TABLE 3.
Evidence for F420 association in PPOX family genes from Mycobacterium smegmatis and M. tuberculosise
| Gene or sequence | M. tuberculosis gene | Found by PPPa | F420-specific clade HMMb | SIMBAL peak 1 |
SIMBAL peak 2 |
||
|---|---|---|---|---|---|---|---|
| Score | Sequencec | Score | Sequencec | ||||
| M. smegmatis genes | |||||||
| MSMEG_3380 | Rv2074 | Yes | TIGR03618 | 45.0 | RPDGTPQVNAMW | 14.5 | RQKYRNIKANPA |
| MSMEG_0048 | Rv2991 | Yes | TIGR03618 | 44.6 | LPDGRPHLVAMW | 29.8 | SQKAVNLRRDPT |
| MSMEG_6526 | Rv0121c | No | TIGR03668 | 39.7 | NADGAPHLVPVV | 6.6 | LRRLANIDRDSR |
| MSMEG_3863 | Rv2061c | Yes | TIGR03666 | 38.2 | TKDGRPKPTAIW | 16.4 | SWKVKRIRNTPR |
| MSMEG_5819 | - | No | TIGR04023 | 37.2 | QPDGTPQNSPVG | 6.3 | SQKYRNIARNNR |
| MSMEG_6576 | - | Yes | TIGR03618 | 32.5 | KANGLPQLSPVT | 42.0 | RAKTANLRRDPR |
| MSMEG_3880 | - | No | TIGR03618 | 31.1 | RSDGSPHVVAVG | 2.6 | SQKAVNAQERGV |
| MSMEG_3179 | - | No | TIGR03666 | 30.7 | RRDGTAVDTPIW | 2.3 | GPKTKRLAARPE |
| MSMEG_2791 | - | No | TIGR03618 | 28.5 | NPDGSPQATLVW | 50.8 | HKKVRNVRRDPR |
| MSMEG_6848 | - | No | TIGR03618 | 24.2 | DPDGAPQQSVVW | 38.8 | SRKERNLRRDPR |
| MSMEG_6485 | - | No | TIGR03618 | 20.0 | RADGSLQSSPVT | 35.3 | RAKSANIRRTPR |
| MSMEG_5170 | Rv1155 | Yes | TIGR03618 | 16.8 | KQDGRPQLSNVS | 42.0 | RAKTRNLRRDPR |
| MSMEG_5717 | - | No | - | 12.8 | GDKRGPLTVPIW | 6.5 | SRKHRLIESAGR |
| - | Rv3369 | No | TIGR03667 | 9.6 | ARSGQPVPRLVW | 1.6 | AAKVAHITAHPQ |
| MSMEG_4975 | - | No | - | 8.1 | VRDGHPVAFPIG | 1.0 | SPWLRALAEGAP |
| - | Rv1875 | No | TIGR03618 | 6.6 | RADGTVQASLVN | 5.6 | KVKLGNLRARPQ |
| MSMEG_1668 | - | No | TIGR03666 | 4.1 | KRSGEAVPSPIN | 8.9 | TAKVKRIRNNPN |
| MSMEG_5136 | - | No | - | 3.5 | TEDALPAVQPVN | 1.3 | GGKLSAAAKNQV |
| MSMEG_1061 | - | No | - | 1.8 | DAEGRVDVSPKG | 4.3 | VDGYLNVLQQPH |
| MSMEG_6744 | - | No | - | 1.8 | DDAGRVWAGPLT | 2.3 | YMTLGNLEVDSR |
| MSMEG_6519 | - | No | - | 1.5 | TTEGDPWASFVT | 3.1 | AEHGRNLAHDPR |
| MSMEG_0964 | - | No | - | 0.9 | DADGRPRSRVLH | 2.3 | PVKRAHLAEHPY |
| Negative control sequencesd | |||||||
| Mycobacterial PdxH (MSMEG_5675; Rv2607) | 2.6 | DADGRPVTRSVL | 0.7 | SAKGEHLAVNAY | |||
| Escherichia coli PdxH | 0.0 | DEHGQPYQRIVL | 0.0 | SRKAHQIENNPR | |||
| PdxH model TIGR00558 consensus | 0.7 | ePeGRPssRmVL | 0.0 | SRKGhqieeNPn | |||
| Non-F420-producing species PPOX family consensus | 0.1 | dddGrPyaRpvl | 0.2 | srkarnlaanPr | |||
Genes identified among the top 63 PPP hits versus an F420 producer profile (see Table S1 in the supplemental material).
TIGRFAMs HMMs built to represent clades of PPOX genes consisting only of genes from F420-producing organisms.
Twelve-mer sequences corresponding to the centers of the two prominent SIMBAL peaks. Residues in bold are observed primarily in the highest-scoring sequences, and underlined residues are those typical of low-scoring and known FMN-binding sequences.
These sequences are presumed to correspond to non-F420-binding enzymes. PdxH is a characterized FMN-binding enzyme. The non-F420-binding PPOX family consensus was constructed from a multiple sequence alignment of all PPOX family proteins from non-F420-producing species in our data set. Conserved residues are in uppercase; consensus residues are in lowercase.
Items in bold represent items in evidence of F420 binding for the respective gene.