Align L-iditol 2-dehydrogenase (EC 1.1.1.14) (characterized)
to candidate WP_012585753.1 C665_RS06220 3-oxoacyl-ACP reductase FabG
Query= BRENDA::Q1J2J0 (255 letters) >NCBI__GCF_000310185.1:WP_012585753.1 Length = 236 Score = 158 bits (400), Expect = 8e-44 Identities = 102/240 (42%), Positives = 137/240 (57%), Gaps = 11/240 (4%) Query: 16 LDGRHALVTGGAQGIGFEIARGLAQAGARVTIADLNPDVGEGAARELDGTFERLNVTDAD 75 L G+ A+VTGGA+GIG I L +GARV + D+ D E A G R+NV DA Sbjct: 7 LAGKVAIVTGGARGIGRTITDALVASGARVHVFDMT-DSNESA-----GVLHRVNVADAQ 60 Query: 76 AVADLARRLPD-VDVLVNNAGIVRNAPAEDTPDDDWRAVLSVNLDGVFWCCREFGRTMLA 134 +VAD +LP+ +LVNNAGI R+ D++WR+VL VNL G F R M+A Sbjct: 61 SVADAVAQLPEPATLLVNNAGITRDRSLLKMSDEEWRSVLDVNLSGAFHMLRACAPGMIA 120 Query: 135 RGRGAIVSTASMSGLISNHPQPQAAYNASKAAVIHLTRSLAGEWASRGVRVNAVAPGYTA 194 GRG +V+ S++GL QA Y A+KA +I LT++ A E +G+ VNAVAPG Sbjct: 121 AGRGRVVNITSINGLRGKF--GQANYTAAKAGMIGLTKTAARELGPKGITVNAVAPGMVM 178 Query: 195 TPLTRRGLETPEWRETWLKETPLGRLAEPREIAPAVLYLASDAASFVTGHTLVVDGGYTV 254 T + R E E L+E+ + LA P +IA AV++L SD A +TG + VD G V Sbjct: 179 TEMAR--ALPAEVLERALQESVMRELATPDDIAAAVVFLLSDMARMITGEVIRVDAGQYV 236 Lambda K H 0.319 0.134 0.408 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: 182 Number of extensions: 11 Number of successful extensions: 4 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: 255 Length of database: 236 Length adjustment: 24 Effective length of query: 231 Effective length of database: 212 Effective search space: 48972 Effective search space used: 48972 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 (21.8 bits) S2: 46 (22.3 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