Align L-iditol 2-dehydrogenase (EC 1.1.1.14) (characterized)
to candidate WP_011384971.1 AMB_RS13035 NAD(P)-dependent oxidoreductase
Query= BRENDA::Q1J2J0 (255 letters) >NCBI__GCF_000009985.1:WP_011384971.1 Length = 248 Score = 139 bits (351), Expect = 4e-38 Identities = 88/249 (35%), Positives = 140/249 (56%), Gaps = 13/249 (5%) Query: 15 RLDGRHALVTGGAQGIGFEIARGLAQAGARVTIADLNPDVGEGAAREL-----DGTFERL 69 + + + AL+TGGA GIG+ + +A+ GA V IAD+N + GE AA EL F RL Sbjct: 2 KFEDKVALITGGASGIGYCTVKSMAELGADVLIADINVEAGEKAAAELTAKGFKAEFVRL 61 Query: 70 NVTDADAVADLARRL----PDVDVLVNNAGIVRNAPAEDTPDDDWRAVLSVNLDGVFWCC 125 +VTD +A + + +D+L N AG P D D V+S+NL G Sbjct: 62 DVTDKANIARVKEHVVATRGRLDILCNVAGWGHIQPFVDNDDAFIAKVMSLNLTGPIELI 121 Query: 126 REFGRTMLARGRGAIVSTASMSGLISNHPQPQAAYNASKAAVIHLTRSLAGEWASRGVRV 185 R F M+ + G IV+ AS +G + + ++ Y+A+K +I +++LA E A + V Sbjct: 122 RAFFPLMIEKKTGKIVNVASDAGRVGS--LGESVYSAAKGGLIAFSKALAREGARFNINV 179 Query: 186 NAVAPGYTATPLTRRGLETPEWRETWLKETPLGRLAEPREIAPAVLYLASDAASFVTGHT 245 NA+ PG T TPL + E ++ E +LK P+ R +P+E+A +++++AS+ A ++TG Sbjct: 180 NAICPGPTDTPLLKS--EPEKFLEAFLKVIPMRRFGQPQEVADSIVFMASNRADYITGQV 237 Query: 246 LVVDGGYTV 254 L V+GG T+ Sbjct: 238 LSVNGGITM 246 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: 140 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: 248 Length adjustment: 24 Effective length of query: 231 Effective length of database: 224 Effective search space: 51744 Effective search space used: 51744 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