Align lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate WP_057507192.1 ABB28_RS02945 aldehyde dehydrogenase
Query= BRENDA::Q58806 (463 letters) >NCBI__GCF_001431535.1:WP_057507192.1 Length = 460 Score = 253 bits (646), Expect = 9e-72 Identities = 161/462 (34%), Positives = 252/462 (54%), Gaps = 15/462 (3%) Query: 13 MDVINPYSLEVIKKIPALSREEAKEAIDTAEK-YKEVMKNLPITKRYNILMNIAKQIKEK 71 + V+ + I +I + ++ + AE+ +K+ LP +R IL +A + K Sbjct: 2 LTVVQAFDRAPITEIGFDTAAALEQKLSAAERVFKDRDGWLPPHERIAILRRLAALMDAK 61 Query: 72 KEELAKILAIDAGKPIKQARVEVERSIGTFKLAAFYVKEHRDEVIPSD------DRLIFT 125 ++ LA +A + GKP+ A +E R+I AA ++ IP R FT Sbjct: 62 RDHLALQIAREGGKPLPDAIIETTRAIDGVHNAADELRNFGGREIPMGLSAAAVGRWAFT 121 Query: 126 RREPVGIVGAITPFNFPLNLSAHKIAPAIATGNVIVHHPSSKAPLVCIELAKIIENALKK 185 REP+GIV AI+ FN PLNL H++APAIA G ++ P+S PL C++L ++ A Sbjct: 122 TREPIGIVAAISAFNHPLNLIVHQVAPAIAVGCPVIIKPASATPLSCLDLVAMVHEA--- 178 Query: 186 YNVPLGVYNLLTGAGEVVGDEIVVNEKVNMISFTGSSKVG-ELITKKAGFKKIALELGGV 244 +P G + + + +++V +SF GS++VG L +K A + ALE GGV Sbjct: 179 -GLPEPWCQSFMPEGNDLAEALATDKRVAFLSFIGSARVGWSLHSKLAHGARSALEHGGV 237 Query: 245 NPNIVLKDADLNKAVNALIKGSFIYAGQVCISVGMILVDESIADKFIEMFVNKAKVLNVG 304 P IV ++ADL++ + ++KG + +AGQVC+S I V + IAD F E V + + L G Sbjct: 238 APAIVDRNADLSRIIEPIVKGGYYHAGQVCVSTQRIFVHDDIADDFTEALVARVERLRTG 297 Query: 305 NPLDEKTDVGPLISVEHAEWVEKVVEKAIDEGGKLLLGGKR-DKALFYPTI-LEVDRDNI 362 +P + TDVGPLI A+ V + +++A+ G KL GGKR + PT+ L+ D Sbjct: 298 DPTLKDTDVGPLIQPREADRVAEWIDEAVKGGAKLATGGKRLSETTLQPTVLLDPASDAR 357 Query: 363 LCKTETFAPVIPIIR-TNEEEMIDIANSTEYGLHSAIFTNDINKSLKFAENLEFGGVVIN 421 + E F PV+ + R + +E I ANS ++IFT DI+ +L+ A L+ V+IN Sbjct: 358 VTTQEVFGPVVAVYRYADLDEAISRANSLPTAFQASIFTQDIDIALRAANRLDASAVMIN 417 Query: 422 DSSLFRQDNMPFGGVKKSGLGREGVKYAMEEMSNIKTIIISK 463 D++ FR D MPF G ++SG G G+ Y M +MS K I++ + Sbjct: 418 DATAFRTDWMPFAGRRESGYGTGGIPYTMRDMSQEKMILMHR 459 Lambda K H 0.317 0.137 0.381 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: 467 Number of extensions: 22 Number of successful extensions: 4 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: 463 Length of database: 460 Length adjustment: 33 Effective length of query: 430 Effective length of database: 427 Effective search space: 183610 Effective search space used: 183610 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 (21.6 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