Align L-iditol 2-dehydrogenase (EC 1.1.1.14) (characterized)
to candidate WP_040534726.1 L248_RS03880 2-dehydro-3-deoxy-D-gluconate 5-dehydrogenase KduD
Query= BRENDA::Q1J2J0 (255 letters) >NCBI__GCF_000469325.1:WP_040534726.1 Length = 274 Score = 129 bits (324), Expect = 6e-35 Identities = 83/255 (32%), Positives = 133/255 (52%), Gaps = 15/255 (5%) Query: 11 LDLFRLDGRHALVTGGAQGIGFEIARGLAQAGARVTIA-------DLNPDVGEGAARELD 63 ++ F+LDG+ A+VTGG G+G LA+AGA + +A D + E R ++ Sbjct: 23 MNWFKLDGKVAIVTGGNTGLGQGYVVALAEAGADILVAAHGTEQWDQTRAMVEKRGRRIE 82 Query: 64 GTFERLNVTDADAVADLARRLPD----VDVLVNNAGIVRNAPAEDTPDDDWRAVLSVNLD 119 F ++++TD DA + + D +D+LVNNAG+++ P ++ + DW V+++NL Sbjct: 83 --FLQVDLTDEDAPERVMQTALDKFGHIDILVNNAGMIKRNPLLESKEQDWNNVIAINLT 140 Query: 120 GVFWCCREFGRTMLARGRGAIVSTASMSGLISNHPQPQAAYNASKAAVIHLTRSLAGEWA 179 V+ + M + G I++ SM P +Y A+K V LT++ A E Sbjct: 141 AVYRLSLAAAKIMAKQKSGKIINIGSMLSFQGGKFIP--SYTAAKHGVAGLTKAFASELG 198 Query: 180 SRGVRVNAVAPGYTATPLTRRGLETPEWRETWLKETPLGRLAEPREIAPAVLYLASDAAS 239 + ++VNA+APGY T T + L P G AEP E+ ++LASDAA+ Sbjct: 199 AYNIQVNAIAPGYIKTANTAPIRADKARNQEILDRIPAGHWAEPYELMGIAVFLASDAAN 258 Query: 240 FVTGHTLVVDGGYTV 254 ++ G + VDGGY V Sbjct: 259 YLNGAIIPVDGGYLV 273 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: 171 Number of extensions: 9 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: 274 Length adjustment: 25 Effective length of query: 230 Effective length of database: 249 Effective search space: 57270 Effective search space used: 57270 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: 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