Align L-piperidine-6-carboxylate dehydrogenase; EC 1.2.1.21 (characterized, see rationale)
to candidate PfGW456L13_3932 Aldehyde dehydrogenase A (EC 1.2.1.22)
Query= uniprot:Q88CC3 (496 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3932 Length = 477 Score = 198 bits (504), Expect = 3e-55 Identities = 142/448 (31%), Positives = 214/448 (47%), Gaps = 28/448 (6%) Query: 23 VHTPIDGSQIASVKLLGKAETIARIDQAQSAFEAWRSVPAPRRGELVRLFGEVLREHKAD 82 V P G+ ++ V + + A +A + W PA R +R LRE+ A Sbjct: 24 VINPATGAVLSKVPASTAEDVERALAAACAAQKGWARKPANDRAGYLRRIAAKLRENVAH 83 Query: 83 LGELVSIEAGKITQEGLGEVQEMIDICDFAVGLSRQLYGLTIASERPGHHMRETWHPLGV 142 L +++E GKI+ EV D D+ +R++ G I S+R ++ PLGV Sbjct: 84 LARTITLEQGKISGLAEVEVNFTADYLDYMAEWARRIEGEIITSDRQNENIFLFRKPLGV 143 Query: 143 VGVISAFNFPVAVWAWNTALALVAGNSVVWKPSEKTPLTALACQALFEKA-LKAFGDAPA 201 V I +NFP + A A AL+ GN++V KPSE+TP FE A L A D P Sbjct: 144 VAGILPWNFPFFLIARKMAPALLTGNTIVIKPSEETPNNC------FEFARLVAETDLPP 197 Query: 202 GLAQLVIGGREAGEAMVDDPRVPLVSATGSTRMGREVGPRVAARFGRSILELGGNNAMIL 261 G+ +V G + G A+ V ++S TGS G + A + LELGG I+ Sbjct: 198 GVFNVVCGDGKVGAALSSHKGVDMISFTGSVDTGSRIMAAAAPNITKLNLELGGKAPAIV 257 Query: 262 APSADLDLAVRGILFSAVGTAGQRCTTLRRLIVHRSIKDEVVARVKAAYGKVRIGDP--R 319 ADLDLAVR I S + +GQ C R+ V R + D+ + R+ AA R GDP + Sbjct: 258 LADADLDLAVRAIRDSRIINSGQVCNCAERVYVERKVADQFIERIAAAMSATRYGDPIAQ 317 Query: 320 KDNLVGPLIDKQSFDAMQGALAKARDEGGQVFGGERQLADQYPNAYYVSPAI-AEMPAQS 378 D +GPLI++Q D++ + A +G + G Q+AD PN ++ P + A A Sbjct: 318 PDVEMGPLINRQGLDSVNRKVRTALSQGASLISG-GQMAD-LPNGFHFQPTVLAGCRADM 375 Query: 379 DVVRHETFAPILYVLAYDDFEEALRLNNEVPQGLSSCIFTTDIREA-------------- 424 +++R E F P+L + DD +EA+ L N+ GL+S I+T D+ + Sbjct: 376 EIMREEIFGPVLPIQIIDDLDEAIALANDCDYGLTSSIYTRDLSKTMQAMRELDFGETYV 435 Query: 425 --ERFQSASGSDCGIANVNIGTSGAEIG 450 E F++ G G+ IG + + G Sbjct: 436 NRENFEAMQGFHAGVRKSGIGGADGKHG 463 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: 494 Number of extensions: 24 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: 477 Length adjustment: 34 Effective length of query: 462 Effective length of database: 443 Effective search space: 204666 Effective search space used: 204666 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