Align Probable galactose dehydrogenase GalD; EC 1.1.1.- (characterized)
to candidate WP_057508628.1 ABB28_RS10765 NAD(P)-dependent oxidoreductase
Query= SwissProt::Q92RN6 (256 letters) >NCBI__GCF_001431535.1:WP_057508628.1 Length = 252 Score = 117 bits (294), Expect = 2e-31 Identities = 83/246 (33%), Positives = 128/246 (52%), Gaps = 5/246 (2%) Query: 11 LRDRGVLVTGGGSGIGAALVEAFARQGARVAFVDIAAESSLALCEKVAAQTGQAPHFIQA 70 L+ + +VTGG SGIG A+ E A GA ++ D+ E+ A E + + G I Sbjct: 6 LKGKTAIVTGGVSGIGLAVAEMLAASGAAISVWDLKQEAVDATTEALRGK-GVKAIGIAL 64 Query: 71 DLRNVEAVRAAADEAVAKLGSVRVLVNNAARDDRQALEA-VTEESWDESLSVNLRHLFFM 129 D+ + AV AA VA+LGSV + VNNA A+ + W + + VNL +F Sbjct: 65 DVTDEAAVEAAVARTVAELGSVDIAVNNAGIAGPAAISGDYPVDGWRKVIDVNLTSVFLC 124 Query: 130 CQAVAPHMQRQG-GGSIVNFSSIAFLLNMPEIPAYSTAKAGIIGLTKSLAGKLGPDNIRV 188 +A M+ G GGSI+N +SI + AY+ AK G++GLT++ A + D IR+ Sbjct: 125 QRAQIQAMRDAGNGGSIINMASILGQVGYAGSVAYAAAKHGVVGLTQTAAWEHASDQIRI 184 Query: 189 NAILPGMIVTERQRRLWLTEESIARMQERQCLKRMLVADDLVGPCLFLASDSSAAMTAQA 248 NA+ PG I T + + + A ++ R LKR+ +++ +LASD+++ T Sbjct: 185 NAVGPGFISTPLLEQ--MDPKVRATLESRHALKRLGTPEEVAALVAWLASDAASFATGTY 242 Query: 249 MIIDGG 254 IDGG Sbjct: 243 YAIDGG 248 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: 126 Number of extensions: 6 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: 252 Length adjustment: 24 Effective length of query: 232 Effective length of database: 228 Effective search space: 52896 Effective search space used: 52896 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