Align phenylpyruvate decarboxylase (EC 4.1.1.43) (characterized)
to candidate WP_005456123.1 SACCYDRAFT_RS10835 pyruvate dehydrogenase (acetyl-transferring) E1 component subunit alpha
Query= BRENDA::A0A222AKA3 (368 letters) >NCBI__GCF_000244975.1:WP_005456123.1 Length = 347 Score = 157 bits (397), Expect = 4e-43 Identities = 116/350 (33%), Positives = 166/350 (47%), Gaps = 18/350 (5%) Query: 23 VTAAPAAAAPAAAGVPPDRQLLMYRAMVVGRAFNRQATAFSRQGRLAVYPS-SRGQEACQ 81 +T A+ PA G P+ YR MV+ R F +A Q ++ Y + G+EA Sbjct: 1 MTETIEASRPALPGEDPETLRRYYRDMVLVRRFEERAAQGYTQAKIGGYCHLNLGEEATV 60 Query: 82 VGSALAVRPTDWLFPTYRESVALLTRGIDPVQVLTL-----------FRGDQHCGYDPVT 130 VG A+RPTD+LF YRE L +GI+P +V+ + G H +D V Sbjct: 61 VGLLAAMRPTDYLFTNYREHGYALAKGIEPGRVMAELYGRTTGTSKGWGGSMHL-FD-VP 118 Query: 131 EHTAPQCTPLATQCLHAAGLADAARMAGDPIVALAYIGDGATSEGDFHEALNYAAVRRAP 190 + Q A G A A D V + +GDG T+ G FHE+LN AA+ R P Sbjct: 119 SRLLGGYGIVGGQLPLAVGAALAVDYRRDDDVVVCQMGDGTTNIGAFHESLNLAALWRLP 178 Query: 191 VVFLVQNNQYAISVPLAKQTAARTLADKAAGYGMPGVRIDGNDVLQVYRAVHDAAERARA 250 VVF+V NN + + + +A L +AA Y MPG R+DG D+L V ++AR Sbjct: 179 VVFVVINNNLGMGTTVERSSAEPELFRRAAAYRMPGERVDGTDLLAVRDTARRLIDQARE 238 Query: 251 GHGPTLIEAVTYRIDAHTNADDDTRYRPAGEADVWAAQDPVDRLERDLLAAGVLDRAAAD 310 P L+E V++R+ H + D +YR E A DP+ R +L+AAGV+D AD Sbjct: 239 EGTPALLETVSHRLKGH-SVVDPAKYRSETEIAAARAADPLIRFRAELVAAGVVDDDGAD 297 Query: 311 GIAAAADAFAGELSARFSAPPTGDPMQMFRHVYHHLPPHLREQSERLAAE 360 + +A A A P +P +F H Y +R + RL A+ Sbjct: 298 ALEQSAAEEVDAAVAFAEASPHPEPSSLFDHTY---ATPVRGEDRRLPAD 344 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: 309 Number of extensions: 12 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 368 Length of database: 347 Length adjustment: 29 Effective length of query: 339 Effective length of database: 318 Effective search space: 107802 Effective search space used: 107802 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 24 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