Align L-piperidine-6-carboxylate dehydrogenase; EC 1.2.1.21 (characterized, see rationale)
to candidate WP_078210708.1 BXU11_RS01185 aldehyde dehydrogenase family protein
Query= uniprot:Q88CC3 (496 letters) >NCBI__GCF_002017945.1:WP_078210708.1 Length = 517 Score = 555 bits (1429), Expect = e-162 Identities = 288/476 (60%), Positives = 353/476 (74%), Gaps = 4/476 (0%) Query: 24 HTPIDGSQIASVKLLGKAETIARIDQAQSAFEAWRSVPAPRRGELVRLFGEVLREHKADL 83 ++P+DG IASV A+ + A +AF+ +R +PAP+RGE+VR FGE LR++K L Sbjct: 42 YSPVDGQLIASVTTSSAADYEKVMQTATAAFKTFRLMPAPQRGEIVRQFGEKLRKNKEAL 101 Query: 84 GELVSIEAGKITQEGLGEVQEMIDICDFAVGLSRQLYGLTIASERPGHHMRETWHPLGVV 143 G+LVS E GK QEG GEVQEMIDICDFAVGLSRQL+GLT+ SERPGH M E +H LGVV Sbjct: 102 GKLVSYEMGKSLQEGYGEVQEMIDICDFAVGLSRQLHGLTMHSERPGHRMYEQYHSLGVV 161 Query: 144 GVISAFNFPVAVWAWNTALALVAGNSVVWKPSEKTPLTALACQALFEKALKAFGDAPAGL 203 G+ISAFNFPVAVWAWNTALA + G+ VWKPSEKTPL +ACQ + + LK + P G+ Sbjct: 162 GIISAFNFPVAVWAWNTALAWICGDVCVWKPSEKTPLCGVACQNIIAEVLKE-NNLPEGI 220 Query: 204 AQLVIGGREAGEAMVDDPRVPLVSATGSTRMGREVGPRVAARFGRSILELGGNNAMILAP 263 + L+ G GE + D RVPL+SATGSTRMG+ V VA R G+S+LELGGNNA+I+ P Sbjct: 221 SCLINGDYTIGEMLTKDTRVPLISATGSTRMGKIVAQTVAGRLGKSLLELGGNNAIIVTP 280 Query: 264 SADLDLAVRGILFSAVGTAGQRCTTLRRLIVHRSIKDEVVARVKAAYGKVRIGDPRKD-N 322 AD+ + V G +F AVGTAGQRCT+ RRLI+H S+ D+V + AAYG++RIG+P + N Sbjct: 281 DADIKMTVIGAVFGAVGTAGQRCTSTRRLIIHESMYDKVKDTIVAAYGQLRIGNPLDEKN 340 Query: 323 LVGPLIDKQSFDAMQGALAKARDEGGQVF-GGERQLADQYPNAYYVSPAIAEMPAQSDVV 381 VGPLIDKQ+ + AL K EGG++ G + Y + YV PAIAE ++V Sbjct: 341 HVGPLIDKQAVEMYNQALTKVVAEGGKILVEGGVLSGEGYESGCYVKPAIAEAQNSFEIV 400 Query: 382 RHETFAPILYVLAYD-DFEEALRLNNEVPQGLSSCIFTTDIREAERFQSASGSDCGIANV 440 +HETFAP+LY+L Y D + A++L N V QGLSS I T ++REAERF S +GSDCGIANV Sbjct: 401 QHETFAPVLYLLKYSGDVDNAIKLQNGVAQGLSSAIMTNNLREAERFLSVAGSDCGIANV 460 Query: 441 NIGTSGAEIGGAFGGEKETGGGRESGSDAWKGYMRRQTNTVNYSRELPLAQGIVFD 496 NIGTSGAEIGGAFGGEKETGGGRESGSDAWK YMRRQTNT+NY+ LPLAQGI FD Sbjct: 461 NIGTSGAEIGGAFGGEKETGGGRESGSDAWKVYMRRQTNTINYTTNLPLAQGIKFD 516 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: 737 Number of extensions: 32 Number of successful extensions: 5 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: 517 Length adjustment: 34 Effective length of query: 462 Effective length of database: 483 Effective search space: 223146 Effective search space used: 223146 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 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