Align Lmo2663 protein (characterized, see rationale)
to candidate 3607519 Dshi_0931 Alcohol dehydrogenase GroES domain protein (RefSeq)
Query= uniprot:Q8Y414 (343 letters) >FitnessBrowser__Dino:3607519 Length = 339 Score = 119 bits (298), Expect = 1e-31 Identities = 89/273 (32%), Positives = 136/273 (49%), Gaps = 18/273 (6%) Query: 1 MKAVVKTNPGYDQMELKDVEEPQVYGDKVKIKVAFTGICGSDIHTFKGEYK-NPTTPVTL 59 MKA + T+ +E+++V +P V + +K+ G+C +D+H +G++ P P Sbjct: 4 MKAALVTDFS-KPLEIREVRKPTVTDGNILVKIEACGVCHTDLHAARGDWPVKPEPPFIP 62 Query: 60 GHEFSGVVVEVGPDVTSIKVGDRVTSETTFETCGECIYCKEHDYNLC-SNRRGIGTQANG 118 GHE GVVVEVG +VTS+K GDRV CG C C LC + G NG Sbjct: 63 GHEGVGVVVEVGHNVTSVKEGDRVGVPWLHHACGHCTACVTGWETLCRTEPEYTGYTVNG 122 Query: 119 SFAEFVLSREESCHVLDERISLEAAALTEPLACC---VHSALEKTTIRPDDTVLVFGPGP 175 FAE+V + L +++ AA P+ C V+ L++ + P TV++ G G Sbjct: 123 GFAEYVEADPTYVGHLPDKLDFAPAA---PILCAGVTVYKGLKECDLHPGQTVVISGIGG 179 Query: 176 IGLLLAQVVKAQGATVIMAGITKDSDRLRLAKELGMDRIVDTLKED-LAEVV-LGMTGGY 233 +G L Q +A G VI + + D+L LA++LG ++ +D +AEV LG Sbjct: 180 LGHLAVQYARAMGLHVIAVDVAE--DKLALARDLGAGVAINAATQDPVAEVARLG----- 232 Query: 234 GAERVFDCSGAVPAVNQGLPLTKKKGDFVQVGL 266 GAE V + + A +QG+ + G VGL Sbjct: 233 GAEGVLVTAVSNTAFSQGVGMLAPGGTMSLVGL 265 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: 285 Number of extensions: 22 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: 343 Length of database: 339 Length adjustment: 29 Effective length of query: 314 Effective length of database: 310 Effective search space: 97340 Effective search space used: 97340 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 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