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) | GTTGGTTGGAGCTG CCAGCTCCAACCAAC TGAGACACTT CAAGTGTCTCA | 29 21 |
Mmm SC PG1 | MSC_1021 (LppQ) plus MSC_1005 (LppC) | 14 | (a) | GGAAAAAGC ATGGTTAAAATGTTTTGCG CCGCAAAACATTTTAACCA AGCTTTTTCC | 57 |
Mcc Kid | MCAP_0311 (in Tra I) | 10 | (a) | TGAAACACTCCGCCCGTA AC CG ATACGGGCGGAGTGTTTCA | 41 |
Salinibacter ruber | SRU_p0003 | 12 | (a) (b) | GAAAC CTTCAACCAA CATATATCTTGGTTGAACGTTTC T ACAATCGAAATATCC CAA CTT CGGATATTTCGATTG AA | 38 39 |
Vibrionales bacterium SWAT-3 | VSWAT3_25559 | 16 | (a) | TG ACCGTAGGCGTATGCC ATTCACCAATCGATTGGTGAA AGGCATACGCCTACGCACA | 58 |
Ostreococcus lucimarinus | OSTLU_3281 | 9 | (a) (b) | C CACGAG CTTCAA CTTCGACATGTCGAA CTTGAA CCTCG ACG GAACATGTC AGACATGTTC | 42 19 |
Micromonas sp. RCC299 | MICPUN_102633 | 9 | (a) | CAAATT ATCC CAAAAGCCGATG CGTT CA AT CAAC CCATCGGCTTTT CGGA AAATTTG | 57 |
Helicobacter hepaticus | HH0050 | 19 | (a) (b) (c) | CTAACGTTGGA AACATGCCAG CT AT CT AAGGGGTGGCT CAGGT ATTTAGCC AGCCCA AA CAT AAC ACG CATAC AAGCAACGTTGC AAGTAT CC CAG AAAT CT ATGGGC AGGCTAAAAACCT CAGCCACCCC AAA CA AA CCTGGCATGT ATCCAACGTTAG CATGTGTGGAACGTTGCTTGTGTCCCATTTATCTAAC CG CC CGTTAGATAAATGGGACACAAGCAACGT ACCACACATG CCAGCCTTC AGAAGGCTGG | 160 79 19 |
Psychroflexus torquis | P700755_04362 | 17 | (a) | CTT ACA ACCCACCCCTCGAGGGGTGGG ATG AAAG AAGTGGCACTAATA AGCATGGCATGC ATATTAGTGCCACT ACTT ACA ACCCACCTCTTAAGAGGTGGG ATG AAAG AAGTGGCACTAATA AGCATGCCATGC ATATTAGTGCCACTACTT ACA ACCCACCCCTCGAGGGGTGGG ATG AAAG | 184 |