Align Probable galactose dehydrogenase GalD; EC 1.1.1.- (characterized)
to candidate WP_077274914.1 BW732_RS00300 D-threitol dehydrogenase
Query= SwissProt::Q92RN6 (256 letters) >NCBI__GCF_001998885.1:WP_077274914.1 Length = 254 Score = 127 bits (318), Expect = 3e-34 Identities = 77/244 (31%), Positives = 132/244 (54%), Gaps = 5/244 (2%) Query: 11 LRDRGVLVTGGGSGIGAALVEAFARQGARVAFVDIAAESSLALCEKVAAQTGQAPHFIQA 70 L ++ ++TGG SGIG+A+ E + ++GA++A DI ++ E V Q G Sbjct: 12 LENKVAIITGGLSGIGSAIGELYVKKGAKLAIFDINPDTP----ELVEEQFGTKAIGFAV 67 Query: 71 DLRNVEAVRAAADEAVAKLGSVRVLVNNAARDDRQALEAVTEESWDESLSVNLRHLFFMC 130 D+ + E V A E + + +LVN+A E ++E WD + ++N++ F + Sbjct: 68 DVTSKEQVMNAVKETMNHFKKIDILVNSAGVCFLDDAENLSETEWDLTFNINVKGSFLVA 127 Query: 131 QAVAPHMQRQGGGSIVNFSSIAFLLNMPEIPAYSTAKAGIIGLTKSLAGKLGPDNIRVNA 190 QAV M + GGG I+N +S A L+ + AY+ +K I+ +TK LA + +I VN Sbjct: 128 QAVGNEMIQSGGGKIINMASQAALVALDNHVAYAASKGAILSMTKVLAYEWAQYSINVNC 187 Query: 191 ILPGMIVTERQRRLWLTEESIARMQERQCLKRMLVADDLVGPCLFLASDSSAAMTAQAMI 250 + P +++TE ++ W + M+++ + R +++ LFLASD+S MT + M+ Sbjct: 188 LSPTIVLTELGKKAWAGQVG-EDMKQQIPIGRFGYPEEVAASALFLASDASNLMTGENMV 246 Query: 251 IDGG 254 IDGG Sbjct: 247 IDGG 250 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: 7 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: 254 Length adjustment: 24 Effective length of query: 232 Effective length of database: 230 Effective search space: 53360 Effective search space used: 53360 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 Sep 24 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