Align phenylpyruvate decarboxylase (EC 4.1.1.43) (characterized)
to candidate N515DRAFT_0356 N515DRAFT_0356 pyruvate dehydrogenase E1 component alpha subunit
Query= BRENDA::A0A222AKA3 (368 letters) >FitnessBrowser__Dyella79:N515DRAFT_0356 Length = 361 Score = 207 bits (527), Expect = 4e-58 Identities = 122/320 (38%), Positives = 177/320 (55%), Gaps = 6/320 (1%) Query: 40 DRQLLMYRAMVVGRAFNRQATAFSRQGRLAVYPSSRGQEACQVGSALAVRPTDWLFPTYR 99 D + +Y+ M+ R F+ ++ A R G+L Y S G EA VG A++P D P+YR Sbjct: 34 DHMVELYKLMMSTRVFDAKSVALQRTGKLGTYASCLGHEAAHVGIGSAMKPEDVFAPSYR 93 Query: 100 ESVALLTRGIDPVQVLTLFRGDQHCGYDPVTE---HTAPQCTPLATQCLHAAGLADAARM 156 E A L RG+ P +V + GD+ G D E H P+ATQCLHAAG A A ++ Sbjct: 94 EYGAQLYRGVQPREVYMYWGGDER-GNDYQKEPARHDFAWSVPIATQCLHAAGSALAFKI 152 Query: 157 AGDPIVALAYIGDGATSEGDFHEALNYAAVRRAPVVFLVQNNQYAISVPLAKQTAARTLA 216 + VA+ IGDG +S+GDF+ A+N + P+V ++ NNQ+AISVP Q+ A TLA Sbjct: 153 RNEKRVAVCTIGDGGSSKGDFYGAINITGAQNLPMVAVIVNNQWAISVPRKIQSGAPTLA 212 Query: 217 DKAAGYGMPGVRIDGNDVLQVYRAVHDAAERARAGHGPTLIEAVTYRIDAHTNADDDTRY 276 K G+ +++DGND++ V +A+ DA +RAR G G +++E VTYR+ HT ADD RY Sbjct: 213 QKGIAAGLFSIQVDGNDIIAVRKAMEDALDRARNGQGGSVLELVTYRLSDHTTADDARRY 272 Query: 277 RPAGEA-DVWAAQDPVDRLERDLLAAGVLDRAAADGIAAAADAFAGELSARFSAPPTGDP 335 R E D W A++P+ RL L+A V D A + A D + + T Sbjct: 273 RGEQEVKDAW-AKEPMKRLRAWLVAKNVWDDAKEEAWKAECDEWMDNEVNAYLETKTQPV 331 Query: 336 MQMFRHVYHHLPPHLREQSE 355 MF + + +P L +Q + Sbjct: 332 TAMFDYTFAEVPADLAKQRD 351 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: 271 Number of extensions: 7 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: 361 Length adjustment: 29 Effective length of query: 339 Effective length of database: 332 Effective search space: 112548 Effective search space used: 112548 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