Align aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) (characterized)
to candidate CCNA_01274 CCNA_01274 piperideine-6-carboxylate dehydrogenase
Query= BRENDA::Q69P84 (509 letters) >FitnessBrowser__Caulo:CCNA_01274 Length = 507 Score = 450 bits (1157), Expect = e-131 Identities = 229/471 (48%), Positives = 306/471 (64%), Gaps = 4/471 (0%) Query: 42 PTNNQVIAEVVEASAREYEEGMRACYDAAKTWMAIPAPKRGEIVRQIGDALRAKLHHLGR 101 P + ++ VV AR+ E + A A W +PAP+RGE+VR G+ LRA L Sbjct: 35 PIDGAILGHVVYDDARQIEAKVAAACRAFADWRVVPAPRRGELVRLFGEELRAAKADLAA 94 Query: 102 LVSLEMGKILPEGIGEVQEIIDMCDYAVGLSRQLNGSIIPSERPNHMMMEVWNPLGVVGV 161 LV+LE GKI E GEVQE+ID+CD+AVGLSRQL+G I SERP H M E W+PLG V V Sbjct: 95 LVTLEAGKIASEAAGEVQEMIDICDFAVGLSRQLHGLTIASERPGHAMRETWHPLGPVAV 154 Query: 162 ITAFNFPCAVLGWNACIALVCGNCVVWKGAPTTPLITIAMTKIVASVLER-NNLPGSIFT 220 I+AFNFP AV WNAC+ALVCG+ V+WK + TPL +A I+ L R + P + + Sbjct: 155 ISAFNFPVAVWAWNACLALVCGDPVIWKPSEKTPLTALATQAILERALARFRDAPQGLSS 214 Query: 221 AFCGGADIGQAISLDTRIPLVSFTGSTKVGLMVQQQVNARFGKCLLELSGNNAIIVMDDA 280 G D G+ ++ D RIPLVS TGST++G V V RFG+ +LEL GNNA+IV A Sbjct: 215 VVLGARDAGERLARDPRIPLVSATGSTRMGRAVAPMVAERFGRSILELGGNNAMIVTPSA 274 Query: 281 DIQLAVRSVLFAAVGTAGQRCTTCRRLLLHESIYRTFLDQLVEVYKQVRIGDPLENGTLL 340 D+ LA+R+++F+A GTAGQRCT+ RRL++HES+ D + ++++ +GDP + TLL Sbjct: 275 DLSLALRAIVFSAAGTAGQRCTSLRRLIVHESLVDKVSDAVEAAFQRLSVGDPRDPKTLL 334 Query: 341 GPLHTPASRDAFLKGIQTIRSQGGKILYGGSAIESE---GNFVQPTIVEISPSAPVVREE 397 GPL A+ DAF+ + +R++GG + G + E +V+P + + AP ++ E Sbjct: 335 GPLIDKAAYDAFIAAMNQVRAEGGSVAGGERVLIDEHPDAYYVRPALARLPAPAPCMQRE 394 Query: 398 LFGPVLYVMKVQNLKEAVEINNSVPQGLSSSIFTKRPDIIFKWIGPHGSDCGIVNVNIPT 457 F P+L+V+ + A+ I N VPQGLSS + T +++ GSDCGI NVNI Sbjct: 395 TFAPLLHVVPYNSFDMAIAIQNDVPQGLSSCVMTNDVREAERFLAAAGSDCGIANVNIGP 454 Query: 458 NGAEIGGAFGGEKATGGGREAGSDSWKQYMRRATCTINYGSELPLAQGINF 508 +GAEIGGAFGGEK TGGGRE+GSDSWKQYMRR T T+NY LPLAQG+ F Sbjct: 455 SGAEIGGAFGGEKETGGGRESGSDSWKQYMRRQTATVNYSGALPLAQGVRF 505 Lambda K H 0.320 0.137 0.416 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: 674 Number of extensions: 25 Number of successful extensions: 3 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: 509 Length of database: 507 Length adjustment: 34 Effective length of query: 475 Effective length of database: 473 Effective search space: 224675 Effective search space used: 224675 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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