Align Lmo2663 protein (characterized, see rationale)
to candidate WP_086510920.1 BZY95_RS16145 alcohol dehydrogenase
Query= uniprot:Q8Y414 (343 letters) >NCBI__GCF_002151265.1:WP_086510920.1 Length = 343 Score = 137 bits (346), Expect = 3e-37 Identities = 96/306 (31%), Positives = 150/306 (49%), Gaps = 6/306 (1%) Query: 18 DVEEPQVYGDKVKIKVAFTGICGSDIHTFKGEYKNPTTPVTLGHEFSGVVVEVGPDVTSI 77 + E P+ +V +KVAF GICGSD+H G+ P GHEF+G V +G V I Sbjct: 16 ETEAPRAAAGEVLVKVAFAGICGSDMHIIHGDNAFVRFPRITGHEFAGTVEALGEGVEGI 75 Query: 78 KVGDRVTSETTFETCGECIYCKEHDYNLCSNRRGIGTQANGSFAEFVLSREESCHVLDER 137 ++G RV + +CG C C+ N+CS + IG +G F E+V + H+L E Sbjct: 76 EIGARVCIDPVV-SCGRCYPCRIGRPNVCSALQVIGVHRDGGFEEWVNVPAANVHLLPEG 134 Query: 138 ISLEAAALTEPLACCVHSALEKTTIRPDDTVLVFGPGPIGLLLAQVVKAQGATVIMAGIT 197 + LEA AL EP + + LE+ D +L++G G IGL + Q+ +A G I I Sbjct: 135 LGLEAGALVEPYSIAA-NVLERMQPLRGDRLLIYGAGVIGLTILQMARALGLEDITV-ID 192 Query: 198 KDSDRLRLAKELGMDRIVDTLKEDLAEVVLGMTGGYGAERVFDCSGAVPAVNQGLPLTKK 257 +RL A+ELG R KED+ +TGG G + D + + Q L + Sbjct: 193 LIEERLATARELGATRTWHG-KEDVEAAAHELTGGEGMPLIADAACVPALLPQMLRIASP 251 Query: 258 KGDFVQVGLFAEKKNAIDEESIIQREIAYIGSRSQKPSSWILALDLLANGKIDTDKMITK 317 G +G + + E +I++E+ +GSR + L+ +A+G++D +++ Sbjct: 252 AGRIGLLGFNPTPSDLVQLE-VIKKELTLVGSRLNN-RKFPEVLERMASGRLDPLALVSH 309 Query: 318 VYGLDD 323 DD Sbjct: 310 RLPFDD 315 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: 293 Number of extensions: 20 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: 343 Length of database: 343 Length adjustment: 29 Effective length of query: 314 Effective length of database: 314 Effective search space: 98596 Effective search space used: 98596 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: 49 (23.5 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