Align L-iditol 2-dehydrogenase (EC 1.1.1.14) (characterized)
to candidate N515DRAFT_2826 N515DRAFT_2826 3-oxoacyl-[acyl-carrier-protein] reductase
Query= BRENDA::Q1J2J0 (255 letters) >FitnessBrowser__Dyella79:N515DRAFT_2826 Length = 247 Score = 145 bits (366), Expect = 8e-40 Identities = 101/244 (41%), Positives = 137/244 (56%), Gaps = 13/244 (5%) Query: 16 LDGRHALVTGGAQGIGFEIARGLAQAGARVTIADLNPDVGEGAAREL----DGTFERLNV 71 L G ALVTG ++GIG IA LA GA V I + G A E G LNV Sbjct: 5 LQGEIALVTGASRGIGAAIADELAAQGATV-IGTATSESGAAAIGERLAPHGGQGRVLNV 63 Query: 72 TDADAVADLA----RRLPDVDVLVNNAGIVRNAPAEDTPDDDWRAVLSVNLDGVFWCCRE 127 T+ A+ L + + + +LVNNAGI R+ D+DW+A+L NL V+ + Sbjct: 64 TEPGAIEALVDAIGKDVGALSILVNNAGITRDQLLMRMRDEDWQAILDTNLTSVYRASKA 123 Query: 128 FGRTMLARGRGAIVSTASMSGLISNHPQPQAAYNASKAAVIHLTRSLAGEWASRGVRVNA 187 R M+ +G IVS AS+ GL N Q+ Y A+KA +I ++SLA E SRG+ VN Sbjct: 124 VMRGMMKARKGRIVSIASVIGLTGN--PGQSNYAAAKAGIIAFSKSLAREIGSRGITVNV 181 Query: 188 VAPGYTATPLTRRGLETPEWRETWLKETPLGRLAEPREIAPAVLYLASDAASFVTGHTLV 247 VAPG+ T +TR E E ++ L + LGRL E ++IA AV +LAS AA+++TG TL Sbjct: 182 VAPGFIDTDMTRALPE--ESKQALLGQIALGRLGEAQDIAKAVAFLASPAAAYITGETLH 239 Query: 248 VDGG 251 V+GG Sbjct: 240 VNGG 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: 182 Number of extensions: 15 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: 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