Align acetaldehyde dehydrogenase (acetylating) (EC 1.2.1.10) (characterized)
to candidate WP_083758718.1 VEIS_RS03235 aldehyde dehydrogenase family protein
Query= BRENDA::B0K315 (466 letters) >NCBI__GCF_000015565.1:WP_083758718.1 Length = 526 Score = 186 bits (473), Expect = 1e-51 Identities = 127/399 (31%), Positives = 194/399 (48%), Gaps = 9/399 (2%) Query: 47 AKEAQKKFALMDLEKREEIIAAIREACVNNARLLAEIACSETGRGRVEDKVAKN-ILAAK 105 A+ A + FA D E+ + A+ +A +NA AE A ETG G VE K KN +A Sbjct: 25 AEWAARDFAQFDREQVLRVAEAVAKAAHDNAAFYAEWAVRETGYGVVEHKQKKNESVAYP 84 Query: 106 KTPGTEDLKPTAWTGDRGLTLVEMA-PVGVIASITPVTNPTATIINNTISMLAAGNAVVF 164 DL D +VE+ P G++ ++TP TNP AT+ + L + NA+V Sbjct: 85 LLDFYRDLDLVHPRVDEARKMVEIPKPAGIVLALTPATNPVATVYYKVMLALLSRNAIVI 144 Query: 165 NPHPSAKKTSNKAVEIINEAILKVGAPNGLVCSINNPTIQTAQKLMEHPEVNMVVVTGGK 224 +PHP+A + N A ++ A GAP GL+ I P+I LM P+V +V+ TGG Sbjct: 145 SPHPAASRCCNDAARKLDAAAHAAGAPPGLIQCIERPSIPLVDTLMRSPQVAVVMATGGG 204 Query: 225 AVVQTALRCGKKVIGAGAGNPPVVVDETADIVKAAHDIACGASFDNNLPCIAEKEIIAVE 284 +V+ A G IG G GN P +D +AD+ KAA I SFDN++ C +E ++ + Sbjct: 205 PMVRAAYSSGNPAIGVGPGNAPAYIDTSADMRKAARMIVSSKSFDNSVLCTSESVLLVQQ 264 Query: 285 RIADTLLERMKREGAYVLHGKDIDRMTELIFQGGAINKDLIGRDAHFILSQIGIETGKDI 344 + A ++ GA++ ++++R+ +F G +N IG+ A +I + G++ Sbjct: 265 KDAQRFERELRAAGAHLCQEREVERLRAYLFPDGDLNPAAIGKSAVWIAREAGLKVLPAT 324 Query: 345 RLVVMPVD---VSHPLVYHEQLMPVIPFVTVPTVEEAINLA--VKAEGGNRHTAMMHSKN 399 +++V V V PL E+L PV+ V + E A A + G H+A H + Sbjct: 325 QVLVANVQHIGVDEPLT-KEKLCPVLALYAVDSFERATRSAQMILRLSGAGHSAAFHGND 383 Query: 400 VENMTAFARAIQTTIFVKNAPSYAGI-GFGGEGYTTFTI 437 + FA + V NAP G GF TF I Sbjct: 384 PQKALDFAARLNVYRVVVNAPCAQGASGFATHLPPTFMI 422 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: 527 Number of extensions: 23 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: 526 Length adjustment: 34 Effective length of query: 432 Effective length of database: 492 Effective search space: 212544 Effective search space used: 212544 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: 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