Align NAD(P)-dependent dehydrogenase (Short-subunit alcohol dehydrogenase family) (characterized, see rationale)
to candidate SMc00268 SMc00268 oxidoreductase
Query= uniprot:A0A4R8NY47 (263 letters) >FitnessBrowser__Smeli:SMc00268 Length = 252 Score = 134 bits (337), Expect = 2e-36 Identities = 97/249 (38%), Positives = 125/249 (50%), Gaps = 8/249 (3%) Query: 17 LAGKRVVITGGGS--GIGAALVEAFVGQGAQVCFLDIATEPSEALVASLKDAAVAPRFFP 74 L G VITG S G+G A F GA V LD+ + ASL V Sbjct: 6 LEGNFAVITGAASRRGLGKATARLFAEHGATVAILDLDEADAREAAASLGPRHVG---MA 62 Query: 75 CNLMNLEALRATFTEIETVMGGVDILINNAANDDRHKSEDVTPAYWDERLAVNLRHQFFC 134 CN+ +L ++R + + G +DIL+NNA K ++ P +D L VNLR +C Sbjct: 63 CNVTDLASVRTVMDALVSQWGRIDILVNNAGITQPLKIMEIAPENYDAVLDVNLRGTLYC 122 Query: 135 AQAVLPGMRERKGGVILNFGSISWHL--GLPDLTLYMTAKAGIEGMTHGMARDFGRDGVR 192 +QAV+P MR RK G I+N S+S G+ Y AKAG+ G+T MAR+ D VR Sbjct: 123 SQAVIPHMRSRKQGKIVNLSSVSAQRGGGIFGGPHYSAAKAGVLGLTKAMARELAPDNVR 182 Query: 193 VNAIIPGAIRTPRQTLLWHTPEEEAKILAAQCLPVRVDPHDVAALALFLSSDSGAKCTGR 252 VNAI PG I T L TPE+ +I A + DVA ALFL+SD A TG Sbjct: 183 VNAICPGFIATDITGGLL-TPEKLEEIKAGIPMGRPGTADDVAGCALFLASDLSAYVTGS 241 Query: 253 EYYVDAGWL 261 E V+ G L Sbjct: 242 EVDVNGGSL 250 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: 180 Number of extensions: 11 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: 263 Length of database: 252 Length adjustment: 24 Effective length of query: 239 Effective length of database: 228 Effective search space: 54492 Effective search space used: 54492 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