Align L-iditol 2-dehydrogenase (EC 1.1.1.14) (characterized)
to candidate WP_035218082.1 G491_RS0106845 3-oxoacyl-ACP reductase
Query= BRENDA::Q1J2J0 (255 letters) >NCBI__GCF_000429905.1:WP_035218082.1 Length = 258 Score = 169 bits (428), Expect = 5e-47 Identities = 99/251 (39%), Positives = 147/251 (58%), Gaps = 9/251 (3%) Query: 12 DLFRLDGRHALVTGGAQGIGFEIARGLAQAGARVTIADLNPDVGEGAARELDGTFE---- 67 +LF L G+ A++TG + G+G A+GLA AGA V +A D + A L+ T Sbjct: 6 ELFDLTGKTAVITGASSGLGVAFAQGLAAAGANVVLAARRTDRLKDLAANLEKTGVGAEP 65 Query: 68 -RLNVTDADAVADLARRLPD----VDVLVNNAGIVRNAPAEDTPDDDWRAVLSVNLDGVF 122 +VT + V ++ + D +D+LVNNAG+ PAE P + ++ V+ +N++ F Sbjct: 66 VTCDVTLENDVDNMVKATTDRFGRLDILVNNAGVAIPHPAETEPYESFKMVMDINVNAQF 125 Query: 123 WCCREFGRTMLARGRGAIVSTASMSGLISNHPQPQAAYNASKAAVIHLTRSLAGEWASRG 182 C + GR ML G+I++ ASM GL+ PQA+YNASKAA+I++TR LA +W+ RG Sbjct: 126 LCSQRCGRIMLEARSGSIINIASMLGLVGLGSIPQASYNASKAAMINMTRELAAQWSKRG 185 Query: 183 VRVNAVAPGYTATPLTRRGLETPEWRETWLKETPLGRLAEPREIAPAVLYLASDAASFVT 242 VRVNA+APG+ + +T K + L R E+ A+L LAS+A S++T Sbjct: 186 VRVNAIAPGWFPSEMTTDMFGDERSEAFMEKRSLLRRGGRTEELIGALLLLASEAGSYIT 245 Query: 243 GHTLVVDGGYT 253 G T+VVDGG+T Sbjct: 246 GQTIVVDGGWT 256 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: 160 Number of extensions: 8 Number of successful extensions: 3 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: 258 Length adjustment: 24 Effective length of query: 231 Effective length of database: 234 Effective search space: 54054 Effective search space used: 54054 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