Align Short-chain dehydrogenase (characterized, see rationale)
to candidate GFF2316 PGA1_c23480 putative D-beta-hydroxybutyrate dehydrogenase
Query= uniprot:A0A2E7P8M8 (258 letters) >FitnessBrowser__Phaeo:GFF2316 Length = 257 Score = 96.7 bits (239), Expect = 4e-25 Identities = 82/256 (32%), Positives = 121/256 (47%), Gaps = 18/256 (7%) Query: 4 NLQDKVVIVTGGASGIGGAISLQLAAEGAIPVVFARSEPDPQFWARLTGLQPRAALFQLE 63 +L + V+VTGG SG+G A++ A GA + R Q A TG P A Sbjct: 8 DLAGRHVVVTGGGSGVGAALARSFAGGGARLTLLGRRIEPLQEVAAETGALPLACDVT-- 65 Query: 64 LQDEARCGEAVAETVRR-FGRLDGLVNNAGVNDS---VGLDAGRNEFVASLERNLIHYYV 119 EA A +T R+ G + + NAG S +D +F A+L NL + Sbjct: 66 ---EAEAVRAALDTARQQHGPVSVAIANAGAAPSKPFAKMDLA--DFEAALAVNLSGVFN 120 Query: 120 MAHYCVPHLKATR-GAILNVSSKTALTGQGNTSGYCASKGAQLSLTREWAAALRDDGVRV 178 + +P +K+ G ++ V+S L G SGYCA+K + LTR A L G+ V Sbjct: 121 LWQAALPDMKSAGWGRMIAVASTAGLKGYPYVSGYCAAKHGVVGLTRSLAQELARSGITV 180 Query: 179 NALIPAEVMTPLYEKWIATF-----ENPQEKLDAITSKIPLGKRFTTSEEMADMAVFLLS 233 NA+ P + TPL E+ IAT + +E ++ + P G RF EE+AD A+FL S Sbjct: 181 NAICPGFIETPLLERSIATIVSTTGMSEEEAAKSLRAGNPQG-RFIQPEEVADAALFLAS 239 Query: 234 GRSSHTTGQWVFVDGG 249 ++ G + + GG Sbjct: 240 SSAASINGSALPITGG 255 Lambda K H 0.318 0.134 0.394 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: 142 Number of extensions: 7 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: 258 Length of database: 257 Length adjustment: 24 Effective length of query: 234 Effective length of database: 233 Effective search space: 54522 Effective search space used: 54522 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 47 (22.7 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