Align D-gluconate dehydrogenase 21.7 kD subunit (EC 1.1.99.3) (characterized)
to candidate BPHYT_RS23030 BPHYT_RS23030 gluconate 2-dehydrogenase
Query= metacyc::MONOMER-12747 (251 letters) >FitnessBrowser__BFirm:BPHYT_RS23030 Length = 246 Score = 262 bits (669), Expect = 5e-75 Identities = 136/242 (56%), Positives = 171/242 (70%), Gaps = 6/242 (2%) Query: 10 RREFLRKSLTLIPVVTVASTGLGGSLLAAASETAIAATPATPGKQPAGSGQGYEPGYFTA 69 RR FLR ++ L+P T+A + S +A ++ A A G+ SG Y+P +F A Sbjct: 9 RRGFLRTAIALVPAGTLAGCEVKQSTTTSAPGSSEGAD-ANAGR---ASGVDYKPHFFDA 64 Query: 70 EEWAFIKAAVERLIPADEMGPGALEAGVPEYIDRQMNTPYAAGALWYMQGPFKADAAPEM 129 +EWAFI AAV+RLIP+D GPGA+EAGVPE+IDRQM+TPYA GALWYMQGPF APE+ Sbjct: 65 KEWAFIHAAVDRLIPSDSEGPGAVEAGVPEFIDRQMDTPYAHGALWYMQGPF-TQGAPEL 123 Query: 130 GWQSKLVPKDIYRLGIAATDAWCKELKGQTFAAQDSATRDDLLKQLEAGTPQFDAVPAKL 189 G+Q KLVP+D+YRLGIAA +A+C + F A D ATRD +L LE G D VPA + Sbjct: 124 GYQLKLVPRDLYRLGIAAINAYCTKTYAHPFDALDPATRDTVLGALEKGNVDLDNVPAGV 183 Query: 190 FFNLLLQNTKEGFFSDPIHGGNKGLVGWTLIGFPGARADFMDWVERN-EQYPFPAVSIRG 248 FF LLQNT+EG+F DPIHGGN+ + GW +IGFPGARADFMD+V +N YP+ VSI G Sbjct: 184 FFGQLLQNTREGYFCDPIHGGNRDMGGWKMIGFPGARADFMDFVNQNGAAYPYGPVSIEG 243 Query: 249 ER 250 +R Sbjct: 244 KR 245 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: 259 Number of extensions: 15 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: 246 Length adjustment: 24 Effective length of query: 227 Effective length of database: 222 Effective search space: 50394 Effective search space used: 50394 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