Align D-xylose 1-dehydrogenase (EC 1.1.1.175) (characterized)
to candidate WP_043743408.1 AMB_RS04300 beta-ketoacyl-ACP reductase
Query= BRENDA::B8H1Z0 (248 letters) >NCBI__GCF_000009985.1:WP_043743408.1 Length = 240 Score = 102 bits (253), Expect = 9e-27 Identities = 72/241 (29%), Positives = 115/241 (47%), Gaps = 11/241 (4%) Query: 11 GKRVVITGGGSGIGAGLTAGFARQGAEVIFLDIADEDSRALEAELAGSPIPP----VYKR 66 G+ ++TGG GIG ++ + G +V+ ++++ A G P Y Sbjct: 2 GRLAIVTGGTRGIGREISVTLKKAGYKVVANYGGNDEAAAKFTAETGIPSMKWDVGSYPA 61 Query: 67 CDLMNLEAIKAVFAEIGDVDVLVNNAGNDDRHKLADVTGAYWDERINVNLRHMLFCTQAV 126 C+ AI + AE G V+++VNNAG L ++ W+E I+ NL + Sbjct: 62 CEA----AIAKIVAEHGPVEIIVNNAGITRDATLHRMSYQMWEEVIHTNLTSCFNMARLA 117 Query: 127 APGMKKRGGGAVINFGSISWHLGLEDLVLYETAKAGIEGMTRALARELGPDDIRVTCVVP 186 M++RG G ++N GSI+ G V Y AK+GI G T+ALA+E +I V + P Sbjct: 118 IDSMRERGFGRIVNIGSINGQAGQYGQVNYAAAKSGIHGFTKALAQEGAAKNITVNAIAP 177 Query: 187 GNVKTKRQEKWYTPEGEAQIVAAQCLKGRI-VPENVAALVLFLASDDASLCTGHEYWIDA 245 G V T P + + A+ GR+ E++A V+FL +D+A TG ++ Sbjct: 178 GYVDTDMVRA--VPPAVLEKIIAKIPVGRLGRAEDIARCVMFLIADEADFITGSTLSVNG 235 Query: 246 G 246 G Sbjct: 236 G 236 Lambda K H 0.319 0.137 0.416 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: 127 Number of extensions: 10 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: 248 Length of database: 240 Length adjustment: 24 Effective length of query: 224 Effective length of database: 216 Effective search space: 48384 Effective search space used: 48384 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: 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