Align L-iditol 2-dehydrogenase (EC 1.1.1.14) (characterized)
to candidate N515DRAFT_2873 N515DRAFT_2873 3-oxoacyl-[acyl-carrier-protein] reductase
Query= BRENDA::Q1J2J0 (255 letters) >FitnessBrowser__Dyella79:N515DRAFT_2873 Length = 247 Score = 152 bits (384), Expect = 6e-42 Identities = 104/245 (42%), Positives = 136/245 (55%), Gaps = 15/245 (6%) Query: 19 RHALVTGGAQGIGFEIARGLAQAGARVTIADLNPDVGEGAA-----RELDGT--FERLNV 71 R A+VTGG G+G EI R LA AG +V ADL AA +LDG FE ++V Sbjct: 3 RIAIVTGGIGGLGTEICRQLALAGRQVIAADLPARADRVAAFQAELADLDGAVRFEPVDV 62 Query: 72 TDADAVADLARRLPD----VDVLVNNAGIVRNAPAEDTPDDDWRAVLSVNLDGVFWCCRE 127 +D + ++L R+ VDVLVN AGI R+ W+ ++ VNLDGVF CR Sbjct: 63 SDFASCSELIARVEAAHGRVDVLVNAAGITRDTTLRKMDPQHWQELMRVNLDGVFNMCRH 122 Query: 128 FGRTMLARGRGAIVSTASMSGLISNHPQPQAAYNASKAAVIHLTRSLAGEWASRGVRVNA 187 M ARG G IV+ +S++G Q Y A+KA V +LA E A +GV VN Sbjct: 123 VVEGMSARGFGRIVNLSSVNGQTGQFGQTN--YAAAKAGVHGFGMALARETARKGVTVNT 180 Query: 188 VAPGYTATPLTRRGLETPEWRETWLKETPLGRLAEPREIAPAVLYLASDAASFVTGHTLV 247 V+PGY TPL R E R L++ P+GRL P +IA AV +LA+D A ++TG L Sbjct: 181 VSPGYCDTPLVAR--VPAEIRAQILEDIPVGRLGSPADIARAVCFLAADDAGYITGANLP 238 Query: 248 VDGGY 252 V+GGY Sbjct: 239 VNGGY 243 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: 185 Number of extensions: 11 Number of successful extensions: 5 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 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