Align Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 (characterized)
to candidate WP_075619573.1 GY23_RS12590 aldehyde dehydrogenase family protein
Query= SwissProt::A1B4L2 (508 letters) >NCBI__GCF_001939075.1:WP_075619573.1 Length = 506 Score = 809 bits (2090), Expect = 0.0 Identities = 389/492 (79%), Positives = 435/492 (88%) Query: 17 FEERYDNFIGGEWVAPVSGRYFTNTTPITGAEIGQIARSEAGDIELALDAAHAAKEKWGA 76 F+E+YDN+I G+W APV G YF N TP+TG QIARS + DIELALDAAHAAK+ WG Sbjct: 15 FKEKYDNYINGQWTAPVKGEYFDNVTPVTGKSFTQIARSTSEDIELALDAAHAAKDAWGK 74 Query: 77 TSPAERANIMLKIADRMERNLELLATAETWDNGKPIRETMAADLPLAIDHFRYFAGVLRA 136 TS AERA I+ KIADRME NLE+LA AETWDNGK +RET+ ADLPLAIDHFRYFAG +RA Sbjct: 75 TSVAERAIILNKIADRMEENLEMLAVAETWDNGKAVRETLNADLPLAIDHFRYFAGAIRA 134 Query: 137 QEGSISQIDDDTVAYHFHEPLGVVGQIIPWNFPLLMACWKLAPAIAAGNCVVLKPAEQTP 196 QEGS+SQID+DTVAYHFHEP+GVVGQIIPWNFPLLMA WKLAPA+AAGNCVVLKPAEQTP Sbjct: 135 QEGSLSQIDNDTVAYHFHEPIGVVGQIIPWNFPLLMAVWKLAPALAAGNCVVLKPAEQTP 194 Query: 197 AGIMVWANLIGDLLPPGVLNIVNGFGLEAGKPLASSNRIAKIAFTGETTTGRLIMQYASE 256 A I+V+A L+GDLLP GVLNIVNGFGLEAGKPLAS+ RI KIAFTGETTTGR+IMQYAS+ Sbjct: 195 ASILVFAELVGDLLPAGVLNIVNGFGLEAGKPLASNPRIGKIAFTGETTTGRMIMQYASQ 254 Query: 257 NLIPVTLELGGKSPNIFFADVAREDDDFFDKALEGFTMFALNQGEVCTCPSRVLIQESIY 316 NLIPVTLELGGKSPNIFF DV +DD F DKA+EGF +FALNQGEVCTCPSR L+QESIY Sbjct: 255 NLIPVTLELGGKSPNIFFEDVMDKDDAFLDKAVEGFVLFALNQGEVCTCPSRALVQESIY 314 Query: 317 DKFMERAVQRVQAIKQGDPRESDTMIGAQASSEQKEKILSYLDIGKKEGAEVLTGGKAAD 376 DKFME+ + RV+AIK G+P + +TM+GAQAS+EQ EKILSYLDIGK+EGAE LTGG+ + Sbjct: 315 DKFMEKVIARVEAIKTGNPLDPNTMMGAQASNEQLEKILSYLDIGKQEGAECLTGGERNN 374 Query: 377 LGGELSGGYYIEPTIFRGNNKMRIFQEEIFGPVVSVTTFKDQAEALEIANDTLYGLGAGV 436 LG E +GGYY++PT+F+GNNKMRIFQEEIFGPVVSVTTFK Q EALEIANDTLYGLGAGV Sbjct: 375 LGDEFAGGYYVKPTVFKGNNKMRIFQEEIFGPVVSVTTFKTQEEALEIANDTLYGLGAGV 434 Query: 437 WSRDANTCYRMGRGIKAGRVWTNCYHAYPAHAAFGGYKQSGIGRETHKMMLDHYQQTKNM 496 WSR+ NT YR GR I+AGRVWTNCYHAYPAHAAFGGYK SGIGRE H MML+HYQQTKN+ Sbjct: 435 WSRNMNTAYRFGRAIQAGRVWTNCYHAYPAHAAFGGYKMSGIGRENHLMMLNHYQQTKNL 494 Query: 497 LVSYSPKKLGFF 508 LVSYS KLGFF Sbjct: 495 LVSYSEDKLGFF 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: 915 Number of extensions: 24 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