Detailed information    

experimental Experimentally validated

Overview

Name   clpC   Type   Regulator
Locus tag   SPD_RS10700 Genome accession   NC_008533
Coordinates   2000462..2002894 (-) Length   810 a.a.
NCBI ID   WP_001109677.1    Uniprot ID   A0A0H2ZP24
Organism   Streptococcus pneumoniae D39     
Function   degradation of ComW   
Competence regulation

Function

ComW is a target of the Clp machinery and was shown to be degraded by ClpCP.


Genomic Context

Location: 1995462..2007894
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  SPD_RS10675 (SPD_2018) - 1997229..1997756 (-) 528 WP_000241918.1 isoprenylcysteine carboxyl methyltransferase family protein -
  SPD_RS10680 (SPD_2019) hk06 1997839..1999170 (-) 1332 WP_000594665.1 two-component system sensor histidine kinase HK06 -
  SPD_RS10685 (SPD_2020) rr06 1999167..1999820 (-) 654 WP_001024075.1 two-component system response regulator RR06 -
  SPD_RS10700 (SPD_2022) clpC 2000462..2002894 (-) 2433 WP_001109677.1 ATP-dependent Clp protease ATP-binding subunit Regulator
  SPD_RS10705 (SPD_2023) - 2002896..2003354 (-) 459 WP_001211279.1 CtsR family transcriptional regulator -
  SPD_RS10710 (SPD_2024) - 2003473..2004201 (-) 729 WP_000136224.1 ABC transporter ATP-binding protein -
  SPD_RS10715 (SPD_2025) - 2004201..2005208 (-) 1008 WP_000754546.1 ABC transporter substrate-binding protein -
  SPD_RS10720 (SPD_2026) - 2005246..2006004 (-) 759 WP_001245132.1 ABC transporter permease -
  SPD_RS10725 (SPD_2027) - 2005967..2006257 (-) 291 WP_000647661.1 thiamine-binding protein -
  SPD_RS10730 (SPD_2028) cbpD 2006513..2007859 (-) 1347 WP_000698544.1 choline binding-anchored murein hydrolase CbpD Auxiliary factor

Regulatory network

Positive effect      
Negative effect
Regulator Target Regulation
  clpC comW negative effect
  comW comX/comX1 positive effect
  comX/comX1 late competence genes positive effect
  comX/comX2 late competence genes positive effect
  comX/comX2 late competence genes positive effect
  comW comX/comX2 positive effect
  clpE comX/comX2 negative effect
  clpP comX/comX2 negative effect
  comE comX/comX2 positive effect
  comX/comX1 late competence genes positive effect
  clpE comX/comX1 negative effect
  comE comX/comX1 positive effect
  clpP comX/comX1 negative effect
  mecA comW negative effect
  comE comW positive effect
  comE comM positive effect
  comE comA positive effect
  comE comB positive effect
  comE comE positive effect
  comE comD/comD1 positive effect
  comE comC/comC1 positive effect
  comD/comD1 comE positive effect
  stkP comE positive effect
  ccpA comE positive effect
  clpP comW negative effect
  comM cbpD negative effect
  comA comC/comC1 positive effect
  comB comC/comC1 positive effect
  comC/comC1 comD/comD1 positive effect
  ccpA comD/comD1 positive effect
  ccpA comC/comC1 positive effect
  htrA comC/comC1 negative effect
  ciaR comC/comC1 negative effect
  ciaH comC/comC1 negative effect
  cbpD lytA positive effect
  cbpD lytC positive effect
  htrA comEA/celA/cilE negative effect
  htrA comEC/celB negative effect
  ciaR htrA positive effect
  ciaH htrA positive effect

Sequence

Protein


Download         Length: 810 a.a.        Molecular weight: 90179.96 Da        Isoelectric Point: 5.8612

