Align Malonate-semialdehyde dehydrogenase 1; MSA dehydrogenase 1; EC 1.2.1.-; Methylmalonate-semialdehyde dehydrogenase 1; MMSA dehydrogenase 1; MSDH 1; EC 1.2.1.27 (uncharacterized)
to candidate WP_046008427.1 OLEAN_RS05680 aldehyde dehydrogenase
Query= curated2:Q5L025 (488 letters) >NCBI__GCF_000967895.1:WP_046008427.1 Length = 453 Score = 197 bits (502), Expect = 5e-55 Identities = 138/444 (31%), Positives = 225/444 (50%), Gaps = 19/444 (4%) Query: 23 SGTETLEVPNPATGEVLARVPISTKEDVDQAVQAAKKAFATWKDVPVPKRARIMFSFHHL 82 S + LE +P+ GEV+ V I+ + + V+ A +A W P+ +R+ ++ + Sbjct: 7 SSAQILESIDPSNGEVVGSVAITNEAALKTIVERAAQAQVNWGQRPLHERSSLVQQAYAA 66 Query: 83 LNQHHEELAELVVQENGKAYKEAYGEIQRGIECVEF-AAGAPTLLMGESLSNIAEEIDSE 141 L E +A L+ +E GK + A E + + AA + L+ +SE Sbjct: 67 LEDAEESMAMLISREMGKDTRRAGYEASGTLHGGRYLAAETAKAFASQRLAG-----NSE 121 Query: 142 MFRYPLGVVAGITPFNFPMMVPLWMFPLAIVCGNTFVLKPSERTPILANKLAELFTEAGA 201 + P+G VA I+P+N+P+ + + A+V GN+ +LKPSE TP++A+ L + E Sbjct: 122 IQYRPVGTVAVISPWNYPLAMANNLIVPALVAGNSVILKPSEETPLVADMLVNILNET-L 180 Query: 202 PPGVLNVVHGAHEVVNALIDHEDIRAISFVGSQPVAKYVYERTAAQGKRVQALSGAKNHH 261 P GVL + HG +V AL+ +I ++F GS + + A Q KR+ G + Sbjct: 181 PSGVLQIAHGGGDVGEALV-KSNINMVAFTGSLQTGRNIMANAAPQLKRLVMELGGNDPM 239 Query: 262 IVMPDADVETAVQHVISSAFGSAGQRCMACSAVVIVGE-NETFVRRLKQKADELIIGNGM 320 IV+ DADV A Q ++S+F +AGQ C + V + + E F + + A + +G+ Sbjct: 240 IVLDDADVFAAAQFAVASSFENAGQMCTSTERVYVDEKIAEQFEQAVVSIASQYKVGSWR 299 Query: 321 DPEVLLTPVIRQSHREKVLGYIQKGIEEGAVLLRDGRKEMDDRPEGNFLGPTIFDYVTPD 380 D V + P++ KV+ +I+ +++GA LL RK P F+ PT+ + P Sbjct: 300 DSRVNIGPLVNAKQHAKVVSHIEDALDKGATLLFGERK-----PLLPFIPPTVISNINPT 354 Query: 381 MTIAKEEIFAPVLSLLRANDLDEALSYIRKSRYGNGATIY-TKDAKAVRKFREEADAGML 439 M I EE F PV+++ R LD+ + S YG GA ++ +DAK K ++ AGM+ Sbjct: 355 MIIESEETFGPVVAIDRFGSLDDVIKRANDSVYGLGAVVFGDRDAK---KVAQQLQAGMI 411 Query: 440 GINVGVPATMAFFPFSGWKDSFYG 463 GIN GV A P+ G K S +G Sbjct: 412 GINQGVGAG-GDAPWVGAKQSGFG 434 Lambda K H 0.319 0.136 0.396 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: 451 Number of extensions: 26 Number of successful extensions: 7 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: 488 Length of database: 453 Length adjustment: 33 Effective length of query: 455 Effective length of database: 420 Effective search space: 191100 Effective search space used: 191100 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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