Align D-gluconate dehydrogenase 21.7 kD subunit (EC 1.1.99.3) (characterized)
to candidate HSERO_RS16745 HSERO_RS16745 gluconate 2-dehydrogenase
Query= metacyc::MONOMER-12747 (251 letters) >FitnessBrowser__HerbieS:HSERO_RS16745 Length = 240 Score = 271 bits (693), Expect = 9e-78 Identities = 134/248 (54%), Positives = 178/248 (71%), Gaps = 12/248 (4%) Query: 4 QDRDNPRREFLRKSLTLIPVVTVASTGLGGSLLAAASETAIAATPATPGKQPAGSGQGYE 63 QD++ PRR FLR+ L ++P A++ LGG+ A S+ A+A + + PGK A Y Sbjct: 3 QDKE-PRRRFLRQVLAIVP----AASTLGGATTVAVSQAAMADS-SEPGKPRA-----YT 51 Query: 64 PGYFTAEEWAFIKAAVERLIPADEMGPGALEAGVPEYIDRQMNTPYAAGALWYMQGPFKA 123 P YFTA EWAF+ AAV+ LIP+D+ G GALE GVPE+IDRQM TPY AG LWYMQGPF Sbjct: 52 PTYFTAAEWAFLNAAVDHLIPSDQYGAGALETGVPEFIDRQMETPYGAGKLWYMQGPFHP 111 Query: 124 DAAPEMGWQSKLVPKDIYRLGIAATDAWCKELKGQTFAAQDSATRDDLLKQLEAGTPQFD 183 D+ PE+G+Q LVP+DIYR GIAA + WC + G+ FA D A + ++LK ++ G F+ Sbjct: 112 DSVPELGYQLSLVPRDIYRQGIAACNDWCSKNHGKVFAELDKAKQLEVLKMMDGGKISFE 171 Query: 184 AVPAKLFFNLLLQNTKEGFFSDPIHGGNKGLVGWTLIGFPGARADFMDWVER-NEQYPFP 242 VPAK FFN +L NTKEG+F+DP++GGN+ + GW ++GFPGARADF DWV++ N +YP+ Sbjct: 172 TVPAKTFFNFMLGNTKEGYFADPMYGGNQKMGGWKMVGFPGARADFADWVDQYNVKYPYG 231 Query: 243 AVSIRGER 250 VSI GE+ Sbjct: 232 PVSILGEK 239 Lambda K H 0.317 0.135 0.414 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: 262 Number of extensions: 14 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: 251 Length of database: 240 Length adjustment: 24 Effective length of query: 227 Effective length of database: 216 Effective search space: 49032 Effective search space used: 49032 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: 46 (22.3 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