Align L-iditol 2-dehydrogenase (EC 1.1.1.14) (characterized)
to candidate WP_027723082.1 H589_RS0116710 3-oxoacyl-ACP reductase FabG
Query= BRENDA::Q1J2J0 (255 letters) >NCBI__GCF_000425265.1:WP_027723082.1 Length = 240 Score = 117 bits (292), Expect = 3e-31 Identities = 87/242 (35%), Positives = 123/242 (50%), Gaps = 20/242 (8%) Query: 21 ALVTGGAQGIGFEIARGLAQAGARVTIADLNPDVGEGAAREL------DGTFERLNVTDA 74 AL+TG ++GIG IA LA+ G + + + D G E T + +VTD Sbjct: 5 ALITGASKGIGAAIAVQLAEDGYDIWLNYRSDDAGAHKTAEQIKQHGQQCTLLKFDVTDE 64 Query: 75 DAVAD-----LARRLPDVDVLVNNAGIVRNAPAEDTPDDDWRAVLSVNLDGVFWCCREFG 129 AV + L +++P + +VNNAG R++ DW VL V+L G F + Sbjct: 65 KAVEENLSSLLEKKVPYI--VVNNAGFTRDSIMMMMDSSDWNKVLQVHLTGFFNVTKPVV 122 Query: 130 RTMLARGRGAIVSTASMSGLISNHPQPQAAYNASKAAVIHLTRSLAGEWASRGVRVNAVA 189 ML + G I++ AS SG Q Y A+KA +I T+SLA E A R + VNAV Sbjct: 123 SRMLRKRTGRIINIASTSG--ETGVAGQTNYCAAKAGLIGATKSLAMEVAKRNILVNAVT 180 Query: 190 PGYTATPLTRRGLETPEWRETWLKETPLGRLAEPREIAPAVLYLASDAASFVTGHTLVVD 249 PG+ T + L E + T PL RL P+E+A V +L SD AS++TG T+ V+ Sbjct: 181 PGFIDTDMLSE-LPVDEIKNT----IPLKRLGTPKEVAGVVSFLCSDKASYITGQTIAVN 235 Query: 250 GG 251 GG Sbjct: 236 GG 237 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: 137 Number of extensions: 11 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: 240 Length adjustment: 24 Effective length of query: 231 Effective length of database: 216 Effective search space: 49896 Effective search space used: 49896 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