Align L-iditol 2-dehydrogenase (EC 1.1.1.14) (characterized)
to candidate WP_078715956.1 B5D49_RS01965 3-oxoacyl-[acyl-carrier-protein] reductase
Query= BRENDA::Q1J2J0 (255 letters) >NCBI__GCF_900167125.1:WP_078715956.1 Length = 247 Score = 134 bits (338), Expect = 1e-36 Identities = 94/242 (38%), Positives = 136/242 (56%), Gaps = 16/242 (6%) Query: 21 ALVTGGAQGIGFEIARGLAQAGARVTIADLN-PDVGEGAAREL---DGTFE--RLNVTDA 74 ALVTGG++GIG A LA G V + ++ P+ E + + GT +L+ +D Sbjct: 8 ALVTGGSRGIGRACAERLAADGFEVWLTYVSKPEAAETVVQTIADAGGTARAVQLDSSDR 67 Query: 75 DAVA----DLARRLPDVDVLVNNAGIVRNAPAEDTPDDDWRAVLSVNLDGVFWCCREFGR 130 +AVA D + + LVNNAGI R+ +DW +VL +NL G F C +E + Sbjct: 68 EAVASFFKDEIKGKVHLAALVNNAGITRDGLLIRMKPEDWDSVLDINLTGAFSCLQEAAK 127 Query: 131 TMLARGRGAIVSTASMSGLISNHPQPQAAYNASKAAVIHLTRSLAGEWASRGVRVNAVAP 190 M + G+I++ +S+ G + N QA Y A+KA +I LT++ A E A RGVRVNAVAP Sbjct: 128 IMARQRGGSIINISSVVGQMGN--AGQANYVAAKAGLIGLTKAAARELAGRGVRVNAVAP 185 Query: 191 GYTATPLTRRGLETPEWR-ETWLKETPLGRLAEPREIAPAVLYLASDAASFVTGHTLVVD 249 G+ T +T+ + PE E+ PL RL P +IA AV +LA + A ++TG L V+ Sbjct: 186 GFIETDMTK---DLPEKTVESMKTMIPLSRLGSPGDIAAAVSFLAGNGAGYITGQVLAVN 242 Query: 250 GG 251 GG Sbjct: 243 GG 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: 183 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: 247 Length adjustment: 24 Effective length of query: 231 Effective length of database: 223 Effective search space: 51513 Effective search space used: 51513 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 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