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_011373513.1 SUDEN_RS09855 aldehyde dehydrogenase family protein
Query= curated2:Q81QR5 (486 letters) >NCBI__GCF_000012965.1:WP_011373513.1 Length = 471 Score = 191 bits (485), Expect = 5e-53 Identities = 132/428 (30%), Positives = 211/428 (49%), Gaps = 17/428 (3%) Query: 19 ESTGTEVEAVPNPATGKIIAYVPLSPKEDVEKAVEAAKAAYETWSKVPVPNRSRQLYKYL 78 ES G V NP G++ + +D +KA+ A A + SK + R L Sbjct: 15 ESVGKRV----NPYNGEVASEFVTCNADDAKKALNIALLASKEASKTTIAQRCSWLLDVA 70 Query: 79 QLLQENKEELAKIITLENGKTLTDATGEVQRGIEAVELATSAPNLMMGQALPN--IASGI 136 L +NKE++AK IT E GK +T + EV+R IE V LA M G+ + ASG Sbjct: 71 SKLAQNKEDIAKTITDEVGKPITYSRIEVERCIETVTLAAETMRTMHGETVNTDAFASGK 130 Query: 137 DGSIW--RYPIGVVAGITPFNFPMMIPLWMFPLAIACGNTFVLKTSERTPLLAERLVELF 194 + R P GVV ITPFNFP+ + A+ GN +LK + PL A + +LF Sbjct: 131 KTISFFSRVPCGVVVAITPFNFPLNLIAHKIAPALVAGNAVILKPTPEAPLTAYKFAKLF 190 Query: 195 YEAGFP-KGVLNLVQGGKDVVNSILENKDIQAVSFVGSEPVARYVYETGTKHGKRVQALA 253 E+ F K L++V G DV +++ ++ + +SF GS V + T + K+V Sbjct: 191 IESEFAIKDALSVVYGDADVGGTLVTSEIPRVISFTGSVGVGEII--TKSAGIKKVSLEL 248 Query: 254 GAKNHAIVMPDCNLEKTVQGVIGSAFASSGERCMACSVVAVVDEIADEFIDVLVAETKKL 313 G + NL+ Q AF +SG+ C++ + V +I EF + TKKL Sbjct: 249 GGNAATFIDKSANLDLAAQRCAIGAFVNSGQVCISLQRIYVHKDIYSEFALKIAEATKKL 308 Query: 314 KVGDGFHEDNYVGPLIRESHKERVLGYINSGVADGATLLVDGRKIKEEVGEGYFVGATIF 373 VG + ED ++GPL+ + +R + ++ S + +GAT +++ R EG + Sbjct: 309 VVGSPYEEDTFMGPLVNDEAAKRAMEWVQSAIKEGATPILEPRV------EGRVFYPCVM 362 Query: 374 DGVNQEMKIWQDEIFAPVLSIVRVKDLEEGIKLTNQSKFANGAVIYTSNGKHAQTFRDNI 433 V ++M I E+FAP++S++ VKD +E + + N S + I+T++ + + + Sbjct: 363 ADVKEDMAIVCQEVFAPIVSLIEVKDFDEALPMMNNSPYGLQFSIFTNDLNLTKRAINEL 422 Query: 434 DAGMIGVN 441 DAG I +N Sbjct: 423 DAGGIVIN 430 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: 478 Number of extensions: 23 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: 486 Length of database: 471 Length adjustment: 34 Effective length of query: 452 Effective length of database: 437 Effective search space: 197524 Effective search space used: 197524 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: 51 (24.3 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