Align L-iditol 2-dehydrogenase (EC 1.1.1.14) (characterized)
to candidate AZOBR_RS24695 AZOBR_RS24695 3-oxoacyl-ACP reductase
Query= BRENDA::Q1J2J0 (255 letters) >FitnessBrowser__azobra:AZOBR_RS24695 Length = 256 Score = 162 bits (411), Expect = 5e-45 Identities = 108/248 (43%), Positives = 139/248 (56%), Gaps = 14/248 (5%) Query: 15 RLDGRHALVTGGAQGIGFEIARGLAQAGARVTIADLNPDVGEGAARELDGTFER-----L 69 RL GR A VTGG GIG + LA GA V +AD+ +V E A L + L Sbjct: 10 RLAGRVAFVTGGGGGIGRAVCERLAAEGAAVVVADIGAEVAETVAAALRAEGAQAHATAL 69 Query: 70 NVTDAD----AVADLARRLPDVDVLVNNAGIVRNAPAEDTPDDDWRAVLSVNLDGVFWCC 125 NV D + AV L VD++VN AGIVR+ D +W AV+ VNL G + C Sbjct: 70 NVADRESWGAAVTGLPEAFRGVDIMVNVAGIVRDRSLPKMTDAEWSAVIDVNLRGTWLGC 129 Query: 126 REFGRTMLARGRGAIVSTASMSGLISNHPQPQAAYNASKAAVIHLTRSLAGEWASRGVRV 185 + R + RG G IV+ AS + L + QA Y+ASKA V+ LTR+ A E A RG+ V Sbjct: 130 QTAFRLVGDRGWGRIVNIASTAILGTFG---QANYSASKAGVVGLTRTAALEGARRGILV 186 Query: 186 NAVAPGYTATPLTRRGLETPEWRETWLKETPLGRLAEPREIAPAVLYLASDAASFVTGHT 245 NAVAPG T + + R WL++TP+GRL +P EIA V +LASD A++VTG T Sbjct: 187 NAVAPGVVETAIVEGVPDAV--RSQWLEKTPIGRLGKPAEIAAVVAFLASDDAAYVTGQT 244 Query: 246 LVVDGGYT 253 +V DGG T Sbjct: 245 IVADGGAT 252 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: 223 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: 256 Length adjustment: 24 Effective length of query: 231 Effective length of database: 232 Effective search space: 53592 Effective search space used: 53592 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