Email updates

Keep up to date with the latest news and content from BMC Microbiology and BioMed Central.

Open Access Highly Accessed Research article

A nested leucine rich repeat (LRR) domain: The precursor of LRRs is a ten or eleven residue motif

Norio Matsushima1*, Hiroki Miyashita1, Tomoko Mikami123 and Yoshio Kuroki3

Author Affiliations

1 Sapporo Medical University Center for Medical Education, Sapporo, Hokkaido 060-8556, Japan

2 Sapporo City University School of Nursing, Sapporo, Hokkaido 060-0011, Japan

3 Sapporo Medical University School of Medicine, Sapporo, Hokkaido 060-8556, Japan

For all author emails, please log on.

BMC Microbiology 2010, 10:235  doi:10.1186/1471-2180-10-235

Published: 9 September 2010

Additional files

Additional file 1:

Table 1: IRREKO@LRR proteins. Database; Protein accession number or identification number in EMBL or NCBI. Consensus; The consensus sequences of complete IRREKO@LRRs with 21 residues are shown. Bold uppercase letters indicate more than 60%, normal uppercase letters indicate more than 50% and less than 60%, and normal lowercase letters indicate less than more than 30% and less than 50%. "L" in the consensus sequence denotes Leu, Val, or Ile. "x" denotes any residues. Length; The length of complete amino acid sequences of proteins. LRR repeat; The repeat number of LRR domain. Number is the repeat number of complete IRREKO@LRRs with 21 residues. The numeral in the parenthesis is total repeat number of LRRs. 1st LRR; The LRR class of the first repeat of LRR domain. SIGNAL; The Occurrence (○) and no-occurrence (-) of signal peptide sequence. LRRNT; The pattern of cysteine clusters of the N-terminal side of LRR domain.

Format: XLS Size: 77KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 2:

Figure S1: Sequence alignments of the LRR domain in seventeen IRREKO@ LRR proteins. (A) Escherichia coli yddk; (B) Bifidobacterium animalis BIFLAC_05879; (C) Vibrio harveyi HY01 A1Q_3393; (D) Shewanella woodyi ATCC 51908 SwooDRAFT_0647; (E) Unidentified eubacterium SCB49 SCB49_09905; (F) Colwellia psychrerythraea CPS_3882; (G) Listeria monocytogenes lmo0331 protein; (H) Treponema denticola TDE_0593; (I) Polaromonas naphthalenivorans Pnap_3264; (J) Ddelta proteobacterium MLMS-1 MldDRAFT_4836; (K) Kordia algicida OT-1 KAOT1_04155; (L) Coprococcus eutactus ATCC 27759 COPEUT_03021; (M) Clostridiales bacterium 1_7_47_FAA Cbac1_010100006401; (N) Listeria lin1204/LMOf6854_0364; (O) Escherichia coli SMS-3-5 EcSMS35_1703; (P) Escherichia coli O157:H7 ECS2075/Z2240; (Q) Trichomonas vaginalis G3 TVAG_084780. Overall consensus sequences of IRREKO@LRRs - LxxLxLxxNxLxxLDLxx(N/L/Q/x)xx or LxxLxLxxNxLxxLDLxx(N/L/Q/x)xx - are shown. The consensus amino acids are highlighted with reverse-contrast. Also the consensus amino acids of "SDS22-like" LRR with the consensus of LxxLxLxxNxLxxLxxLxxLxx and of "Bacterial" LRR with the consensus of LxxLxxNxLxxLPxLPxx are highlighted with reverse-contrast. Cysteines of the cysteine clusters at the N-terminal side of LRR domain are shown by underlined bold letter. Cons., the overall consensus sequences of IRREKO@LRRs; SIGNAL, signal peptide sequence; LRR; leucine rich repeat (LRR); IRREKO, IRREKO LRR; SDS22; "SDS22-like" LRR; BAC; "Bacterial" LRR; ISLAND, Island region interrupting LRRs; N-TERM, the N-terminal region of proteins; C-TERM, the C-terminal region of proteins; LRRNT; the region of cysteine clusters at the N-terminal side of LRR domain.

Format: DOC Size: 209KB Download file

This file can be viewed with: Microsoft Word Viewer

Open Data

Additional file 3:

Figure S2: Self-dot matrices for four IRREKO@LRR proteins. (A) Bifidobacterium animalis BIFLAC_05879; (B) Vibrio harveyi HY01A1Q_3393, (C) Listeria monocytogenes lmo0331 protein; (D) Treponema denticola TDE_0593. A window size of 21 residues was used. The threshold is 30 in the upper panel and 10 or 15 in the lower panel. Residues used are full lengths for the self-dot matrices; residue 1-186, 1-278, 1-633, and 1-631 of BIFLAC_05879, HY01A1Q_3393, lmo0331 protein, TDE_0593, respectively, were used. The abscissa and the ordinate are residues number.

Format: PDF Size: 416KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 4:

Figure S3: Protein secondary structure prediction in five IRREKO@LRR proteins by the Proteus and SSpro4.0 programs. (A) Escherichia coli yddk; (B) Bifidobacterium animalis BIFLAC_05879; (C) Vibrio harveyi HY01 A1Q_3393; (D) Listeria monocytogenes lmo0331 protein; (E) Shewanella woodyi ATCC 51908 SwooDRAFT_0647; (F) Treponema denticola TDE_0593. The highly conserved segment of individual LRRs is highlighted by a shadow. For comparison, its consensus sequence is shown in bold letters. Abbreviations: h/H, helix; c/C, coil; e/E, β-strand.

Format: DOC Size: 97KB Download file

This file can be viewed with: Microsoft Word Viewer

Open Data