Align Probable galactose dehydrogenase GalD; EC 1.1.1.- (characterized)
to candidate GFF2316 PGA1_c23480 putative D-beta-hydroxybutyrate dehydrogenase
Query= SwissProt::Q92RN6 (256 letters) >FitnessBrowser__Phaeo:GFF2316 Length = 257 Score = 140 bits (354), Expect = 2e-38 Identities = 94/254 (37%), Positives = 132/254 (51%), Gaps = 15/254 (5%) Query: 10 DLRDRGVLVTGGGSGIGAALVEAFARQGARVAFVDIAAESSLALCEKVAAQTGQAPHFIQ 69 DL R V+VTGGGSG+GAAL +FA GAR+ + E ++VAA+TG P + Sbjct: 8 DLAGRHVVVTGGGSGVGAALARSFAGGGARLTLLGRRIEP----LQEVAAETGALP--LA 61 Query: 70 ADLRNVEAVRAAADEAVAKLGSVRVLVNNAARDDRQALEAVTEESWDESLSVNLRHLFFM 129 D+ EAVRAA D A + G V V + NA + + ++ +L+VNL +F + Sbjct: 62 CDVTEAEAVRAALDTARQQHGPVSVAIANAGAAPSKPFAKMDLADFEAALAVNLSGVFNL 121 Query: 130 CQAVAPHMQRQGGGSIVNFSSIAFLLNMPEIPAYSTAKAGIIGLTKSLAGKLGPDNIRVN 189 QA P M+ G G ++ +S A L P + Y AK G++GLT+SLA +L I VN Sbjct: 122 WQAALPDMKSAGWGRMIAVASTAGLKGYPYVSGYCAAKHGVVGLTRSLAQELARSGITVN 181 Query: 190 AILPGMIVTERQRRLWLTEESIARMQERQCLK---------RMLVADDLVGPCLFLASDS 240 AI PG I T R T S M E + K R + +++ LFLAS S Sbjct: 182 AICPGFIETPLLERSIATIVSTTGMSEEEAAKSLRAGNPQGRFIQPEEVADAALFLASSS 241 Query: 241 SAAMTAQAMIIDGG 254 +A++ A+ I GG Sbjct: 242 AASINGSALPITGG 255 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: 124 Number of extensions: 7 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: 257 Length adjustment: 24 Effective length of query: 232 Effective length of database: 233 Effective search space: 54056 Effective search space used: 54056 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 17 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