Align NADH-dependent aldehyde reductase (EC 1.1.1.77; EC 1.1.1.244; EC 1.1.1.1) (characterized)
to candidate WP_076477985.1 BW971_RS07365 SDR family oxidoreductase
Query= metacyc::G3O-32155-MONOMER (298 letters) >NCBI__GCF_900156495.1:WP_076477985.1 Length = 293 Score = 189 bits (480), Expect = 7e-53 Identities = 114/295 (38%), Positives = 166/295 (56%), Gaps = 11/295 (3%) Query: 1 MKVFITGASGFIGSAVLSELISSGHEVVGLARSDEAAAKIKSIDPAAKILRGDLKDLEIL 60 M VF+TG +G IGSAV+ EL+++ H V+ LARSD +A + A+++RG + DL+ L Sbjct: 1 MHVFVTGGTGTIGSAVVDELLANDHTVLALARSDASADALARA--GAEVVRGTIADLDTL 58 Query: 61 KKGATESDGVIHLGFVHDFKNFE--QCCEIDRQATVAML-ESLKGSNKPFLYTNGTLSLR 117 A +DGVI L F D+ + ++ A +A L E+L GS +P + +GT + Sbjct: 59 STSAGRADGVISLAFTPDYDTPDGLAAAVVEEGAALASLGEALLGSGRPIVTVSGTPWI- 117 Query: 118 PNKVANEQDGIDEDSKIL-RAVTEQVALSYKDKGVSARIVRLPFSVHGKGDKAFVPILMN 176 P +++ E+D + E+ + RAV+ L +GV A VR+P +VH +G F +L Sbjct: 118 PGRLSTERDPLPEEGPVGGRAVSVNRLLELSSRGVRAVAVRMPRTVHNRGTGGFAGLLTE 177 Query: 177 IAKAAGKSGYVGQGTNAWAAVHRLDTAPLFRLVLEKGKTGQVYHCVGEQGIPFKDIARVI 236 A+ G +GY G G W AVH LD A LFRL LE G +H V ++G +DIA VI Sbjct: 178 QARRTGVAGYPGDGAQRWPAVHALDAAVLFRLALESAPAGTAWHAVADEGDAVRDIASVI 237 Query: 237 GEILNVPVASIPVDDAESHFGFLTCFVTRDGPVSSEGTRKELGWQPQQIGLLEDI 291 G L++PV S+ +E G D P SS TR+ LGW+P +GLLED+ Sbjct: 238 GRRLDLPVESV----SEQSLGPFGPVFALDQPASSAHTRETLGWEPVHLGLLEDL 288 Lambda K H 0.318 0.136 0.393 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: 229 Number of extensions: 7 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: 298 Length of database: 293 Length adjustment: 26 Effective length of query: 272 Effective length of database: 267 Effective search space: 72624 Effective search space used: 72624 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Sep 24 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