Align L-piperidine-6-carboxylate dehydrogenase; EC 1.2.1.21 (characterized, see rationale)
to candidate WP_034273599.1 AMYHA_RS20335 aldehyde dehydrogenase family protein
Query= uniprot:Q88CC3 (496 letters) >NCBI__GCF_000504245.1:WP_034273599.1 Length = 496 Score = 207 bits (528), Expect = 5e-58 Identities = 148/460 (32%), Positives = 228/460 (49%), Gaps = 20/460 (4%) Query: 23 VHTPIDGSQIASVKLLGKAETIARIDQAQSAFE--AWRSVPAPRRGELVRLFGEVLREHK 80 V P + +++A+V + + A + A+ AF+ WR+ A RGEL+R +L+ K Sbjct: 22 VLNPANAAELATVCEADEKDVDAAVAAARRAFDDSPWRATTARERGELLREIARLLQRDK 81 Query: 81 ADLGELVSIEAGKITQEGLGEVQEMIDICDFAVGLSRQLYGLTIASERPGHHMRETWHPL 140 L S++ GK EG +V ++ + + L+ G + + R P+ Sbjct: 82 EHLARTESLDTGKTMAEGRVDVDDVTSVFRYYANLADNEAGRVVDTGDASVISRVVHEPV 141 Query: 141 GVVGVISAFNFPVAVWAWNTALALVAGNSVVWKPSEKTPLTALACQALFEKALKAFGDAP 200 GV +I+ +N+P+ +W A AL AGN+VV KPSE TPLT + L E+A P Sbjct: 142 GVCSLIAPWNYPLLQMSWKLAPALAAGNTVVMKPSEVTPLTTIELMRLVEEA-----GVP 196 Query: 201 AGLAQLVI-GGREAGEAMVDDPRVPLVSATGSTRMGREVGPRVAARFGRSILELGGNNAM 259 AG+ LV+ GG G MV P V LVS TG G+++ A R LELGG N Sbjct: 197 AGVVNLVLGGGANVGAPMVSHPDVDLVSFTGGLETGKKIMAMAAEGVKRVALELGGKNPN 256 Query: 260 ILAPSADLDLAVRGILFSAVGTAGQRCTTLRRLIVHRSIKDEVVARVKAAYGKVRIG--- 316 ++ AD D AV L +A +GQ C+ RLIV I DE VA + +R+G Sbjct: 257 VVFADADFDTAVDYALMAAFAHSGQVCSAGSRLIVESDIHDEFVAELARRADAIRLGDGL 316 Query: 317 DPRKDNLVGPLIDKQSFDAMQGALAKARDEGGQ-VFGGERQLADQYPNAYYVSPAI-AEM 374 DP + GPL + D ++ + +A+ EG + V GG R + + Y++ P + A+ Sbjct: 317 DPATE--CGPLSSAEHRDKVERHIEEAKTEGARLVVGGHRPTEPELADGYFLRPTVFADC 374 Query: 375 PAQSDVVRHETFAPILYVLAYDDFEEALRLNNEVPQGLSSCIFTTDIREAERFQSA-SGS 433 + +V+ E F P++ V +D +EA+RL N+ GL+ ++T+D A+R A Sbjct: 375 DREMRIVQDEVFGPVVTVERFDTEDEAIRLANDTEYGLAGAVWTSDASRAQRVAGALRHG 434 Query: 434 DCGIANVNIGTSGAEIGGAFGGEKETGGGRESGSDAWKGY 473 I + + AE GG FG ++G GRE G + Y Sbjct: 435 TVWINDFHPYLPQAEWGG-FG---KSGIGRELGPSGLEEY 470 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: 571 Number of extensions: 28 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 496 Length of database: 496 Length adjustment: 34 Effective length of query: 462 Effective length of database: 462 Effective search space: 213444 Effective search space used: 213444 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