Align L-iditol 2-dehydrogenase (EC 1.1.1.14) (characterized)
to candidate 206645 3-oxoacyl-(acyl-carrier-protein) reductase
Query= BRENDA::Q1J2J0 (255 letters) >MicrobesOnline__882:206645 Length = 259 Score = 149 bits (377), Expect = 4e-41 Identities = 104/241 (43%), Positives = 146/241 (60%), Gaps = 14/241 (5%) Query: 21 ALVTGGAQGIGFEIARGLAQAGARVTIADLN-PDVGEGAA---RELDG--TFERLNVTDA 74 A+VTGG++GIG +A LA+AG +V + ++ PD E A R+ G T RL+V+DA Sbjct: 20 AIVTGGSRGIGKAVAETLARAGLQVFLTYVSKPDEAEAVAAGIRDAGGSATAFRLDVSDA 79 Query: 75 DAVADLAR-RLPD---VDVLVNNAGIVRNAPAEDTPDDDWRAVLSVNLDGVFWCCREFGR 130 AVA + + D +DVLVNNAGI ++ D+D+ VL VNL G F C RE + Sbjct: 80 AAVAAFFQSEIKDKVRLDVLVNNAGITKDGLIMRMKDEDFERVLDVNLCGAFTCLREASK 139 Query: 131 TMLARGRGAIVSTASMSGLISNHPQPQAAYNASKAAVIHLTRSLAGEWASRGVRVNAVAP 190 M + G I++ S+ G + N QA Y A+KA +I LT+S A E A+R V VNAVAP Sbjct: 140 LMTRQRLGRIINITSVVGQMGN--AGQANYCAAKAGLIGLTKSAAKELAARNVTVNAVAP 197 Query: 191 GYTATPLTRRGLETPEWRETWLKETPLGRLAEPREIAPAVLYLASDAASFVTGHTLVVDG 250 G+ T +T GL E R+ +++ PL RL ++IA AV +LAS+ AS++TG L V+G Sbjct: 198 GFIETDMT-AGL-PEEVRKAYVEAIPLRRLGSAQDIADAVAFLASERASYITGQVLAVNG 255 Query: 251 G 251 G Sbjct: 256 G 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: 5 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: 259 Length adjustment: 24 Effective length of query: 231 Effective length of database: 235 Effective search space: 54285 Effective search space used: 54285 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 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