Align phenylpyruvate decarboxylase (EC 4.1.1.43) (characterized)
to candidate AZOBR_RS25395 AZOBR_RS25395 acetoin dehydrogenase
Query= BRENDA::A0A222AKA3 (368 letters) >FitnessBrowser__azobra:AZOBR_RS25395 Length = 316 Score = 108 bits (270), Expect = 2e-28 Identities = 91/297 (30%), Positives = 127/297 (42%), Gaps = 12/297 (4%) Query: 45 MYRAMVVGRAFNRQATAFSRQGRLAVYPS-SRGQEACQVGSALAVRPTDWLFPTYRESVA 103 +Y M R F A + G++A Y S GQEA +R D L T+R Sbjct: 3 LYATMQRIRVFETLADEAHKAGQVAGYIHLSIGQEAIAAAVGANLRADDVLTSTHRGHGH 62 Query: 104 LLTRGIDPVQVLTLF--RGDQHCGYDPVTEHTAP-QCTPLATQCLHAAGL------ADAA 154 + +G DP+ + R CG + H A L + AAGL A A Sbjct: 63 TIAKGADPLAMFRELCGRAGGTCGGKGGSMHIADFSVGMLGANGVVAAGLPIAVGAAHAI 122 Query: 155 RMAGDPIVALAYIGDGATSEGDFHEALNYAAVRRAPVVFLVQNNQYAISVPLAKQTAART 214 + G+ +A+ + GDGAT+ G F EALN+AA R PV+F+ ++N Y + +A Sbjct: 123 ALKGEDRIAVCFFGDGATNRGPFLEALNWAAAFRLPVLFVCEDNGYGATTRTGSVSAGGG 182 Query: 215 LADKAAGYGMPGVRIDGNDVLQVYRAVHDAAERARAGHGPTLIEAVTYRIDAHTNADDDT 274 +A G+P +DGND+ V A R G GP + A TYR HT++D T Sbjct: 183 PGVRAESLGIPVTVVDGNDLAAVDAAAAALVRAVRDGGGPQFLHARTYRFRGHTSSDPAT 242 Query: 275 RYRPAGEADV-WAAQDPVDRLERDLLAAGVLDRAAADGIAAAADAFAGELSARFSAP 330 YR A E A DP+ R L GV A + A L+ +P Sbjct: 243 -YRDAAEVRAQLAGNDPLQRAAATLAELGVTPDALERVERHERETLAAALATALDSP 298 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: 274 Number of extensions: 14 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: 316 Length adjustment: 29 Effective length of query: 339 Effective length of database: 287 Effective search space: 97293 Effective search space used: 97293 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