Align L-piperidine-6-carboxylate dehydrogenase; EC 1.2.1.21 (characterized, see rationale)
to candidate WP_041097806.1 SUTH_RS05840 aldehyde dehydrogenase family protein
Query= uniprot:Q88CC3 (496 letters) >NCBI__GCF_000828635.1:WP_041097806.1 Length = 479 Score = 190 bits (482), Expect = 1e-52 Identities = 144/456 (31%), Positives = 223/456 (48%), Gaps = 23/456 (5%) Query: 18 QGDYPVHTPIDGSQIASVKLLGKAETIARIDQAQSAFEAWRSVPAPRRGELVRLFGEVLR 77 QG V +P DG+ +A+V A+ + A+ AF+AW PA R ++ E L+ Sbjct: 19 QGTIEVFSPTDGALLATVPQGNAADADKAVTAARGAFDAWSVTPAAERAAYLKKIQESLK 78 Query: 78 EHKADLGELVSIEAG---KITQEGLGEVQEMIDICDFAVGLSRQLYGLTIASERPGHHMR 134 ++ + +++E G K +Q +Q F G+ ++ E+ G+ + Sbjct: 79 ARADEIAKTITLEMGMPYKFSQR----IQVGSPTASF--GMYSKMLADFPFEEKVGNS-K 131 Query: 135 ETWHPLGVVGVISAFNFPVAVWAWNTALALVAGNSVVWKPSEKTPLTALACQALFEKALK 194 +GVV I+ +N+P+ A A AL AG +VV KPSE PL A L + + Sbjct: 132 VVREAVGVVAAITPWNYPLHQIAAKVAAALAAGCTVVLKPSEVAPLNAF----LLAEIIH 187 Query: 195 AFGDAPAGLAQLVIG-GREAGEAMVDDPRVPLVSATGSTRMGREVGPRVAARFGRSILEL 253 A G PAG+ L+ G G GEAMV V +VS TGSTR G V +A R LEL Sbjct: 188 AAG-VPAGVFNLITGYGPVVGEAMVTHREVDMVSFTGSTRAGTRVSELASATVKRVALEL 246 Query: 254 GGNNAMILAPSADLDLAVRGILFSAVGTAGQRCTTLRRLIVHRSIKDEVVARVKAAYGKV 313 GG +A I+ AD ++AV+G++ + +GQ CT R++V + E A Sbjct: 247 GGKSAAIILDDADFNVAVKGVVGNCYLNSGQTCTAHTRMLVPATRYAEAAKLAVEAAQAY 306 Query: 314 RIGDPRKDNL-VGPLIDKQSFDAMQGALAKARDEGGQVFGGERQLADQY-PNAYYVSPAI 371 R+GDP + + +GPL K D ++ + K EG ++ G L + P+ YYV P I Sbjct: 307 RVGDPMAEGVTLGPLASKMQQDRVRDYIGKGIAEGCELLTGGADLPEGVNPDGYYVKPTI 366 Query: 372 -AEMPAQSDVVRHETFAPILYVLAYDDFEEALRLNNEVPQGLSSCIFTTDIREAERFQSA 430 ++ S + + E F P+L +++Y D E+A+ + N GL+ +++ AE Q A Sbjct: 367 FGKVKPDSSIAQEEIFGPVLSIISYADEEDAVSIANGTVYGLAGGVWSATDEHAE--QVA 424 Query: 431 SGSDCGIANVNIGTSGAEIGGAFGGEKETGGGRESG 466 G +N GT + FGG K++G GRE G Sbjct: 425 RRMRTGQVEINGGT--FNMYAPFGGYKQSGNGRELG 458 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: 533 Number of extensions: 27 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: 479 Length adjustment: 34 Effective length of query: 462 Effective length of database: 445 Effective search space: 205590 Effective search space used: 205590 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 Apr 09 2024. 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