Align Aldehyde dehydrogenase; NAD/NADP-dependent aldehyde dehydrogenase; EC 1.2.1.3; EC 1.2.1.4 (characterized)
to candidate 5209190 Shew_1668 methylmalonate-semialdehyde dehydrogenase (RefSeq)
Query= SwissProt::Q8GAK7 (458 letters) >lcl|FitnessBrowser__PV4:5209190 Shew_1668 methylmalonate-semialdehyde dehydrogenase (RefSeq) Length = 501 Score = 183 bits (464), Expect = 1e-50 Identities = 140/466 (30%), Positives = 219/466 (46%), Gaps = 23/466 (4%) Query: 3 IATIDPTTGITLKTFDAHTPEEVENRIARAEAAFRSLQNTSFEERARWMHKAADILESEA 62 I+ +P + T +A T EEVE IA A+ AF + + ERAR M + +L+ Sbjct: 22 ISVTNPANNEVIATINAATVEEVETAIASAKQAFATWKEVPVSERARVMFRYQHLLKLHH 81 Query: 63 DEVARLIATEMGKTLTTAKYEALKSATGMRHFADHAQRYLSPETPVPASEVNASNLHVQF 122 DE+A ++A E GKT AK + + H + A + A ++ + Sbjct: 82 DEIATILAQETGKTFEDAKGDVWRGIEVAEHACNIASLIMGETVENVARSIDT---YSYT 138 Query: 123 DPLGVVLAVMPWNYPLWQAVRFAAPALMAGNTGLLKHASNVPQCALYLGDLFARGGFPEG 182 PLGV + P+N+P + A+ GNT +LK + P L +LF G P+G Sbjct: 139 QPLGVCAGITPFNFPAMIPLWMFPLAIACGNTFVLKPSEQDPLTPQRLVELFEEAGAPKG 198 Query: 183 AFQTLLVEGKDVIPLVDDARIRAVTLTGSVAAGSAIAEAAGRNIKRSVLELGGMDVFIVM 242 Q + + V L+ I+A++ GSV G I + N+KR G + ++M Sbjct: 199 VLQLVHGDKTAVDVLLSHQDIKAISFVGSVGVGQYIYKTGTDNLKRVQAFAGAKNHCVIM 258 Query: 243 PSADIEKAAAQAVIARLQNSGQSCIAAKRFYVHEDVYDRFEHLFVTGMAEAVA----GDP 298 P A+ ++ V A + +GQ C+A + V+ ++ + +A+A G Sbjct: 259 PDANKQQVINNLVGASVGAAGQRCMA-----LSVAVFVGEAKKWIPELRDAIAKVRPGVW 313 Query: 299 LDESTSFGPLATERGRQDVHELVRDAREKGAAVQCGG-----EIPEGEGWYYPATVLTGV 353 D+ ++GP+ + + V +L+ +E+GA G E E W P T+ T V Sbjct: 314 DDKDAAYGPVISPAAKARVLKLIAQGKEEGAECLLDGSDFTVEGYENGNWVGP-TMFTNV 372 Query: 354 TEDMRIYREECFGPVACLYKVSSLQEAIALSNDSDFGLSSSVWTNDETEATEAARSIEAG 413 T DM IY+EE FGPV C +V SL+EAI L N+S +G +S++T A + +IE G Sbjct: 373 TTDMSIYKEEIFGPVLCCMEVESLEEAIELVNNSPYGNGTSIFTACGAAARKYQHNIEVG 432 Query: 414 GVFIN-GLTASFPAVPFGGLKDSGYGRELSAYG---IREFVNIKTV 455 V IN + P F G K S YG + AYG +R + KT+ Sbjct: 433 QVGINVPIPVPLPFFSFTGWKGSFYG-DQHAYGKQAVRFYTETKTI 477 Lambda K H 0.317 0.132 0.386 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: 492 Number of extensions: 26 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: 458 Length of database: 501 Length adjustment: 34 Effective length of query: 424 Effective length of database: 467 Effective search space: 198008 Effective search space used: 198008 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 17 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.
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