Align Lactaldehyde reductase (characterized, see rationale)
to candidate WP_093396479.1 BM091_RS13315 alcohol dehydrogenase
Query= uniprot:Q8A199 (384 letters) >NCBI__GCF_900114975.1:WP_093396479.1 Length = 380 Score = 208 bits (530), Expect = 2e-58 Identities = 126/374 (33%), Positives = 202/374 (54%), Gaps = 7/374 (1%) Query: 12 FGAGCRSVIAVEAARRGFKKAFFVTDKDLIKFGVAAEIIKVFDDNHIPYELYSDVKANPT 71 FG G A+ A R G +K F V+D L K G E+I + + + + + + DV +NP Sbjct: 13 FGRGSMKYTALCARRLGAEKVFLVSDPGLEKVGWVDELINILEAHQLEWVYFGDVVSNPR 72 Query: 72 IANVQNGVAAYKASGADFIVALGGGSSIDTAKGIGIVVNNPDFADVKSLEGVADTKHKAV 131 ++ G Y + AD ++ALGGGS +D AKGI IV +N + EG Sbjct: 73 DYQIERGARLYLSERADVVIALGGGSPMDAAKGIAIVASNG--GSIHDYEGANRIHRPLP 130 Query: 132 PTFALPTTAGTAAEVTINYVIIDEDARKKMVCVDPNDIPAVAIVDPELMYSMPKGLTAAT 191 P LPTTAG+ ++++ +I D R KM + +P ++I+DP + + P+ L ++ Sbjct: 131 PMVFLPTTAGSGSDISQFAIITDTRRRVKMSIISRTLVPNISIIDPLFLQTKPRELVLSS 190 Query: 192 GMDALTHAIESYITPGAWAMSDMFELKAIEMIAQNL-KAAVDNGKDTVAREAMSQAQYIA 250 +DAL+HAIES+++ A ++M LKAIE++A+ L AAV DT+ EA+S A A Sbjct: 191 AIDALSHAIESFVSVIASPFTEMQSLKAIELVAKYLPTAAVSLELDTL--EALSTASTAA 248 Query: 251 GMGFSNVGLGIVHSMAHPLGAFYDTPHGVANALLLPYVMEYNAESPAAPKYIHIAKAMGV 310 M FSN GLG VH+++H +G YD HG + +LLP VM +N E+ K I + + Sbjct: 249 AMAFSNAGLGAVHALSHAIGGMYDVLHGHVHPVLLPPVMRFNMEA-CLDKMAQIGRIISG 307 Query: 311 NTDGMTETEGVKAAIEAVKALSLSIGIPQKLHEINVKEEDIPALAVAAFNDVCTGGNPRP 370 ++ ++ IE ++ + LS+ + +L +I + +I L A DVC NPRP Sbjct: 308 RRRRSKKSTAIE-GIETLREMFLSLNMKVRLRDILPDDHNIELLCRMAIQDVCVVTNPRP 366 Query: 371 TSVAEIEVLYRKAF 384 + ++ + +A+ Sbjct: 367 VTWKDLVKICEEAW 380 Lambda K H 0.317 0.133 0.379 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: 310 Number of extensions: 16 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: 384 Length of database: 380 Length adjustment: 30 Effective length of query: 354 Effective length of database: 350 Effective search space: 123900 Effective search space used: 123900 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 (21.7 bits) S2: 50 (23.9 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