Align Lmo2663 protein (characterized, see rationale)
to candidate N515DRAFT_2489 N515DRAFT_2489 alcohol dehydrogenase, propanol-preferring
Query= uniprot:Q8Y414 (343 letters) >FitnessBrowser__Dyella79:N515DRAFT_2489 Length = 343 Score = 108 bits (271), Expect = 2e-28 Identities = 73/233 (31%), Positives = 107/233 (45%), Gaps = 4/233 (1%) Query: 1 MKAVVKTNPGYDQMELKDVEEPQVYGDKVKIKVAFTGICGSDIHTFKGEYK-NPTTPVTL 59 MKA V G + + +V P +V +K+ G+C +D+H G++ P P Sbjct: 5 MKAAVVRAFG-QPLSIDEVPVPTPGLGEVLVKIEACGVCHTDLHAVDGDWPVKPKPPFIP 63 Query: 60 GHEFSGVVVEVGPDVTSIKVGDRVTSETTFETCGECIYCKEHDYNLCSNRRGIGTQANGS 119 GHE G VV +GP VT +K GDRV + CG C +C LC +++ G NG Sbjct: 64 GHEGVGYVVAIGPGVTHLKEGDRVGIPWLYSACGHCEHCLGGWETLCESQQNTGYSVNGG 123 Query: 120 FAEFVLSREESCHVLDERISLEAAALTEPLACCVHSALEKTTIRPDDTVLVFGPGPIGLL 179 FAE+ L+ + L + I A V+ L+ T RP + V++ G G +G + Sbjct: 124 FAEYALAAADYVGHLPDGIGFVEIAPVLCAGVTVYKGLKVTDTRPGNWVVISGIGGLGHM 183 Query: 180 LAQVVKAQGATVIMAGITKDSDRLRLAKELGMDRIVDTLKEDLAEVVLGMTGG 232 Q A G V A + D +L LA+ LG I++ D VV GG Sbjct: 184 AVQYAAAMGLNV--AAVDIDDAKLDLARRLGAQLIINARHADPVAVVKKEIGG 234 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: 304 Number of extensions: 19 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: 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 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