Align NAD(P)-dependent dehydrogenase (Short-subunit alcohol dehydrogenase family) (characterized, see rationale)
to candidate Pf6N2E2_3703 Oxidoreductase, short chain dehydrogenase/reductase family
Query= uniprot:A0A4R8NY47 (263 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3703 Length = 249 Score = 111 bits (277), Expect = 2e-29 Identities = 84/237 (35%), Positives = 123/237 (51%), Gaps = 12/237 (5%) Query: 15 RSLAGKRVVITGGGSGIGAALVEAFVGQGAQVCFLDIATEPSEALVASLKDA-AVAPRFF 73 + L +R VITG GSGIGAA+ A+ QGA+ L +A +E L A+ D A+A Sbjct: 2 QQLFNRRAVITGAGSGIGAAIARAYAEQGAR---LVLADRDAERLTATANDCRALAVEVH 58 Query: 74 PC--NLMNLEALRATFTEIETVMGGVDILINNAANDDRHKSEDVTPAYWDERLAVNLRHQ 131 C ++ LE +A GG+DIL+NNA + + +++ W++ L V+L Sbjct: 59 ECVADVGTLEGAQAGVDACVEHFGGIDILVNNAGMLTQARCTELSIEMWNDMLRVDLTSV 118 Query: 132 FFCAQAVLPGMRERKGGVILNFGSISWHLGLPDLTLYMTAKAGIEGMTHGMARDFGRDGV 191 F +Q LP M ++ G I+N S G +L+ Y AKAG+ G T +A + D V Sbjct: 119 FIASQRALPHMLAQRWGRIINIASQLGIKGGAELSHYAAAKAGVIGFTKSLALEVAADNV 178 Query: 192 RVNAIIPGAIRTPRQTLLWHTPEEEAKILAAQCLPVRVD--PHDVAALALFLSSDSG 246 VNAI PG I TP L+ E + +A+ LP+R +VA A+ L+SD G Sbjct: 179 LVNAIAPGPIETP---LVAGISESWKQAKSAE-LPLRRFGLATEVAPTAVLLASDPG 231 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: 185 Number of extensions: 6 Number of successful extensions: 1 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: 249 Length adjustment: 24 Effective length of query: 239 Effective length of database: 225 Effective search space: 53775 Effective search space used: 53775 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