Align lactaldehyde dehydrogenase (EC 1.2.1.22); 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized)
to candidate WP_082353398.1 CDES_RS06155 CoA-acylating methylmalonate-semialdehyde dehydrogenase
Query= BRENDA::Q97UA1 (478 letters) >NCBI__GCF_001277995.1:WP_082353398.1 Length = 513 Score = 263 bits (671), Expect = 1e-74 Identities = 156/459 (33%), Positives = 236/459 (51%), Gaps = 7/459 (1%) Query: 23 NPADKDHVLAKIRLYTKDDVKEAINKAVAKFDEWSRTPAPKRGSILLKAGELMEQEAQEF 82 NPA V A + T V A++ A A W T +R +++ K E++ E Sbjct: 44 NPAT-GAVTASLPFATTATVNAAVSAAQAVAPAWRATGLARRAAVMFKLHEIITSRKDEL 102 Query: 83 ALLMTLEEGKTLKDSMFEVTRSYNLLKFYGALAFKISGKTLPSADPNTRIFTVKEPLGVV 142 A L+T E+GK L D+ E+ R ++F L + G+ L A + V++PLGVV Sbjct: 103 AALITEEQGKVLSDAAGEIARGLENVEFCAGLVHHMKGEFLEQAAAGLDVHQVRQPLGVV 162 Query: 143 ALITPWNFPLSIPVWKLAPALAAGNTAVIKPATKTPLMVAKLVEVLSKAGLPEGVVNLVV 202 A ITP+NFP +P+W + A+AAGNT V+KP+ K P V +VE +AGLPEGV+NL+ Sbjct: 163 ACITPFNFPAMVPLWMITTAIAAGNTVVLKPSEKDPSAVNWIVEAFHEAGLPEGVLNLIH 222 Query: 203 GKGSEVGDTIVSDDNIAAVSFTGSTEVGKRIYKLVGNKNRMTRIQLELGGKNALYVDKSA 262 G E + ++ D + AVSF GST + + IY + R+Q G KN + V A Sbjct: 223 G-DREAVEALIDDPRVQAVSFVGSTPIAQSIYTRATALGK--RVQALGGAKNHMVVMPDA 279 Query: 263 DLTLAAELAVRGGFGLTGQSCTATSRLIINKDVYTQFKQRLLERVKKWRVGPGTE-DVDM 321 DL AA+ AV G+G G+ C A S ++ D+ ++ R+ +G GT+ D +M Sbjct: 280 DLDAAADAAVSAGYGAAGERCMAISVVVPVGDIADDLIAKISSRITDLTIGEGTDPDSEM 339 Query: 322 GPVVDEGQFKKDLEYIEYGKNVGAKLIYGGNII--PGKGYFLEPTIFEGVTSDMRLFKEE 379 GPV+ ++ I + GA+++ G + P +G+F+ PT+ + V M ++ EE Sbjct: 340 GPVITSAAKERIEGLIAGSSDSGAEVVVDGRSVDLPDEGFFIGPTLIDHVKPGMPVYDEE 399 Query: 380 IFGPVLSVTEAKDLDEAIRLVNAVDYGHTAGIVASDIKAINEFVSRVEAGVIKVNKPTVG 439 IFGPVLSV DEA+ L+N+ Y + I D + EF +E G++ +N P Sbjct: 400 IFGPVLSVARVGHFDEAVELINSCQYANGTAIFTRDGRTAREFEFAIEVGMVGINVPIPV 459 Query: 440 LELQAPFGGFKNSGATTWKEMGEDALEFYLKEKTVYEGW 478 FGG+K S G ++ FY + K V W Sbjct: 460 PIGAFSFGGWKKSLFGDTHMYGPESFNFYTRRKVVTSRW 498 Lambda K H 0.316 0.135 0.389 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: 31 Number of successful extensions: 6 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: 478 Length of database: 513 Length adjustment: 34 Effective length of query: 444 Effective length of database: 479 Effective search space: 212676 Effective search space used: 212676 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: 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