Align phenylpyruvate decarboxylase (EC 4.1.1.43) (characterized)
to candidate Pf1N1B4_1020 Branched-chain alpha-keto acid dehydrogenase, E1 component, alpha subunit (EC 1.2.4.4)
Query= BRENDA::A0A222AKA3 (368 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1020 Length = 332 Score = 230 bits (586), Expect = 5e-65 Identities = 130/320 (40%), Positives = 171/320 (53%), Gaps = 2/320 (0%) Query: 45 MYRAMVVGRAFNRQATAFSRQGRLAVYPSSRGQEACQVGSALAVRPTDWLFPTYRESVAL 104 +YR MV+ R F+++A A R GR+ Y + GQEA V + D L P YR++ Sbjct: 4 LYRQMVLTRLFDQKAVALQRTGRIGTYAPTLGQEAIGVAVGSLMHAEDVLIPYYRDTAVQ 63 Query: 105 LTRGIDPVQVLTLFRGDQHCG--YDPVTEHTAPQCTPLATQCLHAAGLADAARMAGDPIV 162 L RG+ ++L + GD+ DP P C P+ATQ LHA G+A A ++ G+ V Sbjct: 64 LMRGVRMEEILLYWGGDERGSDFADPAVAQDFPICVPIATQALHACGVASAFKIRGEHRV 123 Query: 163 ALAYIGDGATSEGDFHEALNYAAVRRAPVVFLVQNNQYAISVPLAKQTAARTLADKAAGY 222 A+ GDG TS+GDF EALN A + PVVF+V NNQ+AISVP Q A TLA KA G Sbjct: 124 AVTTCGDGGTSKGDFLEALNVAGAWQLPVVFMVNNNQWAISVPRRIQCGAPTLAQKAIGA 183 Query: 223 GMPGVRIDGNDVLQVYRAVHDAAERARAGHGPTLIEAVTYRIDAHTNADDDTRYRPAGEA 282 G G ++DGND+L VY V A ER R G GP L+E ++YR+ HT ADD TRYR A E Sbjct: 184 GFHGEQVDGNDMLAVYDRVQAALERTRHGKGPVLLECLSYRLGDHTTADDATRYRSADEV 243 Query: 283 DVWAAQDPVDRLERDLLAAGVLDRAAADGIAAAADAFAGELSARFSAPPTGDPMQMFRHV 342 ++P+ RL+R + GV D + + F A P + HV Sbjct: 244 KQAWLEEPIKRLQRFMAGQGVWDEGREQALISECQGLVQRAVDNFEAAGLQAPESVMDHV 303 Query: 343 YHHLPPHLREQSERLAAELA 362 Y P L EQ E +A Sbjct: 304 YAQWPQALAEQREDFLERVA 323 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: 9 Number of successful extensions: 2 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: 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