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_085772038.1 B1812_RS13395 aldehyde dehydrogenase family protein
Query= curated2:Q81QR5 (486 letters) >NCBI__GCF_002117405.1:WP_085772038.1 Length = 506 Score = 201 bits (510), Expect = 6e-56 Identities = 141/466 (30%), Positives = 221/466 (47%), Gaps = 15/466 (3%) Query: 7 KRVKNHINGEWVESTGTEVEAVPNPATGKIIAYVPLSPKEDVEKAVEAAKAAYETWSKVP 66 KR N I G+WV G E +P TG I V DVE A++AA A + W K P Sbjct: 17 KRYDNFIGGQWVAPLGGEYFDNISPITGHPICQVARGRAADVELALDAAHKAKDAWGKTP 76 Query: 67 VPNRSRQLYKYLQLLQENKEELAKIITLENGKTLTDAT-GEVQRGIEAVELATSAPNLMM 125 R+ L K Q L +N LA + T++NGK + + T ++ I+ Sbjct: 77 AAERANMLNKIAQRLDDNLSALALVETIDNGKPIRETTAADIPLAIDHFRYFAGCLRAQE 136 Query: 126 GQALPNIASGIDGSIWRYPIGVVAGITPFNFPMMIPLWMFPLAIACGNTFVLKTSERTPL 185 G +L I + P+GVV I P+NFP+++ W A+A GN VLK +E+TP+ Sbjct: 137 G-SLSEIDHDTVAYHFHEPLGVVGQIIPWNFPILMAAWKLSPALAAGNCVVLKPAEQTPM 195 Query: 186 LAERLVELFYEAGFPKGVLNLVQG-GKDVVNSILENKDIQAVSFVGSEPVARYVYETGTK 244 + EL + P GVLN+V G G + + NK I ++F G R + + + Sbjct: 196 SILAVAELIADL-LPPGVLNIVNGFGVEAGKPLASNKRIAKIAFTGETTTGRLIMQYAAE 254 Query: 245 HGKRVQALAGAKNHAIVM------PDCNLEKTVQGVIGSAFASSGERCMACSVVAVVDEI 298 + V G K+ I D L+K ++G A + GE C S V I Sbjct: 255 NLIPVTLELGGKSPNIFFADVMAEDDAFLDKALEGFASFAL-NQGEVCTCPSRALVQRSI 313 Query: 299 ADEFIDVLVAETKKLKVGDGFHEDNYVGPLIRESHKERVLGYINSGVADGATLLVDGRK- 357 D+F++ +A K++ G +G E++L Y++ G +GA +L+ G + Sbjct: 314 YDKFMEKALARVAKIRQGHPLDPATMIGAQASNDQLEKILSYVDIGRKEGAKVLIGGERS 373 Query: 358 -IKEEVGEGYFVGATIFDGVNQEMKIWQDEIFAPVLSIVRVKDLEEGIKLTNQSKFANGA 416 ++ E+ EGY++ T +G N+ M+++Q+EIF PV+S+ + EE +++ N + + GA Sbjct: 374 VLEGELKEGYYMQPTALEGHNR-MRVFQEEIFGPVVSVTTFETEEEALQIANDTLYGLGA 432 Query: 417 VIYTSNGKHAQTFRDNIDAGMIGVNVNVPAPMAFFAFAGNKASFFG 462 ++T +G A I AG + N P A AF G K S G Sbjct: 433 GLWTRDGSRAYRCGRAIRAGRVWTNCYHAYP-AHAAFGGYKQSGIG 477 Lambda K H 0.317 0.135 0.392 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: 538 Number of extensions: 23 Number of successful extensions: 5 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: 486 Length of database: 506 Length adjustment: 34 Effective length of query: 452 Effective length of database: 472 Effective search space: 213344 Effective search space used: 213344 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 Apr 09 2024. 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