>NTDB_id=289 SPD_RS10700 WP_001109677.1 2000462..2002894(-) (clpC) [Streptococcus pneumoniae D39]
MNYSKALNECIESAYMVAGHFGARYLESWHLLIAMSNHSYSVAGATLNDYPYEMDRLEEVALELTETDYSQDETFTELPF
SRRLQILFDEAEYVASVVHAKVLGTEHVLYAILHDGNALATRILERAGFSYEDKKDQVKIAALRRNLEERAGWTREDLKA
LRQRHRTVADKQNSMANMMGMPQTPSGGLEDYTHDLTEQARSGKLEPVIGRDKEISRMIQILSRKTKNNPVLVGDAGVGK
TALALGLAQRIASGDVPAEMAKMRVLELDLMNVVAGTRFRGDFEERMNNIIKDIEEDGQVILFIDELHTIMGSGSGIDST
LDAANILKPALARGTLRTVGATTQEEYQKHIEKDAALSRRFAKVTIEEPSVADSMTILQGLKATYEKHHRVQITDEAVET
AVKMAHRYLTSRHLPDSAIDLLDEAAATVQNKAKHVKADDSDLSPADKALMDGKWKQAAQLIAKEEEVPVYKDLVTESDI
LTTLSRLSGIPVQKLTQTDAKKYLNLEAELHKRVIGQDQAVSSISRAIRRNQSGIRSHKRPIGSFMFLGPTGVGKTELAK
ALAEVLFDDESALIRFDMSEYMEKFAASRLNGAPPGYVGYEEGGELTEKVRNKPYSVLLFDEVEKAHPDIFNVLLQVLDD
GVLTDSKGRKVDFSNTIIIMTSNLGATALRDDKTVGFGAKDIRFDQENMEKRMFEELKKAYRPEFINRIDEKVVFHSLSS
DHMQEVVKIMVKPLVASLAEKGIDLKLQASALKLLANQGYDPEMGARPLRRTLQTEVEDKLAELLLKGDLVAGSILKIGV
KAGQLKFDIA

Nucleotide


Download         Length: 2433 bp        

>NTDB_id=289 SPD_RS10700 WP_001109677.1 2000462..2002894(-) (clpC) [Streptococcus pneumoniae D39]
ATGAACTATTCAAAAGCATTGAATGAATGTATCGAAAGTGCCTACATGGTTGCTGGACATTTTGGAGCTCGTTATCTAGA
GTCTTGGCACTTGTTGATTGCCATGTCTAATCACAGTTATAGTGTAGCAGGGGCAACTTTAAATGATTATCCGTATGAGA
TGGACCGTTTAGAAGAGGTGGCTTTGGAACTGACTGAAACGGACTATAGCCAGGATGAAACTTTTACGGAATTGCCGTTC
TCCCGTCGTTTGCAGATTCTTTTTGACGAAGCAGAGTATGTAGCGTCAGTGGTCCATGCTAAGGTGCTAGGTACAGAGCA
CGTCCTCTATGCGATTTTGCATGATGGCAATGCCTTGGCGACTCGTATCTTGGAGAGGGCTGGTTTTTCTTATGAAGACA
AGAAAGATCAGGTCAAGATTGCTGCTCTTCGTCGAAATTTAGAAGAACGGGCAGGCTGGACTCGTGAAGATCTCAAGGCT
TTACGCCAACGCCATCGTACAGTAGCTGACAAGCAAAATTCTATGGCCAATATGATGGGCATGCCGCAGACTCCTAGTGG
TGGTCTCGAGGACTATACGCATGATTTGACAGAGCAAGCGCGTTCTGGCAAGTTAGAACCAGTCATCGGTCGGGACAAGG
AAATCTCACGTATGATTCAAATCTTAAGCCGGAAGACTAAGAACAACCCTGTCTTGGTTGGGGATGCTGGTGTCGGGAAA
ACAGCTCTGGCGCTTGGTCTTGCTCAGCGTATTGCCAGTGGTGACGTGCCTGCGGAAATGGCTAAGATGCGCGTGTTAGA
ACTTGATTTGATGAATGTCGTTGCAGGGACACGCTTCCGTGGTGACTTTGAAGAACGCATGAATAATATCATCAAGGATA
TTGAAGAAGATGGCCAAGTCATCCTCTTTATCGATGAACTCCACACCATCATGGGTTCTGGTAGCGGGATTGATTCGACT
CTGGATGCGGCCAATATCTTGAAACCAGCCTTGGCGCGTGGAACTTTGAGAACGGTTGGTGCCACCACTCAGGAAGAATA
TCAAAAACATATCGAAAAAGATGCGGCACTTTCTCGTCGTTTCGCTAAAGTGACGATTGAAGAACCAAGTGTGGCAGATA
GTATGACTATTTTACAAGGTTTGAAGGCGACTTATGAGAAACATCACCGTGTACAAATCACAGATGAAGCGGTTGAAACA
GCGGTTAAGATGGCTCATCGTTATTTAACCAGTCGTCACTTGCCAGACTCTGCTATCGACCTCTTGGACGAAGCAGCAGC
AACAGTGCAAAATAAGGCAAAGCATGTAAAAGCAGACGATTCAGATTTGAGTCCAGCTGACAAGGCCCTGATGGATGGCA
AGTGGAAACAGGCAGCCCAGCTAATCGCAAAAGAAGAGGAAGTACCTGTCTACAAAGACTTGGTGACAGAGTCTGATATT
TTGACCACCTTGAGTCGCTTGTCAGGAATCCCAGTTCAAAAACTGACTCAGACTGACGCTAAGAAATATCTAAATCTTGA
AGCAGAACTCCATAAACGGGTTATCGGTCAAGATCAAGCTGTTTCAAGTATTAGTCGTGCGATTCGCCGTAATCAGTCAG
GAATTCGCAGTCACAAGCGTCCGATCGGTTCCTTTATGTTCCTAGGACCCACAGGTGTCGGTAAGACCGAGTTGGCCAAG
GCTTTGGCAGAAGTTCTCTTTGATGACGAATCAGCCCTTATCCGCTTTGATATGAGTGAGTATATGGAGAAATTCGCAGC
CAGCCGTCTAAATGGAGCTCCTCCAGGCTATGTGGGTTACGAAGAAGGTGGGGAGTTGACAGAGAAGGTTCGCAATAAAC
CCTATTCCGTTCTCCTCTTTGATGAGGTAGAGAAGGCCCACCCAGATATCTTTAATGTTCTCTTGCAGGTTCTGGATGAC
GGTGTCTTGACAGATAGCAAGGGACGCAAGGTCGATTTTTCAAATACCATTATCATTATGACATCGAATCTAGGTGCGAC
TGCCCTTCGTGATGATAAGACTGTTGGTTTTGGGGCTAAGGATATTCGTTTTGACCAGGAAAATATGGAAAAACGCATGT
TTGAAGAACTGAAAAAAGCTTATAGACCGGAATTCATCAACCGTATTGATGAGAAGGTGGTCTTCCATAGCCTATCTAGT
GACCATATGCAGGAAGTGGTGAAGATTATGGTCAAGCCTTTAGTGGCAAGTTTGGCTGAAAAAGGCATTGACTTGAAATT
ACAAGCTTCAGCTCTGAAATTGTTAGCAAATCAAGGATATGACCCAGAGATGGGAGCTCGCCCACTTCGCAGAACCCTGC
AAACAGAAGTGGAGGACAAGTTGGCAGAACTTCTTCTTAAGGGAGATTTAGTGGCAGGCAGCATACTTAAGATTGGTGTC
AAAGCAGGCCAGTTAAAATTTGATATTGCATAA

