Align NADH-dependent aldehyde reductase (EC 1.1.1.77; EC 1.1.1.244; EC 1.1.1.1) (characterized)
to candidate WP_076481215.1 BW971_RS14995 SDR family oxidoreductase
Query= metacyc::G3O-32155-MONOMER (298 letters) >NCBI__GCF_900156495.1:WP_076481215.1 Length = 302 Score = 235 bits (600), Expect = 8e-67 Identities = 135/294 (45%), Positives = 178/294 (60%), Gaps = 8/294 (2%) Query: 1 MKVFITGASGFIGSAVLSELISSGHEVVGLARSDEAAAKIKSIDPAAKILRGDLKDLEIL 60 M+VF+TGASG+IGSAV+ EL+ +GHEVVGLARSD +A I + A++ RG + D E L Sbjct: 1 MRVFVTGASGWIGSAVVPELVQAGHEVVGLARSDASATAIAAA--GARVHRGSIDDPEGL 58 Query: 61 KKGATESDGVIHLGFVHDFKNFEQCCEIDRQATVAMLESLKGSNKPFLYTNGTLSLRPNK 120 A +DGV+HL F HDF +F +R A+ ++L+ S KP L+ G L ++P + Sbjct: 59 AAAAAAADGVVHLAFNHDFSDFVGAGHTERAVITALGDALRDSGKPLLFAAGLL-VKPGQ 117 Query: 121 VANEQDGID---EDSKILRAVTEQVALSYKDKGVSARIVRLPFSVHGKGDKAFVPILMNI 177 V E D DS R E++ALSY + GV +R SVHG GD F+ L+ + Sbjct: 118 VVTENDPTPVSGPDSP--RGGGEELALSYAEHGVRPVSLRFAPSVHGDGDHGFIKTLVEV 175 Query: 178 AKAAGKSGYVGQGTNAWAAVHRLDTAPLFRLVLEKGKTGQVYHCVGEQGIPFKDIARVIG 237 A+ G SG+VG G N WAAVHR D A L RL LE+ G V H V E+ I +DIA IG Sbjct: 176 ARQRGVSGHVGDGGNRWAAVHRSDAARLVRLALERPPVGGVVHAVDEEAITARDIATAIG 235 Query: 238 EILNVPVASIPVDDAESHFGFLTCFVTRDGPVSSEGTRKELGWQPQQIGLLEDI 291 L+VPVASI DD HFG++ F + D P SS+ TR+ L W P GLL+D+ Sbjct: 236 RGLDVPVASIAPDDVTDHFGWIGGFFSLDLPASSDVTRETLNWTPAGPGLLDDL 289 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: 267 Number of extensions: 10 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: 298 Length of database: 302 Length adjustment: 27 Effective length of query: 271 Effective length of database: 275 Effective search space: 74525 Effective search space used: 74525 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