Align Probable galactose dehydrogenase GalD; EC 1.1.1.- (characterized)
to candidate WP_078715956.1 B5D49_RS01965 3-oxoacyl-[acyl-carrier-protein] reductase
Query= SwissProt::Q92RN6 (256 letters) >NCBI__GCF_900167125.1:WP_078715956.1 Length = 247 Score = 119 bits (299), Expect = 5e-32 Identities = 78/240 (32%), Positives = 114/240 (47%), Gaps = 2/240 (0%) Query: 17 LVTGGGSGIGAALVEAFARQGARVAFVDIAAESSLALCEKVAAQTGQAPHFIQADLRNVE 76 LVTGG GIG A E A G V ++ + + A G +Q D + E Sbjct: 9 LVTGGSRGIGRACAERLAADGFEVWLTYVSKPEAAETVVQTIADAGGTARAVQLDSSDRE 68 Query: 77 AVRAAADEAVAKLGSVRVLVNNAARDDRQALEAVTEESWDESLSVNLRHLFFMCQAVAPH 136 AV + + + + LVNNA L + E WD L +NL F Q A Sbjct: 69 AVASFFKDEIKGKVHLAALVNNAGITRDGLLIRMKPEDWDSVLDINLTGAFSCLQEAAKI 128 Query: 137 MQRQGGGSIVNFSSIAFLLNMPEIPAYSTAKAGIIGLTKSLAGKLGPDNIRVNAILPGMI 196 M RQ GGSI+N SS+ + Y AKAG+IGLTK+ A +L +RVNA+ PG I Sbjct: 129 MARQRGGSIINISSVVGQMGNAGQANYVAAKAGLIGLTKAAARELAGRGVRVNAVAPGFI 188 Query: 197 VTERQRRLWLTEESIARMQERQCLKRMLVADDLVGPCLFLASDSSAAMTAQAMIIDGGVF 256 T+ + L E+++ M+ L R+ D+ FLA + + +T Q + ++GG++ Sbjct: 189 ETDMTKD--LPEKTVESMKTMIPLSRLGSPGDIAAAVSFLAGNGAGYITGQVLAVNGGMY 246 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: 142 Number of extensions: 6 Number of successful extensions: 2 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: 247 Length adjustment: 24 Effective length of query: 232 Effective length of database: 223 Effective search space: 51736 Effective search space used: 51736 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: 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