Align Lactaldehyde dehydrogenase; EC 1.2.1.22 (uncharacterized)
to candidate WP_028950880.1 Q385_RS0106445 aldehyde dehydrogenase
Query= curated2:A6UVT6 (465 letters) >NCBI__GCF_000619805.1:WP_028950880.1 Length = 474 Score = 349 bits (895), Expect = e-100 Identities = 190/468 (40%), Positives = 294/468 (62%), Gaps = 13/468 (2%) Query: 1 MFINGEWINRKD-IEVKNPYNNEIIGYIPSLSRNETKEAIKIAEEHKSTMKNLSPTIRYN 59 M I G+ + + + I+V PYN + IG S + ++A++ A+ +K L+ +Y Sbjct: 6 MLIGGKEVFKDEVIDVIYPYNQQKIGEAVKGSVEDVEKAVEKAKIGLKKLKQLTAYEKYK 65 Query: 60 ILMKIASELSKNKRELAKLITIDVGKPIKQSIIEVDRTITTFKFSAFYSRELRGETIPFD 119 +L+K+A L + K E AK+IT++ GK IK+S IEVDR I T FSA ++ + GE + FD Sbjct: 66 MLLKVAQLLEERKEEFAKVITLETGKTIKESRIEVDRAINTITFSAEEAKRIAGEVVHFD 125 Query: 120 DG------MVITKREPVGLVGAITPFNFPLNLFAHKIAPAIAMGNSIVAHPSSKAPMITI 173 R P G+V AITPFNFP+NL AHKIAPAIA G + PS K P+ Sbjct: 126 ASPNGRGKRGYYFRVPAGIVAAITPFNFPVNLTAHKIAPAIAAGCPFILKPSEKTPLSPT 185 Query: 174 ELTKIIEKVLKSKKIPLGVFNLLTGEGHIVGDEIVKNNKINKLSFTGSVEVGESITKKAG 233 L ++ + +P +++ G VG + ++ + +SFTGS++VGE I K+AG Sbjct: 186 MLCQLFLEA----GVPEEAVSIIPGFAD-VGQAMTTHSDVRVVSFTGSLKVGEIIAKQAG 240 Query: 234 FKKITLELGGNNPMIILKDANINKAVESCMSGKFLNSGQVCISVGRVLIEQEVADEFINK 293 KKI +ELG N+ +I+ KDAN+ A + + G F +GQVCISV RVL+ ++VADEF N Sbjct: 241 LKKIVMELGSNSAVIVDKDANLELAAKKSVLGGFALAGQVCISVQRVLVHKDVADEFENL 300 Query: 294 IVEKVKKLKIGNPLDEDTNISSLISLDSAERVEKLINKSIGQGGKLICGGKRENSIIYPT 353 + ++ KLK G+P++EDT++ +IS++ +R++ I++++ +G K+ GG+ E +++ PT Sbjct: 301 LKKEASKLKYGDPMEEDTDVGPVISINEVDRIQTWISEAVMKGAKVSLGGEAEKTLLKPT 360 Query: 354 IL-EITADNILANIEIFAPVLPIIRVNDMNEALNQANNSNYGLHSGVFTQDINKALYFAD 412 I+ EI D+ L E FAPV+ + R + EA+ N +NYGL G+FT ++ A + Sbjct: 361 IVSEIPEDSKLFYEEAFAPVVAVKRFETIEEAVEMVNKTNYGLQVGIFTNNLKNAWKVIE 420 Query: 413 NLEYGGVLINNSPTFRIDNMPFGGIKHSGLGREGIKYAIDEMSEIKTI 460 +E GGV++N+ PTFR DNMP+GG+K SG+GREG K+AI++ +EIK + Sbjct: 421 EVEVGGVMVNDIPTFRADNMPYGGVKGSGIGREGPKFAIEDYTEIKVV 468 Lambda K H 0.316 0.136 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: 600 Number of extensions: 37 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: 465 Length of database: 474 Length adjustment: 33 Effective length of query: 432 Effective length of database: 441 Effective search space: 190512 Effective search space used: 190512 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