TABLE 2.
Characteristics of genes in mel and mrl loci
| Gene locus | Similar organism (gene)a | E value (score)b | % Identity (no. of aa)c | Other similarities or motifsd | Putative activity |
|---|---|---|---|---|---|
| mel3 | |||||
| melL | M. smegmatis (pknD) | 3e-94 (349) | 66 (272) | S_TKc, DUF477 | Serine/threonine kinase |
| mel4 | |||||
| melM | M. tuberculosis (Rv2315c) | 0.0 (859) | 86 (505) | COG0312, Zn-dep.prot. | Protease |
| melN | M. tuberculosis (Rv2314c) | 0.0 (711) | 84 (457) | COG0312, Zn-dep.prot. | Protease |
| melO | M. tuberculosis (Rv2313) | 5e-113 (410) | 84 (283) | COG2128, unchar.cons.prot. | Unknown |
| melP | N. farcinica (nfa42450) | 3e-13 (78.6) | 52 (91) | None | Unknown |
| mrl1 | |||||
| mrlA | Arthrobacter sp. (Arth4051) | 2e-47 (194) | 46 (276) | COG1922, teich.ac.syn. | Cell wall biogenesis |
| mrlB | M. avium subsp. paratuberculosis (MAP0964c) | 0.0 (704) | 71 (507) | COG2148, sug.trans.lps, COG1086, nuc.diph.ep. | Cell wall biogenesis |
| mrlC | M. avium subsp. paratuberculosis (MAP0963c) | 3e-150 (535) | 68 (488) | pfam01943, polys.syn., COG0728, MviN | Cell wall biogenesis |
| mrlD | M. avium subsp. paratuberculosis (MAP0962c) | 0.0 (685) | 63 (663) | COG1216, glyc.tran., pfam00534, glyc.tran1 | Cell wall biogenesis |
| mrlE | M. avium subsp. paratuberculosis (MAP0961c) | 8e-125 (449) | 72 (349) | COG0438, glyc.tran. | Cell wall biogenesis |
| mrl2 | |||||
| mrlF | M. avium subsp. paratuberculosis (MAP3191) | 0.0 (646) | 87 (370) | pfam04209, hom.diox. | Phe and Tyr metabolism |
| mrlG | M. avium subsp. paratuberculosis (MAP3192) | 0.0 (711) | 87 (392) | COG1506, dip.amin.pep. | Amino acid transport/metabolism |
| mrlH | M. avium subsp. paratuberculosis (MAP3193) | 0.0 (685) | 90 (396) | COG1804, acCoA-trans. | Lipid transport/metabolism |
| mrlI | M. avium subsp. paratuberculosis (MAP3194) | 2e-104 (381) | 81 (301) | pfam00682, aldolase | Metabolism |
| mrlJ | M. avium subsp. paratuberculosis (MAP3195) | 1e-87 (325) | 80 (213) | pfam00440, TetR_N, COG1309, AcrR | Transcriptional regulation |
| mrlK | M. avium subsp. paratuberculosis (FadE12-3) | 0.0 (734) | 87 (412) | cd00567, ACAD | Lipid metabolism |
| mrlL | M. avium subsp. paratuberculosis (MAP3197) | 3e-89 (322) | 75 (264) | COG1960, ACAD pfam01636, phosphotr. | Metabolism |
| mrlM | M. avium subsp. paratuberculosis (MAP3198) | 5e-37 (156) | 62 (129) | COG3631, ketost.isom. | Metabolism |
| mrlN | M. avium subsp. paratuberculosis (MAP3199) | 2e-56 (221) | 64 (173) | pfam04264, YceI | Unknown |
| mrlO | M. tuberculosis (Rv3143) | 7e-55 (216) | 88 (130) | Cd00156, sig.rec. | Signal receiver |
That is, the organism that carries the protein most similar to that encoded by the M. marinum gene identified, along with the name of the corresponding gene in that organism in parentheses.
The expectation frequency (E value) is a parameter that describes the significance of the sequence match and the score of the sequence match according to NCBI protein-protein BLAST when it is compared to the closest homologue.
The percent identity at the amino acid (aa) level and the number of amino acids (in parentheses) that could be aligned to show this level of identity.
This column indicates the placement of the putative protein product into a cluster of orthologues (COG or KOG [eukaryotic]) using the CD-Search at NCBI and SignalP v.1.1 at the Center for Biological Sequence Analysis website. COG, clusters of orthologous groups; KOG, clusters of orthologous groups for eukaryotic genomes; pfam, protein family; cd, conserved domain; S_TKc, serine/threonine protein kinase catalytic domain; DUF477, domain of unknown function found in Eukarya and Eubacteria; Zn-dep.prot., Zn-dependent proteases; unchar.cons.prot., uncharacterized conserved protein; teich.ac.syn., teichoic acid synthesis proteins; sug.trans.lps, sugar transferases involved in lipopolysaccharide synthesis; nuc.diph.ep., predicted nucleoside-diphosphate sugar epimerase; polys.syn., polysaccharide biosynthesis protein; MviN, uncharacterized membrane protein thought to be involved in virulence; glyc.tran., predicted glycosyltransferases; glyc.tran1, glycosyl transferases group 1; hom.diox., homogentisate 1,2-dioxygenase involved in the metabolism of Phe and Tyr; dip.amin.pep., dipeptidyl aminopeptidases/acylaminoacyl-peptidases; TetR_N, TetR family bacterial regulatory proteins; AcrR, AcrR family of transcriptional regulators; ACAD, acyl-coenzyme A dehydrogenase; phosphotr., phosphotransferase enzyme family; ketost.isom., ketosteroid isomerase; YceI, E. coli YceI-like family of inducible periplasmic proteins; sig.rec., signal receiver domain.