Align Short-chain dehydrogenase (characterized, see rationale)
to candidate WP_086511368.1 BZY95_RS18525 3-hydroxybutyrate dehydrogenase
Query= uniprot:A0A2E7P8M8 (258 letters) >NCBI__GCF_002151265.1:WP_086511368.1 Length = 257 Score = 95.1 bits (235), Expect = 1e-24 Identities = 78/255 (30%), Positives = 119/255 (46%), Gaps = 20/255 (7%) Query: 8 KVVIVTGGASGIGGAISLQLAAEGAIPVVFARSEPDPQFWARLTGLQPRAALFQLELQDE 67 +V +VTG ASGIG A+ Q G + +E AR AA FQ +L D Sbjct: 10 RVALVTGTASGIGEAVVHQFRELGHQVLAVDFNEQ-----ARAKADAVGAAFFQADLSDG 64 Query: 68 ARCGEAVAETVRRFGRLDGLVNNAGVNDSVGLDAGRNEFVASLERNLIHYYVMAHYCV-- 125 C AVAE ++RFG++D LVNNAG+ ++ +F + R +I + A + + Sbjct: 65 EACKAAVAEAIKRFGKVDILVNNAGIQHVSPIE----DFPEAKWRQIIDLMLTAPFLLTQ 120 Query: 126 ---PHLKATR-GAILNVSSKTALTGQGNTSGYCASKGAQLSLTREWAAALRDDGVRVNAL 181 P ++ G I+N++S A S Y ++K + LT+ A G+ NA+ Sbjct: 121 AVWPSMRENGWGRIVNIASVHAQVASPGKSAYISAKHGMIGLTKTAALEGGPQGITANAI 180 Query: 182 IPAEVMTPLYEKWIATFE-----NPQEKLDAITSKIPLGKRFTTSEEMADMAVFLLSGRS 236 PA V TPL E IA + Q+ ++ I K KR EE++ + +L S + Sbjct: 181 CPAYVKTPLVENQIADQARLHNMDEQDVVEQIMLKNAAVKRLIDPEEVSALVAYLASDAA 240 Query: 237 SHTTGQWVFVDGGYT 251 TG +D G+T Sbjct: 241 GAVTGSSWNIDLGWT 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: 107 Number of extensions: 4 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: 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 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