Align NAD(P)+-dependent L-rhamnose 1-dehydrogenase (EC 1.1.1.378; EC 1.1.1.173) (characterized)
to candidate GFF1769 PGA1_c17930 3-oxoacyl-[acyl-carrier-protein] reductase FabG
Query= metacyc::MONOMER-16230 (256 letters) >FitnessBrowser__Phaeo:GFF1769 Length = 245 Score = 135 bits (339), Expect = 1e-36 Identities = 92/249 (36%), Positives = 135/249 (54%), Gaps = 10/249 (4%) Query: 3 LIDKTVIVTGASRGIGRAAARECARQGARVVIGHSGSDEGRAGALSLAEEIAAFGGTAIA 62 L K+ ++TGAS GIG AR GA V G SG+ E L E A G A Sbjct: 4 LTGKSALITGASGGIGGDIARALHASGATV--GLSGTREA-----PLQELAAELGERAHV 56 Query: 63 VGADAADLDSGEKLVAAAVEAFGSVDVLVNNAGICPFHSFLDMPRELYLKTVGTNLNGAY 122 + + +D ++ E L A+ A GSVD+LVNNAGI + F+ M E + + NL Sbjct: 57 LPCNLSDAEAVEALPKQAIAAMGSVDILVNNAGITRDNLFMRMKDEEWASVLEVNLTSTM 116 Query: 123 FTVQAAARRMKEQGRGGAIIAVSSISALVGGAMQTHYTPTKAGLLSLMQSCAIALGPYGI 182 + R M + R G II +SSI G Q +Y KAG++ + +S A + GI Sbjct: 117 RLCRGVLRGMMK-ARWGRIINISSIVGATGNPGQGNYAAAKAGMVGMSKSLAYEVANRGI 175 Query: 183 RCNAVLPGTIATDINKEDLSDLEKRERMTSRVPLGRLGEPDDLAGPIVFLASDMARYVTG 242 NAV PG IAT + + L+D +K + + +++P GR+G P+++A +++LAS A YVTG Sbjct: 176 TVNAVAPGFIATAMT-DKLNDAQK-DAILTQIPSGRMGNPEEIASAVLYLASAEAGYVTG 233 Query: 243 ASLLVDGGL 251 +L V+GG+ Sbjct: 234 TTLHVNGGM 242 Lambda K H 0.319 0.136 0.383 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: 152 Number of extensions: 4 Number of successful extensions: 3 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: 256 Length of database: 245 Length adjustment: 24 Effective length of query: 232 Effective length of database: 221 Effective search space: 51272 Effective search space used: 51272 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 Apr 09 2024. 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