Align L-piperidine-6-carboxylate dehydrogenase; EC 1.2.1.21 (characterized, see rationale)
to candidate CA265_RS19780 CA265_RS19780 aldehyde dehydrogenase family protein
Query= uniprot:Q88CC3 (496 letters) >FitnessBrowser__Pedo557:CA265_RS19780 Length = 513 Score = 596 bits (1536), Expect = e-175 Identities = 309/509 (60%), Positives = 374/509 (73%), Gaps = 15/509 (2%) Query: 2 VAGLLERLGVAAE--AYTQG-----DYPVHT-----PIDGSQIASVKLLGKAETIARIDQ 49 + +L +LG+ A AY+ G + V+T P+DG IAS K+ + A + + Sbjct: 5 IQSILNKLGINASNAAYSTGSNWGGELNVNTLESFSPVDGKLIASAKIATADDYDAVVLK 64 Query: 50 AQSAFEAWRSVPAPRRGELVRLFGEVLREHKADLGELVSIEAGKITQEGLGEVQEMIDIC 109 AQ AF AWRSVPAP+RGE+VR FG+ LRE+K LG LVS E GK QEG GEVQEMIDIC Sbjct: 65 AQEAFTAWRSVPAPKRGEIVRQFGDALRENKDALGTLVSYEMGKSLQEGFGEVQEMIDIC 124 Query: 110 DFAVGLSRQLYGLTIASERPGHHMRETWHPLGVVGVISAFNFPVAVWAWNTALALVAGNS 169 DFAVGLSRQLYGLT+ SERP H M E WHPLG+VG+ISAFNFPVAVW+WNTALALV GN Sbjct: 125 DFAVGLSRQLYGLTMHSERPSHRMYEQWHPLGIVGIISAFNFPVAVWSWNTALALVCGNV 184 Query: 170 VVWKPSEKTPLTALACQALFEKALKAFGDAPAGLAQLVIGGREAGEAMVDDPRVPLVSAT 229 +WKPSEKTPLTA+ACQ + K K D G+ L++G RE GE M +D R+PL+SAT Sbjct: 185 CIWKPSEKTPLTAIACQHIIAKVFKD-NDIAEGVCNLILGDREVGERMTNDGRIPLISAT 243 Query: 230 GSTRMGREVGPRVAARFGRSILELGGNNAMILAPSADLDLAVRGILFSAVGTAGQRCTTL 289 GSTRMG+ VG V AR G+S+LELGGNNA+I++ ADLD+++ G +F AVGTAGQRCT+ Sbjct: 244 GSTRMGKAVGAAVGARLGKSLLELGGNNAIIISEHADLDMSLIGAVFGAVGTAGQRCTST 303 Query: 290 RRLIVHRSIKDEVVARVKAAYGKVRIGDP-RKDNLVGPLIDKQSFDAMQGALAKARDEGG 348 RRLI+H S+ D A++ AYG++RIGDP ++N VGPLID + A ++AK + EGG Sbjct: 304 RRLIIHESVYDAFTAKLVKAYGQLRIGDPLDQNNHVGPLIDTDAVAAYLDSIAKCKAEGG 363 Query: 349 Q-VFGGERQLADQYPNAYYVSPAIAEMPAQSDVVRHETFAPILYVLAYDDFEEALRLNNE 407 V G D Y + YV P IAE+ +V+HETFAPILY++ Y +EA+ L N Sbjct: 364 NFVVEGGVLSGDAYTSGCYVKPCIAEVQNDFKIVQHETFAPILYLIKYKTLDEAIALQNG 423 Query: 408 VPQGLSSCIFTTDIREAERFQSASGSDCGIANVNIGTSGAEIGGAFGGEKETGGGRESGS 467 VPQGLSS I T ++REAE+F SA GSDCGIANVNIGTSGAEIGGAFGGEKETGGGRESGS Sbjct: 424 VPQGLSSAIMTLNLREAEQFLSAKGSDCGIANVNIGTSGAEIGGAFGGEKETGGGRESGS 483 Query: 468 DAWKGYMRRQTNTVNYSRELPLAQGIVFD 496 DAW+ YMRRQTNT+NYS LPLAQGI FD Sbjct: 484 DAWRAYMRRQTNTINYSNTLPLAQGIKFD 512 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: 758 Number of extensions: 33 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: 513 Length adjustment: 34 Effective length of query: 462 Effective length of database: 479 Effective search space: 221298 Effective search space used: 221298 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