Align L-piperidine-6-carboxylate dehydrogenase; EC 1.2.1.21 (characterized, see rationale)
to candidate WP_050654861.1 C1M55_RS10170 CoA-acylating methylmalonate-semialdehyde dehydrogenase
Query= uniprot:Q88CC3 (496 letters) >NCBI__GCF_002893965.1:WP_050654861.1 Length = 501 Score = 205 bits (522), Expect = 3e-57 Identities = 136/441 (30%), Positives = 218/441 (49%), Gaps = 11/441 (2%) Query: 22 PVHTPIDGSQIASVKLLGKAETIARIDQAQSAFEAWRSVPAPRRGELVRLFGEVLREHKA 81 PV P G + L + A ID A +AF AWR RR +++ F E+L K Sbjct: 27 PVTNPATGQITGRLALANLEDARAVIDAAAAAFPAWRDTSLARRTQVLFSFRELLNARKG 86 Query: 82 DLGELVSIEAGKITQEGLGEVQEMIDICDFAVGLSRQLYGLTIASERPGHHMRETWHPLG 141 +L E+++ E GK+ + LGE+ ++ +FA G+ L G + + PLG Sbjct: 87 ELAEIITAEHGKVLSDALGEISRGQEVVEFACGIPHLLKGGYTENASTKVDVYSIRQPLG 146 Query: 142 VVGVISAFNFPVAVWAWNTALALVAGNSVVWKPSEKTPLTALACQALFEKALKAFGDAPA 201 VG+IS FNFP V W +A+ AGN+V+ KPSEK P A+ L+ +A P Sbjct: 147 PVGIISPFNFPAMVPMWFFPVAIAAGNTVILKPSEKDPTAAIWLAELWAEA-----GLPP 201 Query: 202 GLAQLVIGGREAGEAMVDDPRVPLVSATGSTRMGREVGPRVAARFGRSILELGG-NNAMI 260 G+ ++ G + A + ++++ V +S GST + + V A G+ + LGG N I Sbjct: 202 GVFNVLQGDKLAVDELLENKAVKAISFVGSTPIAQYVYATGTAN-GKRVQALGGAKNHAI 260 Query: 261 LAPSADLDLAVRGILFSAVGTAGQRCTTLRRLIVHRSIKDEVVARVKAAYGKVRIGDPRK 320 + P ADLDLA ++ + G+AG+RC + L+ I DE+VA++ + GD K Sbjct: 261 VLPDADLDLAADAMVNAGFGSAGERCMAISALVAVGDIADELVAKIVERTTPLVTGDGTK 320 Query: 321 DNLVGPLIDKQSFDAMQGALAKARDEGGQ-VFGGERQLADQYPNAYYVSPAIAE-MPAQS 378 ++ +GPL+ K D + + +G V G AD P+ +++ P + + + Sbjct: 321 NSDMGPLVTKAHRDKVASYVDAGEKDGATIVVDGRTVQADGGPDGFWLGPTLIDHVTTDM 380 Query: 379 DVVRHETFAPILYVLAYDDFEEALRLNNEVPQGLSSCIFTTDIREAERFQSASGSDCGIA 438 + E F P+L V+ D +++AL L N P G + IFT D A RFQ+ + G+ Sbjct: 381 SIYTDEIFGPVLSVVRVDTYDQALELINNNPYGNGTAIFTNDGGAARRFQNE--VEVGMI 438 Query: 439 NVNIGTSGAEIGGAFGGEKET 459 +N+ +FGG K + Sbjct: 439 GINVPIPVPMAYYSFGGWKNS 459 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: 29 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: 501 Length adjustment: 34 Effective length of query: 462 Effective length of database: 467 Effective search space: 215754 Effective search space used: 215754 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 24 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