Align phenylpyruvate decarboxylase (EC 4.1.1.43) (characterized)
to candidate BPHYT_RS29360 BPHYT_RS29360 acetoin:2,6-dichlorophenolindophenol oxidoreductase subunit alpha
Query= BRENDA::A0A222AKA3 (368 letters) >FitnessBrowser__BFirm:BPHYT_RS29360 Length = 327 Score = 112 bits (281), Expect = 1e-29 Identities = 85/282 (30%), Positives = 130/282 (46%), Gaps = 11/282 (3%) Query: 76 GQEACQVGSALAVRPTDWLFPTYRESVALLTRGIDPVQVLTLFRGDQH--CGYDPVTEHT 133 G+EA VG+ L + D++ T+R + +G+D ++ G + C + H Sbjct: 47 GEEASAVGTMLHLNDADYVATTHRGHGHCIAKGVDVRGMMAEIYGRKTGVCHGKGGSMHI 106 Query: 134 APQCTPL--ATQCLHA-----AGLADAARMAGDPIVALAYIGDGATSEGDFHEALNYAAV 186 A + A + A G A AA+ V + + GDGA+++G E+LN A+V Sbjct: 107 ADLSKGMLGANGIVGAGGPLICGAALAAKYKKSGGVGVCFFGDGASNQGVIFESLNLASV 166 Query: 187 RRAPVVFLVQNNQYAISVPLAKQTAARTLADKAAGYGMPGVRIDGNDVLQVYRAVHDAAE 246 R P +F+ +NN YA + A +AD+A+G+GMPGV +DG D V+ A+ +A E Sbjct: 167 WRLPAIFVAENNGYAEATSSTWSVATDNIADRASGFGMPGVIVDGFDFFAVHEALGEAIE 226 Query: 247 RARAGHGPTLIEAVTYRIDAHTNADDDTRYRPAGEAD-VWAAQDPVDRLERDLLAAGVLD 305 RAR G GPTL+E R H D T YR GE + +D + R E ++ A +L Sbjct: 227 RARQGGGPTLVEVKFSRYFGHFEGDAQT-YRAPGEVQKLRDEKDCLKRFEERVVRAEMLS 285 Query: 306 RAAADGIAAAADAFAGELSARFSAPPTGDPMQMFRHVYHHLP 347 G+ A + A P + VY P Sbjct: 286 VDQLRGVDAEVKSLIDSAVTEAKAAPLPTAEDLLSDVYVSYP 327 Lambda K H 0.319 0.132 0.395 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 246 Number of extensions: 12 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 368 Length of database: 327 Length adjustment: 29 Effective length of query: 339 Effective length of database: 298 Effective search space: 101022 Effective search space used: 101022 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory