Align L-iditol 2-dehydrogenase (EC 1.1.1.14) (characterized)
to candidate GFF2840 HP15_2784 3-ketoacyl-(acyl-carrier-protein) reductase
Query= BRENDA::Q1J2J0 (255 letters) >FitnessBrowser__Marino:GFF2840 Length = 247 Score = 137 bits (344), Expect = 3e-37 Identities = 94/247 (38%), Positives = 134/247 (54%), Gaps = 17/247 (6%) Query: 16 LDGRHALVTGGAQGIGFEIARGLAQAGARVTIADLN-PDVGEGAARELDGTFERLNVTDA 74 L G+ ALVTG ++GIG IA LAQ GA V I + GE A+E++ T R A Sbjct: 4 LKGKVALVTGASRGIGRHIALQLAQRGADVAINYRSRQSEGEEVAKEIEATGVRALSFKA 63 Query: 75 DA-----VADLARRLPD----VDVLVNNAGIVRNAPAEDTPDDDWRAVLSVNLDGVFWCC 125 D L R++ + +D+LVNNAGI ++ + DDDW VL NL V+ C Sbjct: 64 DLSKMPEARSLVRQVQEQWGRIDILVNNAGITKDKSMKKLTDDDWNDVLDTNLGSVYATC 123 Query: 126 REFGRTMLARGRGAIVSTASMSGLISNHPQPQAAYNASKAAVIHLTRSLAGEWASRGVRV 185 E + M+ + G I++ S G N QA Y ASK +I T++LA E A + V Sbjct: 124 SEVLKIMMDQKYGRIINITSFVGQAGNF--GQANYAASKGGIIAFTKTLALEMAKYNITV 181 Query: 186 NAVAPGYTATPLTRRGLETPE-WRETWLKETPLGRLAEPREIAPAVLYLASDAASFVTGH 244 NA+APG+T T + + PE RE + P+GR +P EIA AV++LA++ ++TG Sbjct: 182 NAIAPGFTETEML---AQVPENIREQIIARVPMGRFGKPEEIARAVVFLAAE-GDYITGQ 237 Query: 245 TLVVDGG 251 + V+GG Sbjct: 238 QINVNGG 244 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: 162 Number of extensions: 12 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