Align phenylpyruvate decarboxylase (EC 4.1.1.43) (characterized)
to candidate CA265_RS18405 CA265_RS18405 dehydrogenase
Query= BRENDA::A0A222AKA3 (368 letters) >FitnessBrowser__Pedo557:CA265_RS18405 Length = 658 Score = 165 bits (418), Expect = 3e-45 Identities = 98/279 (35%), Positives = 148/279 (53%), Gaps = 11/279 (3%) Query: 36 GVPPDRQLL-MYRAMVVGRAFNRQATAFSRQGRLAVYPSSRGQEACQVGSALAVRPTDWL 94 G D+ LL +YR ++ R + RQGR+ + S GQEA VGS LA++ +++ Sbjct: 6 GDKDDKFLLNLYRRLLYPRMVEDKMLKLLRQGRIGKWFSGIGQEAIAVGSTLAMQSDEYI 65 Query: 95 FPTYRESVALLTRGIDPVQVLTLFRG---------DQHCGYDPVTEHTAPQCTPLATQCL 145 P +R +R I +++ ++G D+ + + L Q Sbjct: 66 LPMHRNLGVFTSRDIPLKKLMAQWQGKITGFSKGRDRSFHFGTQEYKIIGMISHLGPQMA 125 Query: 146 HAAGLADAARMAGDPIVALAYIGDGATSEGDFHEALNYAAVRRAPVVFLVQNNQYAISVP 205 A G+A A + P L Y G+GATSEGDFHEA+N AAV PV+FL++NN Y +S P Sbjct: 126 LADGIALADVLRNQPHATLVYTGEGATSEGDFHEAVNVAAVWNLPVIFLIENNGYGLSTP 185 Query: 206 LAKQTAARTLADKAAGYGMPGVRIDGNDVLQVYRAVHDAAERARAGHGPTLIEAVTYRID 265 ++Q + L DKA GYG+ G++IDGN++L+VY ++ A R P L+E +T+R+ Sbjct: 186 KSEQFRCKNLVDKAIGYGVEGIQIDGNNILEVYDTINQLAMEIRKDPRPVLVECLTFRMR 245 Query: 266 AHTNADDDTRYRPAGEADVWAAQDPVDRLERDLLAAGVL 304 H A T+Y P D W +DP++ E L+ GVL Sbjct: 246 GHEEA-SGTKYVPQELFDEWEKKDPLNNYEAYLIEQGVL 283 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: 476 Number of extensions: 22 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 368 Length of database: 658 Length adjustment: 34 Effective length of query: 334 Effective length of database: 624 Effective search space: 208416 Effective search space used: 208416 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: 52 (24.6 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