Align Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 (characterized)
to candidate WP_059151806.1 V474_RS12520 aldehyde dehydrogenase family protein
Query= SwissProt::A1B4L2 (508 letters) >NCBI__GCF_001046635.1:WP_059151806.1 Length = 506 Score = 784 bits (2024), Expect = 0.0 Identities = 374/489 (76%), Positives = 423/489 (86%) Query: 20 RYDNFIGGEWVAPVSGRYFTNTTPITGAEIGQIARSEAGDIELALDAAHAAKEKWGATSP 79 ++DNFIGG+WVAPV GRYF N +P+TG + Q+AR A DIELALDAAHAAK+ WG SP Sbjct: 18 KFDNFIGGKWVAPVKGRYFDNVSPVTGQVVCQVARGTAEDIELALDAAHAAKDAWGKASP 77 Query: 80 AERANIMLKIADRMERNLELLATAETWDNGKPIRETMAADLPLAIDHFRYFAGVLRAQEG 139 ERAN +L++ADR+E NL+ LA ET DNGKPIRET AAD+PLAIDHFRYFA LRAQEG Sbjct: 78 TERANTLLRVADRLEANLDRLALVETIDNGKPIRETTAADVPLAIDHFRYFASCLRAQEG 137 Query: 140 SISQIDDDTVAYHFHEPLGVVGQIIPWNFPLLMACWKLAPAIAAGNCVVLKPAEQTPAGI 199 SI++ID DTVAYHFHEPLGVVGQIIPWNFP+LMA WKLAPA+AAGNCVVLKPAEQTP I Sbjct: 138 SIAEIDHDTVAYHFHEPLGVVGQIIPWNFPILMAAWKLAPALAAGNCVVLKPAEQTPMSI 197 Query: 200 MVWANLIGDLLPPGVLNIVNGFGLEAGKPLASSNRIAKIAFTGETTTGRLIMQYASENLI 259 +V A L+ D+LPPGVLNIVNGFG+EAGKPLA++ RIAKIAFTGETTTGRLIMQYASENLI Sbjct: 198 LVLAELVADILPPGVLNIVNGFGIEAGKPLAANKRIAKIAFTGETTTGRLIMQYASENLI 257 Query: 260 PVTLELGGKSPNIFFADVAREDDDFFDKALEGFTMFALNQGEVCTCPSRVLIQESIYDKF 319 P TLELGGKSPNIFFADV DDD+ DKALEGFTMFALNQGEVCTCPSR L+ ESIYD F Sbjct: 258 PCTLELGGKSPNIFFADVMDADDDYLDKALEGFTMFALNQGEVCTCPSRALVHESIYDAF 317 Query: 320 MERAVQRVQAIKQGDPRESDTMIGAQASSEQKEKILSYLDIGKKEGAEVLTGGKAADLGG 379 ME+A+ RV+AI+ G P ++ TMIGAQAS++Q EKILSY+ IG+ EGA+VLTGG+ G Sbjct: 318 MEKAIARVEAIRMGSPLDASTMIGAQASNDQLEKILSYIQIGRDEGAKVLTGGERVAHEG 377 Query: 380 ELSGGYYIEPTIFRGNNKMRIFQEEIFGPVVSVTTFKDQAEALEIANDTLYGLGAGVWSR 439 ELS GYY++PT+ G+NKMR+FQEEIFGPV++VT F EAL IANDTLYGLGAGVW+R Sbjct: 378 ELSQGYYVQPTVLEGHNKMRVFQEEIFGPVLAVTKFSTDEEALAIANDTLYGLGAGVWTR 437 Query: 440 DANTCYRMGRGIKAGRVWTNCYHAYPAHAAFGGYKQSGIGRETHKMMLDHYQQTKNMLVS 499 D YR+GRGI+AGRVWTNCYHAYPAHAAFGGYKQSGIGRE HKMMLDHYQQTKN+LVS Sbjct: 438 DGTRAYRIGRGIQAGRVWTNCYHAYPAHAAFGGYKQSGIGRENHKMMLDHYQQTKNLLVS 497 Query: 500 YSPKKLGFF 508 YSPK LGFF Sbjct: 498 YSPKALGFF 506 Lambda K H 0.319 0.136 0.411 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: 853 Number of extensions: 31 Number of successful extensions: 1 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: 508 Length of database: 506 Length adjustment: 34 Effective length of query: 474 Effective length of database: 472 Effective search space: 223728 Effective search space used: 223728 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 (21.7 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