Align phenylpyruvate decarboxylase (EC 4.1.1.43) (characterized)
to candidate WP_011384713.1 AMB_RS11705 pyruvate dehydrogenase (acetyl-transferring) E1 component subunit alpha
Query= BRENDA::A0A222AKA3 (368 letters) >NCBI__GCF_000009985.1:WP_011384713.1 Length = 332 Score = 132 bits (331), Expect = 2e-35 Identities = 96/321 (29%), Positives = 148/321 (46%), Gaps = 14/321 (4%) Query: 34 AAGVPPDRQLLMYRAMVVGRAFNRQATAFSRQGRLAVYPSSR-GQEACQVGSALAVRPTD 92 AA P + YR M++ R F +A G + + GQEA VG D Sbjct: 10 AAEPTPQELIRYYREMLLIRRFEEKAGQLYGMGLINGFCHLYIGQEAVVVGMQAVAGAAD 69 Query: 93 WLFPTYRESVALLTRGIDPVQVLTLFRGDQHCGYDPVTEHTAPQCTP----------LAT 142 +YR+ +L G+DP V+ G + GY + + + Sbjct: 70 SCITSYRDHGHMLVCGMDPKGVMAELTG-RAGGYSRGKGGSMHMFSREKRFYGGHGIVGA 128 Query: 143 QCLHAAGLADAARMAGDPIVALAYIGDGATSEGDFHEALNYAAVRRAPVVFLVQNNQYAI 202 Q GL A + + D VA Y GDGA ++G +EA N AA+ + PVVF+++NN+YA+ Sbjct: 129 QVPLGTGLGFAHKYSKDNGVAHVYCGDGAVNQGQVYEAFNMAALWKLPVVFVIENNKYAM 188 Query: 203 SVPLAKQTAARTLADKAAGYGMPGVRIDGNDVLQVYRAVHDAAERARAGHGPTLIEAVTY 262 + A + L + A YG+PG ++G +++ V A A E AR+G+GP ++E TY Sbjct: 189 GTSTVRHAAGQELYMRGAAYGIPGEPVNGMNIIAVRDAAARALEHARSGNGPYILEMNTY 248 Query: 263 RIDAHTNADDDTRYRPAGEADVWAAQ-DPVDRLERDLLAAGVLDRAAADGIAAAADAFAG 321 R H + D +YR E Q DP+D+L+ LLA G++D A I Sbjct: 249 RYRGH-SMSDPAKYRSKEEVTKMREQHDPIDQLKEKLLAEGLIDEAGLKEIDREVKVIVT 307 Query: 322 ELSARFSAPPTGDPMQMFRHV 342 E + + P DP +++ V Sbjct: 308 EAAEFSQSSPEPDPSELWTDV 328 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: 279 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: 332 Length adjustment: 29 Effective length of query: 339 Effective length of database: 303 Effective search space: 102717 Effective search space used: 102717 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