11975	-	769198..770051 (+)	854	Protein_766	IS630 family transposase	-
SP_RS04015 (SP_0820)	clpE	770258..772516 (-)	2259	WP_000882523.1	ATP-dependent Clp protease ATP-binding subunit	Regulator

Regulatory network

Positive effect      

Negative effect

Regulator	Target	Regulation
clpE	comX/comX1	negative effect
comX/comX1	late competence genes	positive effect
comX/comX2	late competence genes	positive effect
comX/comX1	late competence genes	positive effect
comX/comX2	late competence genes	positive effect
comE	comX/comX2	positive effect
comE	comE	positive effect
comE	comX/comX1	positive effect
comE	comW	positive effect
comE	comA	positive effect
comE	comB	positive effect
comE	comM	positive effect
comE	comD/comD2	positive effect
comE	comC/comC2	positive effect
comD/comD2	comE	positive effect
stkP	comE	positive effect
clpP	comX/comX2	negative effect
clpP	comX/comX1	negative effect
clpP	comW	negative effect
comW	comX/comX2	positive effect
comW	comX/comX1	positive effect
mecA	comW	negative effect
clpC	comW	negative effect
clpE	comX/comX2	negative effect
comA	comC/comC2	positive effect
comB	comC/comC2	positive effect
comM	cbpD	negative effect
comC/comC2	comD/comD2	positive effect
ciaH	comC/comC2	negative effect
htrA	comC/comC2	negative effect
ciaR	comC/comC2	negative effect
cbpD	lytA	positive effect
cbpD	lytC	positive effect
ciaH	htrA	positive effect
htrA	comEC/celB	negative effect
htrA	comEA/celA/cilE	negative effect
ciaR	htrA	positive effect

Sequence

Protein

• Length: 752 a.a.
• Molecular weight: 83814.18 Da
• Isoelectric Point: 5.3713

>NTDB_id=241 SP_RS04015 WP_000882523.1 770258..772516(-) (clpE) [Streptococcus pneumoniae TIGR4]
MLCQNCKINDSTIHLYTNLNGKQKQIDLCQNCYKIIKTDPNNSLFKGMTDLNNRDFDPFGDFFNDLNNFRPSSNTPPIPP
TQSGGGYGGNGGYGSQNRGSAQTPPPSQEKGLLEEFGINVTEIARRGDIDPVIGRDDEIIRVIEILNRRTKNNPVLIGEP
GVGKTAVVEGLAQKIVDGDVPHKLQGKQVIRLDVVSLVQGTGIRGQFEERMQKLMEEIRKREDIILFIDEIHEIVGAGSA
SDGNMDAGNILKPALARGELQLVGATTLNEYRIIEKDAALERRMQPVKVDEPTVDETITILKGIQKKYEDYHHVQYTDAA
IEAAATLSNRYIQDRFLPDKAIDLLDEAGSKMNLTLNFVDPKVIDQRLIEAENLKSQATREEDFEKAAYFRDQIAKYKEM
QKKKITDQDTPSISEKTIEHIIEQKTNIPVGDLKEKEQSQLIHLAEDLKSHVIGQDDAVDKIAKAIRRNRVGLGTPNRPI
GSFLFVGPTGVGKTELSKQLAIELFGSADSMIRFDMSEYMEKHSVAKLVGAPPGYVGYDEAGQLTEKVRHNPYSLILLDE
VEKAHPDVMHMFLQVLDDGRLTDGQGRTVSFKDAIIIMTSNAGTGKTEASVGFGAAREGRTNSVLGELGNFFSPEFMNRF
DGIIEFKALSKDNLLQIVELMLADVNKRLSSNNIRLDVTDKVKEKLVDLGYDPKMGARPLRRTIQDYIEDTITDYYLENP
SEKDLKAVMTSKGNIQIKSAKKAEVKSSEKEK

