Align Lactaldehyde reductase (characterized, see rationale)
to candidate SM_b20147 SM_b20147 alcohol dehydrogenase
Query= uniprot:Q8A199 (384 letters) >FitnessBrowser__Smeli:SM_b20147 Length = 368 Score = 164 bits (415), Expect = 4e-45 Identities = 106/325 (32%), Positives = 164/325 (50%), Gaps = 11/325 (3%) Query: 62 LYSDVKANPTIANVQNGVAAYKASGADFIVALGGGSSIDTAKGIGIVVNN-PDFADVKSL 120 L+ + P I ++ + A + + D IV LGGGS +D AK + ++ ++ ADV Sbjct: 53 LFDAIPGEPDITTLEAALEAARNARPDLIVGLGGGSVMDVAKLVAVLWDSGQSLADVAGP 112 Query: 121 EGVADTKHKAVPTFALPTTAGTAAEVTINYVIIDEDARKKMVCVDPNDIPAVAIVDPELM 180 VA + + TTAGT +E I +I D K+ P+ I +A++DPEL Sbjct: 113 NRVAGRNTRLAQ---VATTAGTGSEAGIRSLITDPGKGSKIAVESPHMIADLAVLDPELT 169 Query: 181 YSMPKGLTAATGMDALTHAIESYITPGAWAMSDMFELKAIEMIAQNLKAAVDNGKDTVAR 240 YS+P +TAATG+DA+ H +E++ A M D F ++ + L AV +G+DT AR Sbjct: 170 YSVPPAVTAATGVDAMAHCVEAFTNRKAHTMIDGFARMGFNLVGKYLARAVRDGEDTEAR 229 Query: 241 EAMSQAQYIAGMGFSNVGLGIVHSMAHPLGAFYDTPHGVANALLLPYVMEYNAESPAAPK 300 E M A Y G+ V H++++PLG PHG+ANA++ P+V+ +N S AA K Sbjct: 230 EGMMLASYYGGICLGPVNTAAGHAISYPLGTLLHLPHGLANAIIFPHVLAFNQPS-AAAK 288 Query: 301 YIHIAKAMGVNTDGMTETEGVKAAIEAVKALSLSIGIPQKLHEINVKEEDIPALAVAAFN 360 +A A+G+ G+++ + + A K +GI L K D+P A A Sbjct: 289 TAEVADALGLG-QGLSQRD----LLSAAKDFCAGLGIEMSLAVNGAKAADLPRFAADAHA 343 Query: 361 -DVCTGGNPRPTSVAEIEVLYRKAF 384 NP S A++ +YR AF Sbjct: 344 IRRLMDNNPVDMSEADVLEIYRAAF 368 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: 341 Number of extensions: 17 Number of successful extensions: 2 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: 368 Length adjustment: 30 Effective length of query: 354 Effective length of database: 338 Effective search space: 119652 Effective search space used: 119652 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 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