Align NAD(P)-dependent dehydrogenase (Short-subunit alcohol dehydrogenase family) (characterized, see rationale)
to candidate 5210421 Shew_2862 short chain dehydrogenase (RefSeq)
Query= uniprot:A0A4R8NY47 (263 letters) >FitnessBrowser__PV4:5210421 Length = 255 Score = 110 bits (276), Expect = 2e-29 Identities = 74/244 (30%), Positives = 121/244 (49%), Gaps = 1/244 (0%) Query: 17 LAGKRVVITGGGSGIGAALVEAFVGQGAQVCFLDIATEPSEALVASLKDAAVAPRFFPCN 76 L+G+ ++TG GIGAA+ E GA V E + + + D + C+ Sbjct: 9 LSGRIALVTGASRGIGAAIAELLAAYGAHVIVASRKAEGCQTVAEQIIDNGGSAEAMACH 68 Query: 77 LMNLEALRATFTEIETVMGGVDILINNAA-NDDRHKSEDVTPAYWDERLAVNLRHQFFCA 135 + +LEA++ATF +I+ G +DIL+NNAA N D +++ + VNLR FF + Sbjct: 69 VGDLEAIQATFEQIQAKHGRLDILVNNAATNPYFGHILDTDLNAFNKTMEVNLRGYFFMS 128 Query: 136 QAVLPGMRERKGGVILNFGSISWHLGLPDLTLYMTAKAGIEGMTHGMARDFGRDGVRVNA 195 MRE+ GVILN S++ +Y +KA + MT A++ G+R NA Sbjct: 129 VTAGRMMREQGHGVILNTASVNALQPGEMQGIYSISKAAVVSMTKAFAKECAPLGIRCNA 188 Query: 196 IIPGAIRTPRQTLLWHTPEEEAKILAAQCLPVRVDPHDVAALALFLSSDSGAKCTGREYY 255 ++PG +T L++ + +++A + P ++A L+L SD+ + TG Sbjct: 189 LLPGFTKTQFAGALFNNDKIYQQLIARIPMGRHAVPSEMAGAVLYLVSDASSYTTGETLV 248 Query: 256 VDAG 259 VD G Sbjct: 249 VDGG 252 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: 154 Number of extensions: 8 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: 255 Length adjustment: 24 Effective length of query: 239 Effective length of database: 231 Effective search space: 55209 Effective search space used: 55209 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