Align L-iditol 2-dehydrogenase (EC 1.1.1.14) (characterized)
to candidate 8502147 DvMF_2858 short-chain dehydrogenase/reductase SDR (RefSeq)
Query= BRENDA::Q1J2J0 (255 letters) >FitnessBrowser__Miya:8502147 Length = 245 Score = 89.7 bits (221), Expect = 5e-23 Identities = 81/247 (32%), Positives = 106/247 (42%), Gaps = 21/247 (8%) Query: 19 RHALVTGGAQGIGFEIARGLAQAGARVTIADLNPDVGEGAARELDGTFERLNVTDADAVA 78 R+A+VTGG++GIG IA LAQ G V + N AA E+ R A Sbjct: 6 RNAIVTGGSRGIGRAIALRLAQDGFCVVV---NYASNAPAALEVVDAIARTGGQAVAVPA 62 Query: 79 DLARR-------------LPDVDVLVNNAGIVRNAPAEDTPDDDWRAVLSVNLDGVFWCC 125 D+ V V+VN+AGI+ P + VL NL G F Sbjct: 63 DVGETGDVEGLFAAAHDAFGQVGVVVNSAGIMPMLPIAGGDTAAFEKVLRTNLTGTFNVL 122 Query: 126 REFGRTMLARGRGAIVSTASMSGLISNHPQPQAAYNASKAAVIHLTRSLAGEWASRGVRV 185 + A GR +ST+ ++ + Y ASKA V L R LA E R + V Sbjct: 123 SRAANALTAGGRIIALSTSVIAKPFPGY----GPYIASKAGVEGLVRVLANELRGRSITV 178 Query: 186 NAVAPGYTATPLTRRGLETPEWRETWLKETPLGRLAEPREIAPAVLYLASDAASFVTGHT 245 NAVAPG AT L G +T E K PL RL P EIA V +L ++ Sbjct: 179 NAVAPGPVATDLFLNG-KTEEQIAAIGKLAPLERLGTPEEIAGVVSFLVGPEGGWINAQV 237 Query: 246 LVVDGGY 252 + V+GG+ Sbjct: 238 VRVNGGF 244 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: 181 Number of extensions: 8 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: 245 Length adjustment: 24 Effective length of query: 231 Effective length of database: 221 Effective search space: 51051 Effective search space used: 51051 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 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