Align acetaldehyde dehydrogenase (acetylating) (EC 1.2.1.10) (characterized)
to candidate WP_015942717.1 DHAF_RS01855 acetaldehyde dehydrogenase
Query= BRENDA::B0K315 (466 letters) >NCBI__GCF_000021925.1:WP_015942717.1 Length = 495 Score = 233 bits (595), Expect = 8e-66 Identities = 140/409 (34%), Positives = 228/409 (55%), Gaps = 22/409 (5%) Query: 33 DLGIFNDVNEAVECAKEAQKKFALMDLEKREEIIAAIREACVNNARLLAEIACSETGRGR 92 DL + V+ AKEAQ A + ++ ++I+A+I A NA LA +AC ET G Sbjct: 6 DLASIQESRNLVQKAKEAQLHLAHFNEQQIDKILASIVAAVEENAEGLARMACQETEYGI 65 Query: 93 VEDKVAKNILAAK---------KTPGTEDLKPTAWTGDRGLTLVEMAPVGVIASITPVTN 143 VE K+AKN+ AA+ KT GT P DR + + AP+GV+ ITP TN Sbjct: 66 VEHKIAKNLFAARDVYESTKHIKTIGTISEDP-----DRKV-IRYAAPMGVLVGITPRTN 119 Query: 144 PTATIINNTISMLAAGNAVVFNPHPSAKKTSNKAVEIINEAILKVGAPNGLVCSINNPTI 203 PT+TII+N + + NA+VF+PHP A + +INEA +K GAP+G+ ++ ++ Sbjct: 120 PTSTIIHNALCAIKGANAIVFSPHPFAVQCGCATASLINEAAVKAGAPDGVCSCLSMTSL 179 Query: 204 QTAQKLMEHPEVNMVVVTGGKAVVQTALRCGKKVIGAGAGNPPVVVDETADIVKAAHDIA 263 Q + +LM HP+V ++ TGG +V++A GK G G+GN PV ++ +ADI +A +DI Sbjct: 180 QASHELMHHPDVAAIIATGGPGLVKSAYSAGKPAFGVGSGNVPVFIERSADIKQAVNDIM 239 Query: 264 CGASFDNNLPCIAEKEIIAVERIADTLLERMKREGAYVLHGKDIDRMTELIFQ-GGAINK 322 +FDN + C +E+ I+A + I D +++ ++ +GAY L +++ ++ ++ G++N Sbjct: 240 VSKTFDNGMICASEQAILADQPIKDEVIKELQNQGAYFLSPEEVQKVGRVVIHANGSMNN 299 Query: 323 DLIGRDAHFILSQIGIETGKDIRLVVMPVD---VSHPLVYHEQLMPVIPFVTVPTVEEAI 379 L+G+ I + GI D L++ P++ +PL HE+L V+ F V +EA Sbjct: 300 ALVGQSPAVIAQRAGISIPADTALLIAPMEGYGKDYPL-SHEKLTTVLGFYVVQDWKEAC 358 Query: 380 NLAVK--AEGGNRHTAMMHSKNVENMTAFARAIQTTIFVKNAPSYAGIG 426 +L+++ GG H+ +HS+N + + F I V + GIG Sbjct: 359 HLSIELLKLGGIGHSCAIHSQNEQVIREFLAKPVFRIIVNTPSALGGIG 407 Lambda K H 0.317 0.133 0.377 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: 493 Number of extensions: 24 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: 466 Length of database: 495 Length adjustment: 34 Effective length of query: 432 Effective length of database: 461 Effective search space: 199152 Effective search space used: 199152 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: 51 (24.3 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