Align acetaldehyde dehydrogenase (acetylating) (EC 1.2.1.10) (characterized)
to candidate WP_092346807.1 BLU87_RS08580 acetaldehyde dehydrogenase
Query= BRENDA::B0K315 (466 letters) >NCBI__GCF_900107645.1:WP_092346807.1 Length = 481 Score = 190 bits (482), Expect = 1e-52 Identities = 132/411 (32%), Positives = 207/411 (50%), Gaps = 16/411 (3%) Query: 33 DLGIFNDVNEAVECAKEAQKKFALMDLEKREEIIAAIREACVNNARLLAEIACSETGRGR 92 DL + + V A+ AQ FA + EK ++++ AI + A LA++A ETG G Sbjct: 5 DLASIQEARDLVRKARVAQCDFAKLSQEKVDQVVQAIAKVMTAMAEDLAKLAVEETGYGN 64 Query: 93 VEDKVAKNILAAKKTPGTEDLKPTAWT--GDRGLTLVEMA-PVGVIASITPVTNPTATII 149 EDK KN+LA++K T DR + ++A P GV+A++ P TNPT+T I Sbjct: 65 WEDKKQKNLLASEKLYQRIHAVKTVGVIAEDREQKIDKIAVPAGVVAALIPSTNPTSTTI 124 Query: 150 NNTISMLAAGNAVVFNPHPSAKKTSNKAVEIINEAILKVGAPNGLVCSINNPTIQTAQKL 209 + L AGN VVF+PHP+A K K V II++ + ++ LV PT++ +L Sbjct: 125 YKAMIALKAGNGVVFSPHPTATKCIGKTVAIIHQILKEMHISEELVSMTTMPTLEGTGEL 184 Query: 210 MEHPEVNMVVVTGGKAVVQTALRCGKKVIGAGAGNPPVVVDETADIVKAAHDIACGASFD 269 M + ++++ TGG +V+ A G +G G GN PV ++++AD+ A I G +FD Sbjct: 185 MR--QADLILATGGPGMVKAAYSSGTPALGVGPGNVPVFIEKSADVQAAVKRIMAGKTFD 242 Query: 270 NNLPCIAEKEIIAVERIADTLLERMKREGAYVLHGKDIDRMTELIF-QGGAINKDLIGRD 328 C +E+ ++ E I + + M EG Y L G D++ L+ G++N ++G+ Sbjct: 243 YGTVCSSEQALVTEESIVAEVKKSMLIEGCYFLEGAAADKVKGLMTGPRGSMNPAIVGQP 302 Query: 329 AHFILSQIGIETGKDIRLVV---MPVDVSHPLVYHEQLMPVIPFVTVPTVEEAINLAVK- 384 A + GIE RL+V V +P Y E+L ++ F TVP + A L + Sbjct: 303 ASVLAQMAGIEIPAGTRLLVYEEQGVGSGYPFSY-EKLTCLLGFYTVPDWQSAGELCTRL 361 Query: 385 -AEGGNRHTAMMHSKNVENMTAFARAIQTTIFVKNAPSYAGIGFGGEGYTT 434 GG H+ +HS N + + FA + + + N PS G G TT Sbjct: 362 LQNGGLGHSMAIHSNNEDIIRHFALSQPVSRLLVNTPS----SLGAVGVTT 408 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: 479 Number of extensions: 19 Number of successful extensions: 5 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: 481 Length adjustment: 33 Effective length of query: 433 Effective length of database: 448 Effective search space: 193984 Effective search space used: 193984 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