Align L-piperidine-6-carboxylate dehydrogenase; EC 1.2.1.21 (characterized, see rationale)
to candidate Echvi_0535 Echvi_0535 NAD-dependent aldehyde dehydrogenases
Query= uniprot:Q88CC3 (496 letters) >FitnessBrowser__Cola:Echvi_0535 Length = 514 Score = 572 bits (1475), Expect = e-168 Identities = 285/475 (60%), Positives = 354/475 (74%), Gaps = 3/475 (0%) Query: 24 HTPIDGSQIASVKLLGKAETIARIDQAQSAFEAWRSVPAPRRGELVRLFGEVLREHKADL 83 ++P+DG ++ V++ + +DQA+ AF+AWR VPAP+RGE+VR G LR K+ L Sbjct: 40 YSPVDGKELGKVQMTTRESYEKVLDQAEKAFKAWRKVPAPQRGEVVRQIGIELRNKKSLL 99 Query: 84 GELVSIEAGKITQEGLGEVQEMIDICDFAVGLSRQLYGLTIASERPGHHMRETWHPLGVV 143 G+LVS E GK QEGLGEVQEMIDICDFAVGLSRQLYGLT+ SERP H M E WHPLG+V Sbjct: 100 GKLVSYEMGKSYQEGLGEVQEMIDICDFAVGLSRQLYGLTMHSERPSHRMYEQWHPLGIV 159 Query: 144 GVISAFNFPVAVWAWNTALALVAGNSVVWKPSEKTPLTALACQALFEKALKAFGDAPAGL 203 GVISAFNFPVAVW+WNT +A V G+ VWKPSEKTPLT++ACQ + G P G+ Sbjct: 160 GVISAFNFPVAVWSWNTMIAWVCGDVCVWKPSEKTPLTSVACQLIAADVFNRNG-FPEGI 218 Query: 204 AQLVIGGREAGEAMVDDPRVPLVSATGSTRMGREVGPRVAARFGRSILELGGNNAMILAP 263 L+IGG G + DPRV L+SATGST+MG+ VG V R G+ +LELGGNNA+I+ Sbjct: 219 TSLLIGGANVGAFLTQDPRVALISATGSTQMGKSVGETVGGRLGKVLLELGGNNAIIITE 278 Query: 264 SADLDLAVRGILFSAVGTAGQRCTTLRRLIVHRSIKDEVVARVKAAYGKVRIGDP-RKDN 322 ADLD+A+RG LF AVGTAGQRCT+ RRLI+H S+ +EV R+ AAY K+ IG+P +DN Sbjct: 279 HADLDIAIRGALFGAVGTAGQRCTSTRRLIIHESVFEEVKERMVAAYSKLTIGNPLDEDN 338 Query: 323 LVGPLIDKQSFDAMQGALAKARDEGG-QVFGGERQLADQYPNAYYVSPAIAEMPAQSDVV 381 +VGPLIDK + A+ + + EGG +V G ++Y + YV P++ E +V Sbjct: 339 IVGPLIDKDAVQNYLTAIERVKAEGGKEVVAGGLLEGEEYVSGCYVRPSVFEAENHFQIV 398 Query: 382 RHETFAPILYVLAYDDFEEALRLNNEVPQGLSSCIFTTDIREAERFQSASGSDCGIANVN 441 + ETF PILY++ Y +F+EA+ + N VPQGLSS I TT++REAER+ S+ GSDCGI+NVN Sbjct: 399 QKETFGPILYLMKYSEFDEAIAMQNNVPQGLSSAIMTTNMREAERYLSSEGSDCGISNVN 458 Query: 442 IGTSGAEIGGAFGGEKETGGGRESGSDAWKGYMRRQTNTVNYSRELPLAQGIVFD 496 IGTSGAEIGGAFGGEKETGGGRESGSDAWK YMRRQTNT+NYS +LPLAQGI FD Sbjct: 459 IGTSGAEIGGAFGGEKETGGGRESGSDAWKAYMRRQTNTINYSTDLPLAQGIKFD 513 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: 780 Number of extensions: 26 Number of successful extensions: 4 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: 514 Length adjustment: 34 Effective length of query: 462 Effective length of database: 480 Effective search space: 221760 Effective search space used: 221760 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