Align L-piperidine-6-carboxylate dehydrogenase; EC 1.2.1.21 (characterized, see rationale)
to candidate Pf1N1B4_3024 4-aminobutyraldehyde dehydrogenase (EC 1.2.1.19)
Query= uniprot:Q88CC3 (496 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3024 Length = 474 Score = 197 bits (502), Expect = 5e-55 Identities = 145/462 (31%), Positives = 217/462 (46%), Gaps = 36/462 (7%) Query: 19 GDYP---VHTPIDGSQIASVKLLGKAETIARIDQAQSAFEAWRSVPAPRRGELVRLFGEV 75 GD P V P G + + +A+ A + A +AF+AW R L+ ++ Sbjct: 14 GDGPAQAVFNPALGRVLVEINEASEAQVDAAVRAADNAFQAWSQTTPKERSLLLLKLADI 73 Query: 76 LREHKADLGELVSIEAGKITQEGLG-EVQEMIDICDFAVGLSRQLYGLTIASERPGHHMR 134 + H +L +L S GK L E+ + D+ F G +R + G PGH Sbjct: 74 IEAHGEELAKLESDNCGKPYSAALNDEIPAIADVFRFFAGANRCMSGALGGEYLPGHTSM 133 Query: 135 ETWHPLGVVGVISAFNFPVAVWAWNTALALVAGNSVVWKPSEKTPLTALACQALFEKALK 194 P+GV+ I+ +N+P+ + AW A AL AGN+VV KPSE+TPLTAL L E A Sbjct: 134 IRRDPVGVIASIAPWNYPLMMVAWKIAPALAAGNTVVLKPSEQTPLTAL---RLAELASD 190 Query: 195 AFGDAPAGLAQLVIG-GREAGEAMVDDPRVPLVSATGSTRMGREVGPRVAARFGRSILEL 253 F PAG+ LV G G G A+V+ P+V +VS TGS G + A R +EL Sbjct: 191 IF---PAGVLNLVYGRGSAVGTALVNHPKVRMVSLTGSIATGSNIISSTAGNVKRLHMEL 247 Query: 254 GGNNAMILAPSADLDLAVRGILFSAVGTAGQRCTTLRRLIVHRSIKDEVVARVKAAYGKV 313 GG +I+ AD+D AV GI AGQ CT R+ I D+ V ++ AA + Sbjct: 248 GGKAPVIIFDDADIDAAVEGIRTFGFYNAGQDCTAACRIYAQAGIYDQFVEKLGAAVSSI 307 Query: 314 RIG---DPRKDNLVGPLIDKQSFDAMQGALAKARDE-------GGQVFGGERQLADQYPN 363 + G DP + +GPLI Q D + + +A + GG+ G N Sbjct: 308 KYGLQDDPSTE--LGPLISAQHRDRVTALVERAMAQPHIRLITGGKAVEG---------N 356 Query: 364 AYYVSPAI-AEMPAQSDVVRHETFAPILYVLAYDDFEEALRLNNEVPQGLSSCIFTTDIR 422 ++ P + A++ ++VR E F P++ V + D +AL N+ GL+S ++TTD+ Sbjct: 357 GFFFEPTVLADVQQDDEIVRREVFGPVVSVTRFTDEAQALAWANDSDYGLASSVWTTDVG 416 Query: 423 EAERFQSASGSDCGIANVNIGTSGAEIGGAFGGEKETGGGRE 464 A R + C N + GG+K +G G++ Sbjct: 417 RAHRLSARLQYGCTWVNTHFMLVSEM---PHGGQKLSGYGKD 455 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: 564 Number of extensions: 26 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: 474 Length adjustment: 34 Effective length of query: 462 Effective length of database: 440 Effective search space: 203280 Effective search space used: 203280 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