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 N515DRAFT_0465 N515DRAFT_0465 aldehyde dehydrogenase (NAD+)
Query= curated2:Q5L025 (488 letters) >FitnessBrowser__Dyella79:N515DRAFT_0465 Length = 511 Score = 210 bits (535), Expect = 8e-59 Identities = 154/487 (31%), Positives = 237/487 (48%), Gaps = 22/487 (4%) Query: 14 YIG-GQWVASSGTETLEVPNPATGEVLARVPISTKEDVDQAVQAAKKAFATWKDVPVPKR 72 Y+G G+W +S L+ NPATGEV+ V S+ D + V+ A++AF TW+ P P+R Sbjct: 19 YLGQGEWSRTSDAGALQPVNPATGEVIGTVHASSAADYETIVKRAQEAFKTWRTTPAPRR 78 Query: 73 ARIMFSFHHLLNQHHEELAELVVQENGKAYKEAYGEIQRGIECVEFAAGAPTLLMGESLS 132 + L +H + L LV E GK E GE+Q I+ +FA G +L G ++ Sbjct: 79 GEAVRLCGEALRKHKDALGSLVALEMGKIKPEGDGEVQEMIDIADFAVGQSRMLYGYTMH 138 Query: 133 NIAEEIDSEMFR--YPLGVVAGITPFNFPMMVPLWMFPLAIVCGNTFVLKPSERTPILA- 189 +E M+ +PLG+V I+ FNFP+ V W LA +CG+ + KPS +TP+ A Sbjct: 139 --SERPGHRMYEQYHPLGLVGIISAFNFPVAVWAWNAFLAAICGDICIWKPSPKTPLSAI 196 Query: 190 --NKLAELFTEAGAPPGVLNVVHGA-HEVVNALIDHEDIRAISFVGSQPVAKYVYERTAA 246 K+ +AG P + + + A ++ +D + I ISF GS V + V ER A Sbjct: 197 ATMKICNEALKAGGFPDIFFLFNDAGTDLSQGFVDDKRIPLISFTGSTKVGRMVGERVAR 256 Query: 247 QGKRVQALSGAKNHHIVMPDADVETAVQHVISSAFGSAGQRCMACSAVV----IVGE-NE 301 + R G N I+ AD++ A+ ++ A G+AGQRC + IVGE + Sbjct: 257 RMGRSLLELGGNNAIILDASADLKLAIPAIVFGAVGTAGQRCTTTRRLFVHESIVGEVTD 316 Query: 302 TFVRRLKQKADELIIGNGMDPEVLLTPVIRQSHREKVLGYIQKGIEEGAVLLRDGRKEMD 361 V KQ + IG+ L+ P+ Q + LG ++K G +L G + Sbjct: 317 KLVAAYKQVEGK--IGDPTLATTLMGPLNSQDAVQAYLGAVEKAKASGGKVLTGG-AALS 373 Query: 362 DRPEGNFLGPTIFDYVTPDMTIAKEEIFAPVLSLLRANDLDEALSYIRKSRYGNGATIYT 421 DR +GNF+ PTI V + + E FAP+L ++ LDEA+ G + I+T Sbjct: 374 DR-KGNFVLPTIVTGVKNSDEVVQTETFAPILYIMPFKSLDEAIELQNDVPQGLSSAIFT 432 Query: 422 KDAKAVRKFREEA--DAGMLGINVGVPATMAFFPFSGWKDSFYGDLHVNGKDGVNFYTRK 479 +D KA ++ A D G+ +N+G F G K++ G +G D Y R+ Sbjct: 433 RDLKAAEQYLSSAGSDCGIANVNIGTSGAEIGGAFGGEKET--GGGRESGSDAWKVYMRR 490 Query: 480 KMITSRF 486 + TS + Sbjct: 491 QTNTSNY 497 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: 547 Number of extensions: 32 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: 488 Length of database: 511 Length adjustment: 34 Effective length of query: 454 Effective length of database: 477 Effective search space: 216558 Effective search space used: 216558 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: 52 (24.6 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:
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