Detailed information    

experimental Experimentally validated

Overview

Name   cbpD   Type   Auxiliary factor
Locus tag   SM12261_RS09205 Genome accession   NZ_CP028414
Coordinates   1829764..1830873 (-) Length   369 a.a.
NCBI ID   WP_000798432.1    Uniprot ID   A0AAX2L5X1
Organism   Streptococcus mitis NCTC 12261     
Function   fratricide process; lyse non-competent cells   
Cell lysis

Function

Upregulated in response to CSP as measured by RNA-seq.


Genomic Context

Location: 1824764..1835873
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  SM12261_RS09180 (SM12261_1770) - 1826149..1826607 (-) 459 WP_001211265.1 CtsR family transcriptional regulator -
  SM12261_RS09185 (SM12261_1771) - 1826726..1827454 (-) 729 WP_000136238.1 ABC transporter ATP-binding protein -
  SM12261_RS09190 (SM12261_1772) - 1827454..1828461 (-) 1008 WP_000754556.1 ABC transporter substrate-binding protein -
  SM12261_RS09195 (SM12261_1773) - 1828500..1829258 (-) 759 WP_161969982.1 ABC transporter permease -
  SM12261_RS09200 (SM12261_1774) - 1829221..1829511 (-) 291 WP_000647684.1 thiamine-binding protein -
  SM12261_RS09205 (SM12261_1775) cbpD 1829764..1830873 (-) 1110 WP_000798432.1 choline binding-anchored murein hydrolase CbpD Auxiliary factor
  SM12261_RS09210 (SM12261_1776) - 1830963..1831229 (-) 267 WP_001278169.1 Veg family protein -
  SM12261_RS09215 (SM12261_1777) dnaB 1831231..1832583 (-) 1353 WP_000852498.1 replicative DNA helicase -
  SM12261_RS09220 (SM12261_1778) rplI 1832627..1833079 (-) 453 WP_000864218.1 50S ribosomal protein L9 -
  SM12261_RS09225 (SM12261_1779) - 1833076..1835049 (-) 1974 WP_000715136.1 DHH family phosphoesterase -
  SM12261_RS09230 (SM12261_1780) hpf 1835185..1835733 (-) 549 WP_000599102.1 ribosome hibernation-promoting factor, HPF/YfiA family -

Regulatory network

Positive effect      
Negative effect
Regulator Target Regulation
  comM cbpD negative effect
  comE comM positive effect
  comE comX/sigX/comX2/sigX2 positive effect
  comE comD positive effect
  comE comE positive effect
  comE comX/sigX/comX1/sigX1 positive effect
  comE comB positive effect
  comE comC positive effect
  comE comW positive effect
  comE comA positive effect
  comD comE positive effect
  comX/sigX/comX2/sigX2 late competence genes positive effect
  comX/sigX/comX2/sigX2 late competence genes positive effect
  comX/sigX/comX1/sigX1 late competence genes positive effect
  comW comX/sigX/comX2/sigX2 positive effect
  comW comX/sigX/comX1/sigX1 positive effect
  comC comD positive effect
  comB comC positive effect
  comA comC positive effect
  comX/sigX/comX1/sigX1 late competence genes positive effect

Sequence

Protein


Download         Length: 369 a.a.        Molecular weight: 41064.36 Da        Isoelectric Point: 9.5489

>NTDB_id=492 SM12261_RS09205 WP_000798432.1 1829764..1830873(-) (cbpD) [Streptococcus mitis NCTC 12261]
MKNSPFKVAETGFSFRKSAKKVVPFLVVGLMLAAGNSVYAYSGGNGSIARGDDYPAHYKNGSQEIDKWRMYSRQCTSFAA
FRLSNVNGFEIPAAYGNANEWGYRARREGYRVDNRPAIGSIAWSTAGTYGHVAWVSNVIGDEIEIEEYNYGIRESYNKRV
VKANTMTGFIHFKDLAGGSVGNSQSSPSTGGTHFFKSKAAIKNQPLASATAIDYYYPGENVHYDQILEKDGYKWLSYTAY
NGSRRYIQLEGVTSSQNQSGNSSNYGSNNGLTIGWKKINGSWYHFKSNGSKSTGWLKDGSSWYYLKSSGEMQTGWLKENG
LWYYLDSSGAMKTGWYQVSGKWYYSYSSGELAVNTTVDGYRVNSDGERV

