Align Lactaldehyde reductase (characterized, see rationale)
to candidate WP_078716111.1 B5D49_RS02645 iron-containing alcohol dehydrogenase
Query= uniprot:Q8A199 (384 letters) >NCBI__GCF_900167125.1:WP_078716111.1 Length = 382 Score = 245 bits (626), Expect = 1e-69 Identities = 147/371 (39%), Positives = 215/371 (57%), Gaps = 8/371 (2%) Query: 12 FGAGCRSVIAVEAARRGFKKAFFVTDKDL-IKFGVAAEIIKVFDDNHIPYELYSDVKANP 70 FG G + + E AR G +A VT K + G + ++ + L+++V+++P Sbjct: 14 FGNGAVAQVGRETARLG-SRALIVTGKSSSTRTGSLEAVTASLNEAGVHPVLFAEVESDP 72 Query: 71 TIANVQNGVAAYKASGADFIVALGGGSSIDTAKGIGIVVNNP-DFADVKSLEGVADTKHK 129 +I V+ G A + + D IV LGGGS +D AKGI +++ +P D D S Sbjct: 73 SIQTVEAGAALARENQCDVIVGLGGGSPLDAAKGIVLLLTHPGDIRDYTS----QPADGP 128 Query: 130 AVPTFALPTTAGTAAEVTINYVIIDEDARKKMVCVDPNDIPAVAIVDPELMYSMPKGLTA 189 +P ++PTTAGTA+E+T VI D + + KM IP+VA++DP+L +MP+ +TA Sbjct: 129 GMPLISIPTTAGTASEITRFTVITDTEQKIKMSLQGTALIPSVALLDPQLTVTMPQHVTA 188 Query: 190 ATGMDALTHAIESYITPGAWAMSDMFELKAIEMIAQNLKAAVDNGKDTVAREAMSQAQYI 249 ATGMDALTHAIE+YI+ A MSD+ L+AI +I NL AVD+ + AREAM + Q Sbjct: 189 ATGMDALTHAIEAYISKLATPMSDLHALEAIRLIGANLIKAVDSPDNMAAREAMLRGQMH 248 Query: 250 AGMGFSNVGLGIVHSMAHPLGAFYDTPHGVANALLLPYVMEYNAESPAAPKYIHIAKAMG 309 AG+ FSN + +VHSM+ PLGA + HG ANA+LLP VM++N S AA +Y HIA+A+G Sbjct: 249 AGLAFSNASVALVHSMSRPLGALFGIAHGQANAMLLPVVMDFN-RSAAADRYRHIAEALG 307 Query: 310 VNTDGMTETEGVKAAIEAVKALSLSIGIPQKLHEINVKEEDIPALAVAAFNDVCTGGNPR 369 N ++ + K + +V+ L G+ Q L V+E+DI LA A T NPR Sbjct: 308 ENVQELSARDAAKTTVLSVEELFEETGLEQHLSAYGVQEKDIARLAKDAMESASTAFNPR 367 Query: 370 PTSVAEIEVLY 380 + + +Y Sbjct: 368 KADLESVAAIY 378 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: 326 Number of extensions: 15 Number of successful extensions: 3 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: 382 Length adjustment: 30 Effective length of query: 354 Effective length of database: 352 Effective search space: 124608 Effective search space used: 124608 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 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