Align GDP-6-deoxy-D-talose 4-dehydrogenase (EC 1.1.1.135); 3-hydroxy-2-methylbutyryl-CoA dehydrogenase (EC 1.1.1.178) (characterized)
to candidate WP_101443621.1 BD749_RS04795 glucose 1-dehydrogenase
Query= BRENDA::Q99714 (261 letters) >NCBI__GCF_002846395.1:WP_101443621.1 Length = 247 Score = 129 bits (323), Expect = 8e-35 Identities = 90/256 (35%), Positives = 130/256 (50%), Gaps = 17/256 (6%) Query: 10 GLVAVITGGASGLGLATAERLVGQGASAVLLDLPNSGGEA---QAKKLGNNCVFAPADVT 66 G VA++TGG+SG+G + A +GA V+ D+ G + ++LG+ +F ADV+ Sbjct: 4 GKVALVTGGSSGIGRSAALLYAREGAKVVVSDIHEESGMQVVREIEQLGSQAIFVAADVS 63 Query: 67 SEKDVQTALALAKGKFGRVDVAVNCAGIAVASKTYNLKKGQTHTLEDFQRVLDVNLMGTF 126 D + + A KFGR+DVA N AGI S T ++E + +V+ +NL F Sbjct: 64 KPADCERMVQQAVEKFGRLDVAFNNAGIGGESNTIG-----DMSIEGWDKVISINLNSVF 118 Query: 127 NVIRLVAGEMGQNEPDQGGQRGVIINTASVAAFEGQVGQAAYSASKGGIVGMTLPIARDL 186 + +M Q QGG G I+N +S+ G AAY A+K G+VG+T + Sbjct: 119 YCMHFQIRQMLQ----QGG--GAIVNNSSILGQVGFANSAAYVAAKHGVVGLTKNGGLEY 172 Query: 187 APIGIRVMTIAPGLFGTPLLTSLPEKVCNFLASQVPFPSRLGDPAEYAHLVQAIIEN--P 244 A GIR+ I P TPLL+ + E+ FL S+ P RLG P E A LV + N Sbjct: 173 ASKGIRINAIGPAFIKTPLLSGMGEETLQFLTSKHPI-GRLGAPEEIAELVIWLSSNKAS 231 Query: 245 FLNGEVIRLDGAIRMQ 260 F++G DGA Q Sbjct: 232 FVSGAYYAADGAYLSQ 247 Lambda K H 0.318 0.135 0.385 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: 153 Number of extensions: 9 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: 261 Length of database: 247 Length adjustment: 24 Effective length of query: 237 Effective length of database: 223 Effective search space: 52851 Effective search space used: 52851 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 (21.7 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