Nucleotide

• Length: 2259 bp

>NTDB_id=241 SP_RS04015 WP_000882523.1 770258..772516(-) (clpE) [Streptococcus pneumoniae TIGR4]
ATGCTTTGTCAAAACTGTAAAATTAACGACTCAACAATTCATCTTTACACCAATCTCAATGGAAAACAAAAACAAATTGA
CCTCTGTCAAAACTGCTATAAGATTATCAAAACAGATCCTAACAATAGCCTCTTCAAAGGTATGACGGATCTGAACAATC
GTGACTTCGATCCCTTTGGTGATTTCTTCAATGATCTAAACAATTTCAGACCTTCTAGCAATACTCCTCCTATTCCCCCA
ACCCAATCAGGTGGAGGTTACGGTGGAAACGGCGGTTATGGTTCCCAAAATCGTGGATCTGCTCAAACTCCGCCACCTAG
CCAAGAAAAAGGCCTGCTGGAAGAATTTGGTATTAATGTAACTGAAATTGCCCGTCGTGGAGACATTGACCCCGTTATTG
GGCGCGACGATGAGATTATCCGTGTCATCGAGATTCTCAATCGTAGAACCAAGAATAATCCTGTCCTTATCGGTGAACCT
GGTGTCGGAAAAACGGCCGTTGTCGAAGGTCTAGCTCAGAAAATTGTCGATGGCGATGTGCCACATAAACTCCAAGGTAA
ACAAGTCATCCGTCTGGATGTGGTTAGCTTAGTTCAAGGAACGGGGATTCGAGGACAATTTGAAGAACGCATGCAAAAAC
TCATGGAAGAAATTCGCAAACGTGAAGACATCATCCTCTTTATCGATGAAATCCATGAAATTGTTGGTGCTGGTTCTGCG
AGTGATGGTAATATGGACGCAGGAAATATCCTCAAGCCAGCCCTTGCTCGTGGAGAACTGCAACTAGTCGGTGCTACTAC
CCTCAATGAATACCGTATCATTGAAAAGGATGCTGCCCTCGAGCGTCGTATGCAGCCTGTTAAAGTCGATGAACCAACGG
TGGACGAAACAATCACTATTCTCAAAGGGATTCAAAAGAAATACGAAGATTACCACCACGTTCAATATACAGATGCTGCG
ATTGAAGCAGCTGCAACTCTTTCCAATCGCTACATCCAAGATCGCTTCTTGCCTGACAAGGCCATTGACCTCCTAGATGA
AGCTGGTTCTAAGATGAACTTGACCTTGAATTTTGTGGATCCTAAAGTAATTGATCAGCGCTTGATTGAGGCTGAAAATC
TCAAGTCTCAAGCTACACGAGAAGAAGATTTTGAGAAGGCGGCCTACTTCCGCGACCAGATTGCCAAGTATAAGGAAATG
CAAAAGAAAAAGATCACAGACCAGGATACTCCTAGCATCAGCGAGAAAACTATTGAGCACATTATCGAGCAGAAAACCAA
TATCCCTGTTGGTGATTTGAAAGAGAAAGAACAATCTCAACTCATCCATCTAGCCGAAGATCTCAAGTCTCATGTTATTG
GTCAAGATGATGCAGTCGATAAGATTGCCAAGGCTATTCGCCGTAATCGTGTCGGACTTGGTACCCCTAACCGCCCAATC
GGAAGCTTCCTCTTCGTTGGGCCAACTGGTGTCGGTAAGACAGAACTTTCCAAACAACTGGCTATCGAACTTTTTGGTTC
TGCTGATAGTATGATTCGCTTTGATATGAGTGAATACATGGAAAAACATAGTGTGGCTAAGTTGGTCGGCGCTCCTCCAG
GTTATGTTGGCTATGATGAGGCTGGTCAATTAACTGAAAAAGTTCGCCACAATCCATATTCTCTCATCCTTCTCGATGAA
GTGGAAAAAGCTCACCCAGATGTTATGCACATGTTTCTTCAAGTCTTGGACGATGGTCGTTTGACAGACGGGCAAGGACG
CACCGTTAGCTTCAAGGATGCCATCATTATCATGACCTCAAATGCAGGTACAGGAAAGACCGAAGCTAGCGTTGGATTTG
GTGCTGCTAGAGAAGGACGTACCAATTCTGTCCTCGGTGAACTCGGTAACTTCTTTAGCCCAGAGTTTATGAACCGTTTT
GATGGCATTATCGAATTTAAGGCTCTCAGCAAGGATAACCTCCTTCAGATTGTCGAGCTCATGCTAGCAGATGTTAACAA
GCGCCTCTCTAGCAACAACATTCGTTTGGATGTAACTGATAAGGTCAAGGAAAAGTTGGTTGACCTAGGTTATGATCCAA
AAATGGGAGCACGCCCACTTCGTCGGACTATTCAAGACTATATTGAGGACACAATCACTGACTACTACCTTGAAAATCCA
AGCGAAAAAGATCTCAAAGCAGTTATGACTAGCAAGGGAAACATTCAGATTAAATCTGCCAAAAAAGCTGAAGTTAAAAG
TTCTGAAAAAGAAAAATAA

Domains

Predicted by InterproScan.

• ATPase family associated with various cellular activities (AAA) (AAA) (155-276)

• C-terminal, D2-small domain, of ClpB protein (ClpB_D2-small) (649-723)

• AAA lid domain (AAA_lid_9) (293-390)

• AAA domain (Cdc48 subfamily) (AAA_2) (478-641)

3D structure

• AlphaFold DB: A0A4J1WRX6

Similar proteins

Only experimentally validated proteins are listed.

Protein	Organism	Identities (%)	Coverage (%)	Ha-value
clpE	Streptococcus pneumoniae R6	99.867	100	0.999
clpE	Streptococcus pneumoniae D39	99.867	100	0.999
clpE	Streptococcus pneumoniae Rx1	99.867	100	0.999
clpE	Streptococcus mutans UA159	82.754	99.336	0.822
clpC	Lactococcus lactis subsp. cremoris KW2	76.839	97.606	0.75
clpC	Bacillus subtilis subsp. subtilis str. 168	52.308	86.436	0.452
clpC	Lactococcus lactis subsp. lactis strain DGCC12653	47.687	83.378	0.398
clpC	Streptococcus pneumoniae Rx1	46.91	83.91	0.394
clpC	Streptococcus pneumoniae D39	46.91	83.91	0.394
clpC	Streptococcus pneumoniae TIGR4	46.91	83.91	0.394
clpC	Streptococcus mutans UA159	47.36	83.112	0.394
clpC	Streptococcus thermophilus LMD-9	46.88	83.112	0.39
clpC	Streptococcus thermophilus LMG 18311	46.486	83.245	0.387

References

• [1]: Andrew Piotrowski et al. (2009) Competence for genetic transformation in Streptococcus pneumoniae: termination of activity of the alternative sigma factor ComX is independent of proteolysis of ComX and ComW. Journal of Bacteriology 191(10):3359-66. [PMID: 19286798]