Align alcohol dehydrogenase (NADP+) (EC 1.1.1.2); alcohol dehydrogenase [NAD(P)+] (EC 1.1.1.71) (characterized)
to candidate WP_011384488.1 AMB_RS10540 KR domain-containing protein
Query= BRENDA::C6A190 (234 letters) >NCBI__GCF_000009985.1:WP_011384488.1 Length = 239 Score = 95.5 bits (236), Expect = 8e-25 Identities = 74/238 (31%), Positives = 121/238 (50%), Gaps = 19/238 (7%) Query: 2 KVAVITGASRGIGEAIARALARDGYALALGARSVDRLEKIAHELMQEQGVEVFYHHLDVS 61 +VA++TGASRGIG A+AR LA +G + AR+ LE++ ++ + G + D+ Sbjct: 8 RVALVTGASRGIGAAVARRLAAEGAEIVAIARTQGALEELDDQIRKAGGKPLVLVPEDLC 67 Query: 62 KAESVEEFSKKVLERFGDVDVVVANAGL--GYFKRLEELSEEEFHEMIEVNLLGVWRTLK 119 K +E+ + + +R+ +D++V NAG G + + + +++ E VN+ WR ++ Sbjct: 68 KPGLIEQVAAAIFQRWARLDILVGNAGAIGGGLTPVAQHAPDDWEEAFAVNVTANWRLIR 127 Query: 120 AFLDSLKR--TGGLALVTTSDVSARLIPYGGGYVSTKWAARALVRTFQIENPDVRFFE-- 175 A D L R G A+ TT+D + P+ G Y ++K A +VRT+ E +V + Sbjct: 128 A-CDPLLRMAPAGRAVFTTADAARHAEPFWGAYAASKAALETMVRTWAAEIANVTSVKAN 186 Query: 176 -LRPGAVDT-----YFGGSKPGKPKEKGYLKPDEIAEAVRCLLKLPKDVRVEELMLRS 227 L PG V T F G P K +PD++A A L LP R E++ S Sbjct: 187 LLDPGVVATRLRSIAFPGEDPAK-----LAQPDDVAGAFLDLC-LPDCTRQGEIIRTS 238 Lambda K H 0.319 0.137 0.391 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: 116 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: 234 Length of database: 239 Length adjustment: 23 Effective length of query: 211 Effective length of database: 216 Effective search space: 45576 Effective search space used: 45576 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 (21.7 bits) S2: 46 (22.3 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