Align L-piperidine-6-carboxylate dehydrogenase; EC 1.2.1.21 (characterized, see rationale)
to candidate GFF519 PS417_02645 aldehyde dehydrogenase
Query= uniprot:Q88CC3 (496 letters) >FitnessBrowser__WCS417:GFF519 Length = 496 Score = 798 bits (2060), Expect = 0.0 Identities = 398/496 (80%), Positives = 431/496 (86%) Query: 1 MVAGLLERLGVAAEAYTQGDYPVHTPIDGSQIASVKLLGKAETIARIDQAQSAFEAWRSV 60 MVA LL+RLGV Y G PVH+PIDGS+I SV G AE ++ +A+ AFEAWR V Sbjct: 1 MVAALLDRLGVNPALYQSGKQPVHSPIDGSRIGSVHWEGAAEVEQQVSRAEHAFEAWRKV 60 Query: 61 PAPRRGELVRLFGEVLREHKADLGELVSIEAGKITQEGLGEVQEMIDICDFAVGLSRQLY 120 PAPRRGELVR FG+VLRE+KADLGELVS EAGKITQEGLGEVQEMIDICDFAVGLSRQLY Sbjct: 61 PAPRRGELVRQFGDVLREYKADLGELVSWEAGKITQEGLGEVQEMIDICDFAVGLSRQLY 120 Query: 121 GLTIASERPGHHMRETWHPLGVVGVISAFNFPVAVWAWNTALALVAGNSVVWKPSEKTPL 180 GLTIASERPGHHMRETWHPLGVVGVISAFNFPVAVWAWNT LALV GN+V+WKPSEKTPL Sbjct: 121 GLTIASERPGHHMRETWHPLGVVGVISAFNFPVAVWAWNTTLALVCGNAVIWKPSEKTPL 180 Query: 181 TALACQALFEKALKAFGDAPAGLAQLVIGGREAGEAMVDDPRVPLVSATGSTRMGREVGP 240 TALACQALFE+ LK F AP L+Q++IGGR+AG A+VDDPRV L+SATGSTRMGREV P Sbjct: 181 TALACQALFERVLKKFDGAPEYLSQVIIGGRDAGAALVDDPRVALISATGSTRMGREVAP 240 Query: 241 RVAARFGRSILELGGNNAMILAPSADLDLAVRGILFSAVGTAGQRCTTLRRLIVHRSIKD 300 +VAARF RSILELGGNNAMIL PSADLD+AVR ILFSAVGTAGQRCTTLRRLI H S+K Sbjct: 241 KVAARFARSILELGGNNAMILGPSADLDMAVRAILFSAVGTAGQRCTTLRRLIAHESVKA 300 Query: 301 EVVARVKAAYGKVRIGDPRKDNLVGPLIDKQSFDAMQGALAKARDEGGQVFGGERQLADQ 360 E+V R+KAAY KVRIG P + NL+GPLIDK FD MQ AL +A EGG+VFGG+RQL DQ Sbjct: 301 EIVTRLKAAYSKVRIGHPLEGNLIGPLIDKHGFDNMQDALEQALSEGGKVFGGKRQLEDQ 360 Query: 361 YPNAYYVSPAIAEMPAQSDVVRHETFAPILYVLAYDDFEEALRLNNEVPQGLSSCIFTTD 420 +PNAYYVSPAI EMP QSDVV ETFAPILYV+ Y DF EALRLNN VPQGLSSCIFTTD Sbjct: 361 FPNAYYVSPAIVEMPEQSDVVCTETFAPILYVIGYSDFNEALRLNNAVPQGLSSCIFTTD 420 Query: 421 IREAERFQSASGSDCGIANVNIGTSGAEIGGAFGGEKETGGGRESGSDAWKGYMRRQTNT 480 +REAE+F SA GSDCGIANVNIG SGAEIGGAFGGEKETGGGRESGSDAW+GYMRRQTNT Sbjct: 421 VREAEQFMSAVGSDCGIANVNIGPSGAEIGGAFGGEKETGGGRESGSDAWRGYMRRQTNT 480 Query: 481 VNYSRELPLAQGIVFD 496 VNYS ELPLAQGI FD Sbjct: 481 VNYSLELPLAQGITFD 496 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: 839 Number of extensions: 21 Number of successful extensions: 1 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: 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 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