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 Dsui_0105 Dsui_0105 NAD-dependent aldehyde dehydrogenase
Query= curated2:Q5L025 (488 letters) >FitnessBrowser__PS:Dsui_0105 Length = 476 Score = 236 bits (601), Expect = 2e-66 Identities = 162/471 (34%), Positives = 231/471 (49%), Gaps = 10/471 (2%) Query: 14 YIGGQWVASSGTETLEVPNPATGEVLARVPISTKEDVDQAVQAAKKAFATWKDVPVPKRA 73 YIGGQWVA G ++V NPAT V+ARVP T D D+A +AA AF W + +R Sbjct: 8 YIGGQWVAPDGNAFIDVENPATETVIARVPEGTATDADRAARAAAAAFPAWAALSGAERG 67 Query: 74 RIMFSFHHLLNQHHEELAELVVQENGKAYKEAYGEIQRGIECVEFAAGAPTLLMGESLSN 133 + L +EL L+ E G K A +Q G FAA A G + Sbjct: 68 AFLQKIADGLKARQDELGRLIASEVGMPVKLAT-RVQAGNPIFTFAACARIAAEGFAEER 126 Query: 134 IAEEIDSEMFRYPLGVVAGITPFNFPMMVPLWMFPLAIVCGNTFVLKPSERTPILANKLA 193 I + + + + P G VA ITP+NFP+ A+ G T VLKPSE P+ A LA Sbjct: 127 IGQSL---VLKVPTGPVACITPWNFPLHQIAAKVGAALAAGCTVVLKPSEVAPLNAFLLA 183 Query: 194 ELFTEAGAPPGVLNVVHGAHEVVN-ALIDHEDIRAISFVGSQPVAKYVYERTAAQGKRVQ 252 E+ AG P GV N+V G VV AL H + A+SF GS K V AA KRV Sbjct: 184 EVIEAAGLPAGVFNLVTGYGPVVGEALAAHPALAAVSFTGSTAAGKRVAAVAAATVKRVS 243 Query: 253 ALSGAKNHHIVMPDADVETAVQHVISSAFGSAGQRCMACSAVVIVGENETFVRRLK-QKA 311 G K+ +V+PDAD+ AV+ ++ F ++GQ C A + +++ E L Q A Sbjct: 244 LELGGKSASVVLPDADLAAAVKGTVAGCFLNSGQACSALTRLLVPQERYAEAAALAVQAA 303 Query: 312 DELIIGNGMDPEVLLTPVIRQSHREKVLGYIQKGIEEGAVLLRDGRKEMDDRPEGNFLGP 371 +G+ + L P++ R++V I++ + +GA LL G + P G ++ P Sbjct: 304 AAYTLGDPLAEGSRLGPLVSGLQRQRVRAMIEQAVADGAELLCGGSAAPEGLPTGYYVRP 363 Query: 372 TIFDYVTPDMTIAKEEIFAPVLSLLRANDLDEALSYIRKSRYGNGATIYTKDAKAVRKFR 431 T+F V PD +A+EE+F PVL++L D EA + + YG A +++ + F Sbjct: 364 TVFGRVRPDAALAREEVFGPVLAILTYRDEAEAEAIANGTDYGLAAAVWSAEEARALAFA 423 Query: 432 EEADAGMLGINVGVPATMAFFPFSGWKDSFYGDLHVNGKDGVNFYTRKKMI 482 AG + IN +A PF G+K S YG G+ GV + + I Sbjct: 424 RRLRAGQVDINGAFFNLLA--PFGGFKQSGYG--RELGRHGVEDFLETQSI 470 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: 520 Number of extensions: 30 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: 488 Length of database: 476 Length adjustment: 34 Effective length of query: 454 Effective length of database: 442 Effective search space: 200668 Effective search space used: 200668 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 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