Nucleotide


Download         Length: 1110 bp        

>NTDB_id=492 SM12261_RS09205 WP_000798432.1 1829764..1830873(-) (cbpD) [Streptococcus mitis NCTC 12261]
ATGAAAAATTCACCATTTAAAGTAGCAGAGACAGGATTTTCTTTTAGAAAATCAGCTAAAAAAGTTGTTCCCTTTTTAGT
AGTAGGATTGATGTTAGCAGCGGGTAATAGTGTATATGCCTATTCCGGAGGAAATGGATCGATTGCGCGTGGGGATGATT
ATCCTGCTCATTATAAAAATGGGAGCCAGGAGATTGATAAGTGGCGCATGTATTCTCGTCAATGTACTTCTTTTGCAGCC
TTTCGTTTGAGTAATGTGAATGGTTTTGAGATTCCGGCTGCTTATGGGAATGCGAATGAATGGGGCTATCGGGCTCGTCG
TGAAGGCTATCGTGTAGATAATAGACCAGCGATTGGCTCCATTGCTTGGTCTACTGCAGGAACTTATGGTCATGTTGCTT
GGGTGTCAAATGTAATAGGAGATGAGATTGAGATTGAAGAATACAACTATGGAATAAGAGAATCTTACAATAAGCGCGTC
GTGAAGGCCAATACCATGACTGGCTTTATTCATTTTAAAGATTTAGCTGGTGGCAGTGTTGGGAATAGTCAATCCTCACC
TTCAACAGGAGGAACACATTTTTTCAAGTCTAAGGCTGCTATCAAAAATCAGCCTCTAGCTAGCGCAACTGCAATTGATT
ACTATTATCCTGGGGAGAATGTTCATTATGATCAAATTCTCGAAAAAGATGGGTACAAGTGGTTGAGTTATACGGCTTAT
AACGGAAGTCGTCGCTATATCCAGCTAGAGGGAGTAACCTCTTCACAGAATCAATCAGGGAATAGTTCTAACTATGGATC
CAATAATGGATTGACTATTGGTTGGAAGAAAATAAATGGTAGTTGGTATCATTTCAAATCAAATGGGTCTAAATCAACAG
GCTGGCTGAAAGATGGATCTAGTTGGTATTATTTGAAATCATCTGGTGAAATGCAAACAGGCTGGTTAAAGGAAAATGGT
CTGTGGTATTATCTAGATAGTTCAGGAGCAATGAAAACAGGTTGGTATCAAGTCTCAGGTAAGTGGTATTATTCTTACTC
TTCAGGTGAGCTAGCTGTTAATACTACAGTGGATGGCTACAGAGTAAACAGTGACGGAGAACGAGTATAG

Domains

Predicted by InterproScan.

Choline-binding repeat (Choline_bind_3)

(274-311)

Choline-binding repeat (Choline_bind_3)

(313-355)

CHAP domain (CHAP)

(68-149)

Bacterial SH3 domain (SH3_5)

(186-249)


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 (%) Ha-value
  cbpD Streptococcus mitis SK321

95.968

100

0.967
  cbpD Streptococcus pneumoniae Rx1

60.889

100

0.743
  cbpD Streptococcus pneumoniae R6

60.889

100

0.743
  cbpD Streptococcus pneumoniae D39

60.667

100

0.74
  cbpD Streptococcus pneumoniae TIGR4

82.061

71.003

0.583
  cbpD/crfP Streptococcus suis strain ZY05719

48.927

76.645

0.375

Multiple sequence alignment    



References

[1] G Salvadori et al. (2018) High-resolution profiles of the Streptococcus mitis CSP signaling pathway reveal core and strain-specific regulated genes. BMC Genomics 19(1):453. [PMID: 29898666]