Align L-piperidine-6-carboxylate dehydrogenase; EC 1.2.1.21 (characterized, see rationale)
to candidate WP_029133105.1 A3GO_RS0108930 CoA-acylating methylmalonate-semialdehyde dehydrogenase
Query= uniprot:Q88CC3 (496 letters) >NCBI__GCF_000428045.1:WP_029133105.1 Length = 497 Score = 206 bits (523), Expect = 2e-57 Identities = 143/470 (30%), Positives = 235/470 (50%), Gaps = 15/470 (3%) Query: 18 QGDYPVHTPIDGSQIASVKLLGKAETIARIDQAQSAFEAWRSVPAPRRGELVRLFGEVLR 77 Q P++ P G V L +A I A++AF AWR P +R +++ + ++L Sbjct: 17 QRTQPIYNPATGETSRQVALASRATVERAIAAAEAAFPAWRETPPLKRAQVMFRYKQLLE 76 Query: 78 EHKADLGELVSIEAGKITQEGLGEVQEMIDICDFAVGLSRQLYGLTIASERPGHHMRETW 137 +H ++ L++ E GK+ + +GE+ I++ ++A G L G S P + Sbjct: 77 QHAEEICGLITDEHGKVLDDAMGELMRGIEVVEYACGAPELLKGEYSKSVGPAIDSWSEF 136 Query: 138 HPLGVVGVISAFNFPVAVWAWNTALALVAGNSVVWKPSEKTPLTALACQALFEKALKAFG 197 PLGVV I+ FNFPV V W +A++ GN+ + KPSE+ P AL L ++A Sbjct: 137 QPLGVVVGITPFNFPVMVPMWMFPMAIICGNTFILKPSERDPSAALRIAELLQQA----- 191 Query: 198 DAPAGLAQLVIGGREAGEAMVDDPRVPLVSATGSTRMGREVGPRVAARFGRSILELGG-N 256 P G+ LV G +EA + +++DPRV S GST M E G+ + LGG Sbjct: 192 GLPDGVFNLVNGDKEAVDTLLNDPRVQAASFVGST-MVAEYIYHTGTAAGKRVQALGGAK 250 Query: 257 NAMILAPSADLDLAVRGILFSAVGTAGQRCTTLRRLI-VHRSIKDEVVARVKAAYGKVRI 315 N ++ P ADLD AV ++ +A G+ G+RC + ++ V ++ D VV + +++ Sbjct: 251 NHAVVMPDADLDNAVNALMGAAYGSCGERCMAISVVVCVGDTVADAVVGGLAEKLAHLKV 310 Query: 316 GDPRKD-NLVGPLIDKQSFDAMQGALAKARDEGGQ-VFGGERQLADQYPNAYYVSPAIAE 373 G R+ + +GPL+ Q ++G + + DEG + V G Q + + +++ + + Sbjct: 311 GPGRESGSEMGPLVTAQHLRKVRGYVDRGLDEGAELVVDGRGQRVEGHAEGFFLGGCLFD 370 Query: 374 -MPAQSDVVRHETFAPILYVLAYDDFEEALRLNNEVPQGLSSCIFTTDIREAERFQSASG 432 + + + R E F P+L V+ ++ ++A+ L + G +CIFT D EA RF S Sbjct: 371 RVTPEMSIYRDEIFGPVLCVVRVENLQQAMTLIDNHEYGNGTCIFTRD-GEAARFFS-DH 428 Query: 433 SDCGIANVNIGTSGAEIGGAFGGEKET--GGGRESGSDAWKGYMRRQTNT 480 G+ VNI +FGG K + G G DA + Y RR+T T Sbjct: 429 IRVGMVGVNIPLPVPVAYHSFGGWKRSLFGDLHAYGPDAVRFYTRRKTIT 478 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: 548 Number of extensions: 36 Number of successful extensions: 5 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: 497 Length adjustment: 34 Effective length of query: 462 Effective length of database: 463 Effective search space: 213906 Effective search space used: 213906 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