Align Probable galactose dehydrogenase GalD; EC 1.1.1.- (characterized)
to candidate AO356_25515 AO356_25515 3-ketoacyl-ACP reductase
Query= SwissProt::Q92RN6 (256 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_25515 Length = 255 Score = 130 bits (327), Expect = 3e-35 Identities = 86/248 (34%), Positives = 131/248 (52%), Gaps = 7/248 (2%) Query: 10 DLRDRGVLVTGGGSGIGAALVEAFARQGARVAFVDIAAESSLALCEKVAAQTGQAPHFIQ 69 D + VLVTGG GIG A+VEAFA +GARV D+ + A+ +++ A G + Sbjct: 6 DFSGQTVLVTGGAQGIGRAIVEAFALRGARVVIADLGLARAEAVADELTA-VGCQVQAVG 64 Query: 70 ADLRNVEAVRAAADEAVAKLGSVRVLVNNAARDDRQALEAVTEESWDESLSVNLRHLFFM 129 DL + A+ +LG + LV+NA +T + +L+VNL LF++ Sbjct: 65 VDLADATAIFEMMSALEQRLGRLDTLVHNAGYFPLTPFAEITPAMLERTLAVNLSALFWL 124 Query: 130 CQAVAPHMQRQGGGSIVNFSSIAF-LLNMPEIPAYSTAKAGIIGLTKSLAGKLGPDNIRV 188 QA P +RQG G ++ SS+ + P + Y+ +KAG+ G ++ A +L +N+RV Sbjct: 125 TQAALPMFRRQGRGCVLVTSSVTGPRVAYPGLSHYAASKAGVNGFIRNAALELAAENVRV 184 Query: 189 NAILPGMIVTERQRRLWLTE--ESIARMQERQCLKRMLVADDLVGPCLFLASDSSAAMTA 246 N + PGMI T L E + IAR R L R+ D+ G LFLAS ++ +T Sbjct: 185 NGVEPGMIATPAMANLGDDEVNQDIAR---RVPLGRLGQPSDIAGAMLFLASSLASYVTG 241 Query: 247 QAMIIDGG 254 Q +++DGG Sbjct: 242 QTLVVDGG 249 Lambda K H 0.321 0.133 0.377 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: 119 Number of extensions: 5 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: 256 Length of database: 255 Length adjustment: 24 Effective length of query: 232 Effective length of database: 231 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 (21.9 bits) S2: 47 (22.7 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