Align phenylpyruvate decarboxylase (EC 4.1.1.43) (characterized)
to candidate WP_041305179.1 BTUS_RS06515 thiamine pyrophosphate-dependent dehydrogenase E1 component subunit alpha
Query= BRENDA::A0A222AKA3 (368 letters) >NCBI__GCF_000092905.1:WP_041305179.1 Length = 330 Score = 222 bits (566), Expect = 1e-62 Identities = 128/321 (39%), Positives = 182/321 (56%), Gaps = 11/321 (3%) Query: 34 AAGVPPDRQLLMYRAMVVGRAFNRQATAFSRQGRLAVYPSSRGQEACQVGSALAV-RPTD 92 A G+ + L MYR M+ R + + +R G++ S +G E QVG+A A+ R D Sbjct: 7 ALGLTGEDLLAMYRVMLTARRVDERLWVLNRAGKIPFVISCQGHEGAQVGAAFALDRQKD 66 Query: 93 WLFPTYRESVALLTRGIDPVQVLTLFRG---DQHCGYDPVTEHTAPQ-------CTPLAT 142 ++ P YR+ +L G P +L D + G + H + +P++T Sbjct: 67 YVLPYYRDVAVVLAFGQTPRDLLLAAYAKADDPNSGGRQMPNHFGSRKHRIVSGSSPVST 126 Query: 143 QCLHAAGLADAARMAGDPIVALAYIGDGATSEGDFHEALNYAAVRRAPVVFLVQNNQYAI 202 Q HAAG+A AA+M GD +VA G+G++++GDFHE LN+AAV R PVVF QNN YAI Sbjct: 127 QIPHAAGIALAAKMRGDDVVAYVSFGEGSSNQGDFHEGLNFAAVHRLPVVFFCQNNGYAI 186 Query: 203 SVPLAKQTAARTLADKAAGYGMPGVRIDGNDVLQVYRAVHDAAERARAGHGPTLIEAVTY 262 SVP +K+ A ++AD+AAGYG+PGV +DG+DVL VY AV A ERAR G GPTL+EA+T Sbjct: 187 SVPASKELATPSVADRAAGYGIPGVVVDGSDVLGVYHAVKTAVERARRGDGPTLVEAMTV 246 Query: 263 RIDAHTNADDDTRYRPAGEADVWAAQDPVDRLERDLLAAGVLDRAAADGIAAAADAFAGE 322 R+ H++ DDD YR E + +DP+ +L L+A+GV D + A E Sbjct: 247 RLTPHSSDDDDRTYRSGEELEDARRRDPLPQLAEYLIASGVADEVLLRALDQEVRAEVDE 306 Query: 323 LSARFSAPPTGDPMQMFRHVY 343 +A DP + R V+ Sbjct: 307 ATAYAEQARDPDPADVLRFVH 327 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: 319 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: 330 Length adjustment: 29 Effective length of query: 339 Effective length of database: 301 Effective search space: 102039 Effective search space used: 102039 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 24 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