Align L-piperidine-6-carboxylate dehydrogenase; EC 1.2.1.21 (characterized, see rationale)
to candidate WP_073950325.1 RH94_RS25575 gamma-aminobutyraldehyde dehydrogenase
Query= uniprot:Q88CC3 (496 letters) >NCBI__GCF_001906585.1:WP_073950325.1 Length = 511 Score = 223 bits (569), Expect = 9e-63 Identities = 153/458 (33%), Positives = 225/458 (49%), Gaps = 15/458 (3%) Query: 21 YPVHTPIDGSQIASVKLLGKAETIARIDQAQSAFEAWRSVPAPRRGELVRLFGEVLREHK 80 + V P G ++ + +L G + A + A+ AF W R + + F EVL + Sbjct: 38 HAVVDPATGEEVHTYELAGPDDVDAAVAAAREAFPGWAGATPGDRSDALHRFAEVLADRA 97 Query: 81 ADLGELVSIEAGK---ITQEGLGEVQEMIDICDFAVGLSRQLYGLTIASERPGHHMRETW 137 D S++ GK +T+E +V ID F G +R L G + H Sbjct: 98 EDFARAESLQCGKPLKLTREF--DVPGTIDNAAFFAGAARHLQGQSAGEYSGDHTSYVRR 155 Query: 138 HPLGVVGVISAFNFPVAVWAWNTALALVAGNSVVWKPSEKTPLTALACQALFEKALKAFG 197 P+GVVG I+ +N+P+ + AW A+ AGN++V KP+E TPLT+L LF +A G Sbjct: 156 EPIGVVGSIAPWNYPLQMAAWKVLPAIAAGNTIVLKPAELTPLTSL----LFAQAATEAG 211 Query: 198 DAPAGLAQLVIG-GREAGEAMVDDPRVPLVSATGSTRMGREVGPRVAARFGRSILELGGN 256 P G+ +V G G+EAGE +V P V +VS TGST +G+ V A R LELGG Sbjct: 212 -IPDGVINIVTGTGKEAGEHLVGHPDVAMVSFTGSTAVGKRVAEIATASVKRLHLELGGK 270 Query: 257 NAMILAPSADLDLAVRGILFSAVGTAGQRCTTLRRLIVHRSIKDEVVARVKAAYGKVRIG 316 ++ ADL+ AV G + A+ GQ CT R V R + +E VAR A VR+G Sbjct: 271 APFVVFDDADLEAAVNGAVAGALINTGQDCTAATRAYVQRPLYEEFVARTAALMETVRLG 330 Query: 317 DPRKDNL-VGPLIDKQSFDAMQGALAKARDEGGQVFGGERQLADQYPNAYYVSPAIAEMP 375 DP +GPLI D + G + +AR V GGE + AYY IA Sbjct: 331 DPFAPGTDLGPLISHVHRDRVAGFVDRARAYARVVTGGEAPQGELKNGAYYRPTLIAGAA 390 Query: 376 AQSDVVRHETFAPILYVLAYDDFEEALRLNNEVPQGLSSCIFTTDIREAERFQSASGSDC 435 S++V+ E F P+L VL +D +E +RL N+ GL++ ++ D+ A R + C Sbjct: 391 QDSEIVQSEIFGPVLVVLPFDSDDEGIRLANDTAYGLAASAWSRDVYRANRATREIKAGC 450 Query: 436 GIANVNIGTSGAEIGGAFGGEKETGGGRESGSDAWKGY 473 N +I GG K++G G++ S +++ Y Sbjct: 451 VWVNDHIPIISEM---PHGGSKQSGFGKDMSSYSFEEY 485 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: 610 Number of extensions: 32 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: 511 Length adjustment: 34 Effective length of query: 462 Effective length of database: 477 Effective search space: 220374 Effective search space used: 220374 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