Align L-piperidine-6-carboxylate dehydrogenase; EC 1.2.1.21 (characterized, see rationale)
to candidate BPHYT_RS32650 BPHYT_RS32650 aldehyde dehydrogenase
Query= uniprot:Q88CC3 (496 letters) >FitnessBrowser__BFirm:BPHYT_RS32650 Length = 499 Score = 649 bits (1674), Expect = 0.0 Identities = 333/493 (67%), Positives = 378/493 (76%), Gaps = 2/493 (0%) Query: 5 LLERLGVAAEAYTQGDYPVHTPIDGSQIASVKLLGKAETIARIDQAQSAFEAWRSVPAPR 64 +L LG+A A GD VH+PI G I V AE + +A+ A+ AWR+VPAPR Sbjct: 6 ILADLGIAHAAQA-GDIAVHSPITGDLIGRVASNTVAEVDTALARAKEAYTAWRNVPAPR 64 Query: 65 RGELVRLFGEVLREHKADLGELVSIEAGKITQEGLGEVQEMIDICDFAVGLSRQLYGLTI 124 RGELVRL G LRE K LG ++++E GKI QEGLGEVQEMIDICDFAVGLSRQLYGLTI Sbjct: 65 RGELVRLLGNRLREKKQALGSIITLETGKILQEGLGEVQEMIDICDFAVGLSRQLYGLTI 124 Query: 125 ASERPGHHMRETWHPLGVVGVISAFNFPVAVWAWNTALALVAGNSVVWKPSEKTPLTALA 184 ASERPGH M ETWHP+G VISAFNFP AVW+WN ALALV GN+V+WKPSEKTPLTALA Sbjct: 125 ASERPGHRMAETWHPMGTCVVISAFNFPAAVWSWNAALALVCGNAVIWKPSEKTPLTALA 184 Query: 185 CQALFEKALKAFGDAPAGLAQLVIGGREAGEAMVDDPRVPLVSATGSTRMGREVGPRVAA 244 + +AL+ FGDAPAGL L+ GGR+ G +V DPR +VSATGST MGR VG VA Sbjct: 185 VNQILTEALQEFGDAPAGLTALINGGRDVGAKLVADPRASIVSATGSTEMGRTVGVEVAK 244 Query: 245 RFGRSILELGGNNAMILAPSADLDLAVRGILFSAVGTAGQRCTTLRRLIVHRSIKDEVVA 304 RFGRS+LELGGNNA I+ +AD +LA+RGILFSAVGTAGQRCT+LRRL VH S+ D+ + Sbjct: 245 RFGRSLLELGGNNAGIVTQTADHELAMRGILFSAVGTAGQRCTSLRRLFVHESVYDKTIE 304 Query: 305 RVKAAYGKVRIGDP-RKDNLVGPLIDKQSFDAMQGALAKARDEGGQVFGGERQLADQYPN 363 R+K Y KV IG+P K L+GPLIDKQS+ MQ AL +A EGG+VFGGER Y N Sbjct: 305 RLKQLYSKVPIGNPLEKGTLMGPLIDKQSYGRMQEALQQATAEGGKVFGGERVDVKGYEN 364 Query: 364 AYYVSPAIAEMPAQSDVVRHETFAPILYVLAYDDFEEALRLNNEVPQGLSSCIFTTDIRE 423 YYV PAI EMP+Q+ VV ETFAPILYVL Y DF +A+ NN GLSSC+FTTD+RE Sbjct: 365 GYYVRPAIVEMPSQTSVVLKETFAPILYVLRYTDFADAVEANNAAVHGLSSCVFTTDLRE 424 Query: 424 AERFQSASGSDCGIANVNIGTSGAEIGGAFGGEKETGGGRESGSDAWKGYMRRQTNTVNY 483 AERF S SGSDCGIANVNIG SGAEIGGAFGGEKETGGGRESGSDAWK YMRR TNTVNY Sbjct: 425 AERFLSDSGSDCGIANVNIGPSGAEIGGAFGGEKETGGGRESGSDAWKAYMRRATNTVNY 484 Query: 484 SRELPLAQGIVFD 496 S LPLAQGI F+ Sbjct: 485 SSALPLAQGIDFN 497 Lambda K H 0.318 0.135 0.396 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: 794 Number of extensions: 41 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: 496 Length of database: 499 Length adjustment: 34 Effective length of query: 462 Effective length of database: 465 Effective search space: 214830 Effective search space used: 214830 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 52 (24.6 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