Align NAD(P)-dependent dehydrogenase (Short-subunit alcohol dehydrogenase family) (characterized, see rationale)
to candidate Dsui_3259 Dsui_3259 dehydrogenase of unknown specificity, short-chain alcohol dehydrogenase like protein
Query= uniprot:A0A4R8NY47 (263 letters) >FitnessBrowser__PS:Dsui_3259 Length = 256 Score = 77.0 bits (188), Expect = 4e-19 Identities = 73/246 (29%), Positives = 109/246 (44%), Gaps = 15/246 (6%) Query: 20 KRVVITGGGSGIGAALVEAFVGQGAQVCFL---DIATEP---SEALVASLKDAAV--APR 71 K ++ITGG GIGAA V G VCF D A +E S +D+ AP Sbjct: 3 KTLLITGGSRGIGAATVRLAARAGYAVCFSYRQDAAAAQQLVAEVTRESSRDSGREGAPI 62 Query: 72 F-FPCNLMNLEALRATFTEIETVMGGVDILINNAANDD-RHKSEDVTPAYWDERLAVNLR 129 F ++ E +RA F E G + L+NNA + + + ED+ A N+ Sbjct: 63 LAFQADISREEEIRALFAAAEQRFGPITALVNNAGILELQTRVEDMDGDRLQRIFATNVI 122 Query: 130 HQFFCAQAVLPGMRERKGG---VILNFGSISWHLGLP-DLTLYMTAKAGIEGMTHGMARD 185 F C + + + R GG I+N S + LG + Y +KA I+ +T G+AR+ Sbjct: 123 GTFLCCREAVRRLSTRHGGHGGAIVNLSSRAARLGAAGEYVDYAASKAAIDTLTLGLARE 182 Query: 186 FGRDGVRVNAIIPGAIRTPRQTLLWHTPEEEAKILAAQCLPVRVDPHDVAALALFLSSDS 245 +G+RVNA+ PG I T P ++ + P +VA L+L S+ Sbjct: 183 VAAEGIRVNAVAPGLIDTDIHA-SGGEPGRVERLRTGIPMQRGGTPEEVAKAILWLLSED 241 Query: 246 GAKCTG 251 + TG Sbjct: 242 ASYTTG 247 Lambda K H 0.322 0.137 0.417 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: 188 Number of extensions: 12 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: 263 Length of database: 256 Length adjustment: 24 Effective length of query: 239 Effective length of database: 232 Effective search space: 55448 Effective search space used: 55448 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