Align phenylpyruvate decarboxylase (EC 4.1.1.43) (characterized)
to candidate AO353_19950 AO353_19950 pyruvate dehydrogenase (acetyl-transferring) E1 component subunit alpha
Query= BRENDA::A0A222AKA3 (368 letters) >FitnessBrowser__pseudo3_N2E3:AO353_19950 Length = 327 Score = 128 bits (322), Expect = 2e-34 Identities = 98/321 (30%), Positives = 148/321 (46%), Gaps = 15/321 (4%) Query: 35 AGVPPDRQLLMYRAMVVGRAFNRQATAFSRQGRLAVYPSSR-GQEACQVGSALAVRPTDW 93 + +P + L + R M+ R +A +G++ + G+EA VG+ A+ D Sbjct: 4 SSLPKELALGLLRDMLRIRRLEERAGELYGEGKIRGFLHLYIGEEAVAVGALHALAANDA 63 Query: 94 LFPTYRESVALLTRGIDPVQVLTLFRGDQH-CG---------YDPVTEHTAPQCTPLATQ 143 L TYRE L +G+ ++ G Q C +D T Sbjct: 64 LVATYREHGHALIKGVPMKTIMAEMYGRQEGCSRGRGGSMHLFDVSTRFFGGNAIVAGGL 123 Query: 144 CLHAAGLADAARMAGDPIVALAYIGDGATSEGDFHEALNYAAVRRAPVVFLVQNNQYAIS 203 L GLA A M G ++ + G+GA +EG FHE++N AA+ + P++F +NN YA+ Sbjct: 124 PL-TVGLALAEHMQGGSRLSTCFFGEGAMAEGAFHESINLAALWQLPMLFCCENNLYAMG 182 Query: 204 VPLAKQTAARTLADKAAGYGMPGVRIDGNDVLQVYRAVHDAAERARAGHGPTLIEAVTYR 263 LA+ + L KA+ Y + +DG DV+ VY A A E RAG GP +E TYR Sbjct: 183 TALARSQSQTDLCSKASAYKVEARSVDGMDVIAVYEATCLAVEHIRAGRGPYFLEFRTYR 242 Query: 264 IDAHTNADDDTRYRPAGEADVWAAQDPVDRLERDLLAAGVLDRAAADGIAAAADAFAGEL 323 AH+ D YR E + W + P+ L A G+LD A I A DA E Sbjct: 243 FRAHSMFDPQL-YRDKAEVEQWKTRGPIHTYSARLKAEGLLDEAGFQAILAEVDAEV-EA 300 Query: 324 SARFSAPPTGDPMQ-MFRHVY 343 + F+ + +P++ + R VY Sbjct: 301 AVVFADSGSLEPVEDLSRDVY 321 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: 229 Number of extensions: 15 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: 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