Align L-iditol 2-dehydrogenase (EC 1.1.1.14) (characterized)
to candidate WP_039103405.1 FPB0191_RS01165 3-oxoacyl-ACP reductase FabG
Query= BRENDA::Q1J2J0 (255 letters) >NCBI__GCF_000807275.1:WP_039103405.1 Length = 244 Score = 150 bits (380), Expect = 2e-41 Identities = 99/243 (40%), Positives = 140/243 (57%), Gaps = 10/243 (4%) Query: 15 RLDGRHALVTGGAQGIGFEIARGLAQAGARVTIADLNPDVGEGAAREL--DGTFERLNVT 72 +L G+ ALVTG ++GIG IA L + GA V E ++ L +G LNVT Sbjct: 2 KLAGKIALVTGASRGIGRAIAEKLVKNGATVIGTATTEKGAEAISQYLGANGKGFLLNVT 61 Query: 73 DA---DAVADLAR-RLPDVDVLVNNAGIVRNAPAEDTPDDDWRAVLSVNLDGVFWCCREF 128 D D+V D + + D+D+LVNNAGI R+ +++W+ +L NL VF + Sbjct: 62 DEKSIDSVIDAVKSQFGDIDILVNNAGITRDNLLMRMKENEWQDILDTNLTSVFRVSKAL 121 Query: 129 GRTMLARGRGAIVSTASMSGLISNHPQPQAAYNASKAAVIHLTRSLAGEWASRGVRVNAV 188 RTM+ + G IV+ S+ G + N QA Y+A+KA +I ++SLA E ASRG+ VN V Sbjct: 122 LRTMMKKRYGRIVTIGSVVGTMGN--AGQANYSAAKAGLIGFSKSLAREVASRGITVNVV 179 Query: 189 APGYTATPLTRRGLETPEWRETWLKETPLGRLAEPREIAPAVLYLASDAASFVTGHTLVV 248 APG+ T +TR + E R L + P RL EP EIA AV +L SD A+++TG TL + Sbjct: 180 APGFIETDMTR--ALSDEQRTAILSQVPANRLGEPEEIANAVAFLVSDDAAYITGETLHI 237 Query: 249 DGG 251 +GG Sbjct: 238 NGG 240 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: 157 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: 244 Length adjustment: 24 Effective length of query: 231 Effective length of database: 220 Effective search space: 50820 Effective search space used: 50820 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 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