Table 1.
Representative palindromic motifs associated with PARCEL coding regions
| Sources and features of input sequences analyzed | Features of derived palindromic motifs | ||||
|---|---|---|---|---|---|
| Taxon | PARCEL-containing ORFs analyzed (Locus_tag) | No. of HMM domains in ORFs | Palindrome motif (MEME) |
Motif sequence (Symmetrical residues underlined) |
Length (nt) |
| Mcc Kid (consensus) | Sum of 42 ORFs listed in Additional file 7 | 226 | (a) (b) |
GTTGGTTGGAGCTGCCAGCTCCAACCAAC TGAGACACTTCAAGTGTCTCA |
29 21 |
| Mmm SC PG1 | MSC_1021 (LppQ) plus MSC_1005 (LppC) | 14 | (a) | GGAAAAAGCATGGTTAAAATGTTTTGCGCCGCAAAACATTTTAACCAAGCTTTTTCC | 57 |
| Mcc Kid | MCAP_0311 (in Tra I) | 10 | (a) | TGAAACACTCCGCCCGTAACCGATACGGGCGGAGTGTTTCA | 41 |
| Salinibacter ruber | SRU_p0003 | 12 | (a) (b) |
GAAACCTTCAACCAACATATATCTTGGTTGAACGTTTC TACAATCGAAATATCCCAACTTCGGATATTTCGATTGAA |
38 39 |
| Vibrionales bacterium SWAT-3 | VSWAT3_25559 | 16 | (a) | TGACCGTAGGCGTATGCCATTCACCAATCGATTGGTGAAAGGCATACGCCTACGCACA | 58 |
| Ostreococcus lucimarinus | OSTLU_3281 | 9 | (a) (b) |
CCACGAGCTTCAACTTCGACATGTCGAACTTGAACCTCGACG GAACATGTCAGACATGTTC |
42 19 |
| Micromonas sp. RCC299 | MICPUN_102633 | 9 | (a) | CAAATTATCCCAAAAGCCGATGCGTTCAATCAACCCATCGGCTTTTCGGAAAATTTG | 57 |
| Helicobacter hepaticus | HH0050 | 19 | (a) (b) (c) |
CTAACGTTGGAAACATGCCAGCTATCTAAGGGGTGGCTCAGGTATTTAGCCAGCCCAAACATAACACGCATACAAGCAACGTTGCAAGTATCCCAGAAATCTATGGGCAGGCTAAAAACCTCAGCCACCCCAAACAAACCTGGCATGTATCCAACGTTAG CATGTGTGGAACGTTGCTTGTGTCCCATTTATCTAACCGCCCGTTAGATAAATGGGACACAAGCAACGTACCACACATG CCAGCCTTCAGAAGGCTGG |
160 79 19 |
| Psychroflexus torquis | P700755_04362 | 17 | (a) | CTTACAACCCACCCCTCGAGGGGTGGGATGAAAGAAGTGGCACTAATAAGCATGGCATGCATATTAGTGCCACTACTTACAACCCACCTCTTAAGAGGTGGGATGAAAGAAGTGGCACTAATAAGCATGCCATGCATATTAGTGCCACTACTTACAACCCACCCCTCGAGGGGTGGGATGAAAG | 184 |
DNA sequences of PARCEL-containing ORFs from several representative sources were analyzed for the occurrence of palindromic motifs as described in Methods. The derived sequences and features of palindrome motifs that correspond to the canonical HMM-defined repeat pattern are described. Additional details are shown in Additional file 6.