Domains

Predicted by InterproScan.

AAA lid domain (AAA_lid_9)

(370-444)

ATPase family associated with various cellular activities (AAA) (AAA)

(231-362)

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

(718-796)

Clp amino terminal domain, pathogenicity island component (Clp_N)

(103-139)

AAA domain (Cdc48 subfamily) (AAA_2)

(540-711)


Secondary structure

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



3D structure

Source ID Structure
  AlphaFold DB A0A0H2ZP24

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 (%) Ha-value
  clpC Streptococcus pneumoniae Rx1

100

100

1
  clpC Streptococcus pneumoniae TIGR4

99.506

100

0.995
  clpC Streptococcus mutans UA159

66.79

100

0.67
  clpC Streptococcus thermophilus LMD-9

66.093

100

0.664
  clpC Streptococcus thermophilus LMG 18311

65.971

100

0.663
  clpC Lactococcus lactis subsp. lactis strain DGCC12653

48.798

100

0.501
  clpC Bacillus subtilis subsp. subtilis str. 168

45.241

99.877

0.452
  clpE Streptococcus mutans UA159

49.355

82.337

0.406
  clpA Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819

36.541

100

0.396
  clpE Streptococcus pneumoniae Rx1

46.91

83.91

0.394
  clpE Streptococcus pneumoniae TIGR4

46.91

83.91

0.394
  clpE Streptococcus pneumoniae R6

46.91

83.91

0.394
  clpE Streptococcus pneumoniae D39

46.91

83.91

0.394
  clpC Lactococcus lactis subsp. cremoris KW2

46.955

83.422

0.392

Multiple sequence alignment    



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]