Align Short-chain dehydrogenase (characterized, see rationale)
to candidate AZOBR_RS16640 AZOBR_RS16640 3-hydroxybutyrate dehydrogenase
Query= uniprot:A0A2E7P8M8 (258 letters) >FitnessBrowser__azobra:AZOBR_RS16640 Length = 261 Score = 104 bits (260), Expect = 2e-27 Identities = 84/260 (32%), Positives = 122/260 (46%), Gaps = 12/260 (4%) Query: 3 LNLQDKVVIVTGGASGIGGAISLQLAAEGAIPVV--FARSEPDPQFWARLTG-LQPRAAL 59 + L KV +VTG SGIG I+ LA GA V+ F + + A L R Sbjct: 1 MTLTQKVAVVTGSTSGIGLGIARALAGAGADVVLNGFGEAAAIEELRAGLAAEFGVRVGY 60 Query: 60 FQLELQDEARCGEAVAETVRRFGRLDGLVNNAGVNDSVGL-DAGRNEFVASLERNLIHYY 118 +L A + FG +D LVNNAG+ + D + A + NL + Sbjct: 61 HGADLSKPAEIAALIGHAEETFGSVDVLVNNAGIQHVAPVEDFPAERWDAVIALNLSAVF 120 Query: 119 VMAHYCVPHLKATR-GAILNVSSKTALTGQGNTSGYCASKGAQLSLTREWAAALRDDGVR 177 H+ +P +K G ILN++S N S Y A+K + LT+ A GV Sbjct: 121 HGTHHALPGMKRRGWGRILNIASVHGHVASVNKSAYVAAKHGVVGLTKTVALETAGTGVT 180 Query: 178 VNALIPAEVMTPLYEKW---IATFEN---PQEKLDAITSKIPLGKRFTTSEEMADMAVFL 231 NA+ P V+TPL +K IA+ +N PQ K + + +K P G F T +E+ +AVFL Sbjct: 181 CNAICPGWVLTPLVQKQIDAIASTKNIPEPQAKAELLGAKQPSG-AFVTPDELGGLAVFL 239 Query: 232 LSGRSSHTTGQWVFVDGGYT 251 S ++ TG + +DGG+T Sbjct: 240 CSDSAAQMTGASLLMDGGWT 259 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: 139 Number of extensions: 8 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: 258 Length of database: 261 Length adjustment: 24 Effective length of query: 234 Effective length of database: 237 Effective search space: 55458 Effective search space used: 55458 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 Apr 09 2024. 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