Align L-piperidine-6-carboxylate dehydrogenase; EC 1.2.1.21 (characterized, see rationale)
to candidate N515DRAFT_0465 N515DRAFT_0465 aldehyde dehydrogenase (NAD+)
Query= uniprot:Q88CC3 (496 letters) >FitnessBrowser__Dyella79:N515DRAFT_0465 Length = 511 Score = 527 bits (1357), Expect = e-154 Identities = 291/510 (57%), Positives = 353/510 (69%), Gaps = 22/510 (4%) Query: 5 LLERLGVAAEA----YTQGDY----------PVHTPIDGSQIASVKLLGKAETIARIDQA 50 +L+ LG+ AE QG++ PV+ P G I +V A+ + +A Sbjct: 5 ILKALGIGAEHSGTYLGQGEWSRTSDAGALQPVN-PATGEVIGTVHASSAADYETIVKRA 63 Query: 51 QSAFEAWRSVPAPRRGELVRLFGEVLREHKADLGELVSIEAGKITQEGLGEVQEMIDICD 110 Q AF+ WR+ PAPRRGE VRL GE LR+HK LG LV++E GKI EG GEVQEMIDI D Sbjct: 64 QEAFKTWRTTPAPRRGEAVRLCGEALRKHKDALGSLVALEMGKIKPEGDGEVQEMIDIAD 123 Query: 111 FAVGLSRQLYGLTIASERPGHHMRETWHPLGVVGVISAFNFPVAVWAWNTALALVAGNSV 170 FAVG SR LYG T+ SERPGH M E +HPLG+VG+ISAFNFPVAVWAWN LA + G+ Sbjct: 124 FAVGQSRMLYGYTMHSERPGHRMYEQYHPLGLVGIISAFNFPVAVWAWNAFLAAICGDIC 183 Query: 171 VWKPSEKTPLTALACQALFEKALKAFGDAPAGLAQLVIGGREAGEAMVDDPRVPLVSATG 230 +WKPS KTPL+A+A + +ALKA G P G + + VDD R+PL+S TG Sbjct: 184 IWKPSPKTPLSAIATMKICNEALKA-GGFPDIFFLFNDAGTDLSQGFVDDKRIPLISFTG 242 Query: 231 STRMGREVGPRVAARFGRSILELGGNNAMILAPSADLDLAVRGILFSAVGTAGQRCTTLR 290 ST++GR VG RVA R GRS+LELGGNNA+IL SADL LA+ I+F AVGTAGQRCTT R Sbjct: 243 STKVGRMVGERVARRMGRSLLELGGNNAIILDASADLKLAIPAIVFGAVGTAGQRCTTTR 302 Query: 291 RLIVHRSIKDEVVARVKAAYGKV--RIGDPR-KDNLVGPLIDKQSFDAMQGALAKARDEG 347 RL VH SI EV ++ AAY +V +IGDP L+GPL + + A GA+ KA+ G Sbjct: 303 RLFVHESIVGEVTDKLVAAYKQVEGKIGDPTLATTLMGPLNSQDAVQAYLGAVEKAKASG 362 Query: 348 GQVFGGERQLADQYPNAYYVSPAIAEMPAQSD-VVRHETFAPILYVLAYDDFEEALRLNN 406 G+V G L+D+ N +V P I SD VV+ ETFAPILY++ + +EA+ L N Sbjct: 363 GKVLTGGAALSDRKGN--FVLPTIVTGVKNSDEVVQTETFAPILYIMPFKSLDEAIELQN 420 Query: 407 EVPQGLSSCIFTTDIREAERFQSASGSDCGIANVNIGTSGAEIGGAFGGEKETGGGRESG 466 +VPQGLSS IFT D++ AE++ S++GSDCGIANVNIGTSGAEIGGAFGGEKETGGGRESG Sbjct: 421 DVPQGLSSAIFTRDLKAAEQYLSSAGSDCGIANVNIGTSGAEIGGAFGGEKETGGGRESG 480 Query: 467 SDAWKGYMRRQTNTVNYSRELPLAQGIVFD 496 SDAWK YMRRQTNT NYS LPLAQGI FD Sbjct: 481 SDAWKVYMRRQTNTSNYSDSLPLAQGIKFD 510 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: 697 Number of extensions: 28 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: 511 Length adjustment: 34 Effective length of query: 462 Effective length of database: 477 Effective search space: 220374 Effective search space used: 220374 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