Detailed information    

experimental Experimentally validated

Overview

Name   cbpD   Type   Auxiliary factor
Locus tag   SMSK321_RS10490 Genome accession   NZ_AEDT01000032
Coordinates   199625..200743 (-) Length   372 a.a.
NCBI ID   WP_000703686.1    Uniprot ID   -
Organism   Streptococcus mitis SK321     
Function   fratricide process; lyse non-competent cells   
Cell lysis

Function

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


Genomic Context

Location: 194625..205743
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  SMSK321_RS10470 (SMSK321_1605) - 196018..196476 (-) 459 WP_001211265.1 CtsR family transcriptional regulator -
  SMSK321_RS0102850 - 196595..197323 (-) 729 WP_000136238.1 ABC transporter ATP-binding protein -
  SMSK321_RS10475 (SMSK321_1606) - 197323..198315 (-) 993 WP_004235755.1 ABC transporter substrate-binding protein -
  SMSK321_RS10480 - 198353..199120 (-) 768 Protein_200 ABC transporter permease -
  SMSK321_RS10485 (SMSK321_1608) - 199083..199373 (-) 291 WP_004235758.1 thiamine-binding protein -
  SMSK321_RS10490 (SMSK321_1609) cbpD 199625..200743 (-) 1119 WP_000703686.1 choline binding-anchored murein hydrolase CbpD Auxiliary factor
  SMSK321_RS10495 (SMSK321_1610) - 200833..201099 (-) 267 WP_001278169.1 Veg family protein -
  SMSK321_RS10500 (SMSK321_1611) dnaB 201101..202453 (-) 1353 WP_000852485.1 replicative DNA helicase -
  SMSK321_RS0102860 rplI 202497..202949 (-) 453 WP_000864214.1 50S ribosomal protein L9 -
  SMSK321_RS10505 (SMSK321_1612) - 202946..204919 (-) 1974 WP_000715142.1 DHH family phosphoesterase -
  SMSK321_RS10510 (SMSK321_1613) hpf 205055..205603 (-) 549 WP_000599100.1 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 comE positive effect
  comE comX/sigX/comX1/sigX1 positive effect
  comE comC positive effect
  comE comD positive effect
  comE comA positive effect
  comE comX/sigX/comX2/sigX2 positive effect
  comE comW positive effect
  comE comB positive effect
  comD comE positive effect
  comX/sigX/comX1/sigX1 late competence genes positive effect
  comW comX/sigX/comX1/sigX1 positive effect
  comC comD positive effect
  comB comC positive effect
  comA comC positive effect
  comX/sigX/comX2/sigX2 late competence genes positive effect
  comW comX/sigX/comX2/sigX2 positive effect
  comX/sigX/comX1/sigX1 late competence genes positive effect
  comX/sigX/comX2/sigX2 late competence genes positive effect

Sequence

Protein


Download         Length: 372 a.a.        Molecular weight: 41446.82 Da        Isoelectric Point: 9.6548

>NTDB_id=520 SMSK321_RS10490 WP_000703686.1 199625..200743(-) (cbpD) [Streptococcus mitis SK321]
MKISPFKVAETRFSFRKSAKKVVPFLVVGLMLAAGNSVYAYSGGNGSIARGDDYPAHYKNGSQEIDKWRMYSRQCTSFAA
FRLSNVNGFEIPAAYGNANEWGYRARREGYRVDNTPTIGSIAWSTAGTYGHVAWVSNVIGDEIEIEEYNYGIRESYNKRI
VKANTMTGFIHFKDLAGGSVGNSQSSASTGGTHFFKSKAAIKNQPLASATAIDYYYPGENVHYDQILEKDGYKWLSYTAY
NGSRRYIQLEGLTSSQNYQNQSGNSSNYGSNNSSTVGWKKINGSWYHFKSNGSKSTGWLKDGSSWYYLKSSGEMQTGWLK
ENGLWYYLDSSGAMKTGWYQVSGKWYYSYSSGALAVNTTVDGYRVNSDGVRV

Nucleotide


Download         Length: 1119 bp        

>NTDB_id=520 SMSK321_RS10490 WP_000703686.1 199625..200743(-) (cbpD) [Streptococcus mitis SK321]
ATGAAAATTTCACCATTTAAAGTAGCAGAGACAAGATTTTCTTTCAGAAAATCAGCTAAAAAGGTTGTTCCCTTTTTAGT
AGTAGGATTGATGTTAGCAGCGGGTAATAGTGTATATGCCTATTCCGGAGGAAATGGATCGATTGCGCGTGGGGATGATT
ATCCTGCTCATTATAAAAATGGGAGCCAGGAGATTGATAAGTGGCGCATGTATTCTCGTCAGTGTACTTCTTTTGCAGCC
TTTCGTTTGAGTAATGTCAATGGTTTTGAGATTCCGGCTGCTTATGGGAATGCGAATGAATGGGGCTATCGTGCTCGTCG
TGAAGGTTATCGTGTCGATAATACACCAACGATTGGCTCTATTGCTTGGTCTACTGCAGGAACTTATGGTCATGTTGCTT
GGGTGTCAAATGTAATAGGAGATGAGATTGAGATTGAAGAATACAATTATGGAATAAGGGAATCTTACAACAAGCGCATC
GTGAAGGCAAATACTATGACGGGGTTTATTCATTTTAAAGATTTAGCTGGTGGCAGTGTTGGGAATAGTCAATCCTCAGC
TTCAACAGGAGGAACACATTTTTTCAAGTCTAAGGCTGCTATCAAAAATCAGCCTCTAGCTAGCGCAACTGCGATTGATT
ACTATTATCCTGGGGAGAATGTTCATTATGATCAAATTCTCGAAAAAGACGGATACAAGTGGTTGAGTTATACGGCTTAT
AATGGAAGTCGTCGCTATATCCAGCTAGAGGGATTGACTTCTTCACAGAATTATCAGAATCAATCAGGAAATAGCTCTAA
CTATGGATCCAATAACAGTTCAACTGTCGGTTGGAAGAAAATAAATGGTAGTTGGTATCATTTTAAATCAAATGGGTCTA
AATCAACAGGCTGGCTGAAAGATGGTTCTAGTTGGTATTATTTGAAATCATCTGGTGAAATGCAGACAGGCTGGTTAAAG
GAAAATGGTCTGTGGTATTATTTAGATAGTTCAGGTGCAATGAAAACGGGCTGGTACCAAGTATCTGGTAAGTGGTATTA
TTCTTACTCTTCAGGCGCCTTAGCTGTCAATACGACAGTGGATGGCTACAGAGTAAATAGTGATGGAGTACGAGTATAG

Domains

Predicted by InterproScan.

Bacterial SH3 domain (SH3_5)

(186-249)

CHAP domain (CHAP)

(68-149)

Choline-binding repeat (Choline_bind_3)

(276-314)

Choline-binding repeat (Choline_bind_3)

(316-358)


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 NCTC 12261

95.968

100

0.967
  cbpD Streptococcus pneumoniae TIGR4

60.706

100

0.739
  cbpD Streptococcus pneumoniae R6

60.265

100

0.734
  cbpD Streptococcus pneumoniae Rx1

60.265

100

0.734
  cbpD Streptococcus pneumoniae D39

60.044

100

0.731
  cbpD/crfP Streptococcus suis strain ZY05719

48.133

79.276

0.382

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]