Align L-iditol 2-dehydrogenase (EC 1.1.1.14) (characterized)
to candidate WP_235215591.1 BS73_RS31130 SDR family oxidoreductase
Query= BRENDA::Q1J2J0 (255 letters) >NCBI__GCF_000744815.1:WP_235215591.1 Length = 263 Score = 161 bits (407), Expect = 1e-44 Identities = 106/253 (41%), Positives = 138/253 (54%), Gaps = 11/253 (4%) Query: 8 PHILD---LFRLDGRHALVTGGAQGIGFEIARGLAQAGARVTIADLNPDVGEGAARELDG 64 PH +D LFRLDGR V GG GIG E AR LA GA V +AD + D A EL G Sbjct: 5 PHPVDYSRLFRLDGRRIAVVGGGSGIGREAARALAAQGADVLVADRDQDAACETA-ELAG 63 Query: 65 ---TFERLNVTDADAVADLARRLPDVDVLVNNAGIVRNAPAEDTPDDDWRAVLSVNLDGV 121 T +RL+V D DAV + A +D LV AG+ D ++ V+ +NL + Sbjct: 64 PTATAQRLDVLDPDAVREAAEGWGVLDGLVVTAGVNVRKRIADYTLAEFDRVIGLNLRAM 123 Query: 122 FWCCREFGRTMLARGRGAIVSTASMSGLISNHPQP-QAAYNASKAAVIHLTRSLAGEWAS 180 + M A GRG++V ASM +P Q+AY ASKA ++ R+ A EW + Sbjct: 124 LVLTQSVAPRMAAAGRGSVVGVASMRAF---QVEPGQSAYAASKAGLVQFLRTAAAEWGA 180 Query: 181 RGVRVNAVAPGYTATPLTRRGLETPEWRETWLKETPLGRLAEPREIAPAVLYLASDAASF 240 GVR NA+APG TPLT + +W E + + + L R A EIA AV+YL SDA++F Sbjct: 181 EGVRFNAIAPGVVRTPLTDQIAADKDWYEAYAQASALRRWAGAEEIAGAVVYLVSDASTF 240 Query: 241 VTGHTLVVDGGYT 253 TG L VDGG+T Sbjct: 241 TTGSVLTVDGGWT 253 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: 227 Number of extensions: 7 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 255 Length of database: 263 Length adjustment: 24 Effective length of query: 231 Effective length of database: 239 Effective search space: 55209 Effective search space used: 55209 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 Apr 09 2024. 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