Align NADH-dependent aldehyde reductase (EC 1.1.1.77; EC 1.1.1.244; EC 1.1.1.1) (characterized)
to candidate WP_076481840.1 BW971_RS16580 SDR family oxidoreductase
Query= metacyc::G3O-32155-MONOMER (298 letters) >NCBI__GCF_900156495.1:WP_076481840.1 Length = 301 Score = 214 bits (546), Expect = 1e-60 Identities = 127/300 (42%), Positives = 172/300 (57%), Gaps = 15/300 (5%) Query: 1 MKVFITGASGFIGSAVLSELISSGHEVVGLARSDEAAAKIKSIDPAAKILRGDLKDLEIL 60 M+VF+TGA+G+IG+A + ELIS+GH+VVGLARSD +A ++++ AA L GDL DLE L Sbjct: 1 MRVFVTGATGWIGTATVHELISAGHDVVGLARSDSSADRLRTAGAAA--LPGDLDDLESL 58 Query: 61 KKGATESDGVIHLGFVHDFKNFEQCCEIDRQATVAMLESLKGSNKPFLYTNGTLSLRPNK 120 ++GA +D +IHL HD+ + +R A +MLE + G++K FL NG L + Sbjct: 59 RRGAVGADAIIHLANKHDWADPGGTDRAERAAVESMLEVVSGTDKAFLVANGLSGLVVGR 118 Query: 121 VANEQD-------GIDEDSKILRAVTEQVALSYKDKGVSARIVRLPFSVHGKGDKAFVPI 173 A E D G D R +E + L GV +R SVHG GD FV Sbjct: 119 AAVESDPSPAIGPGAD------RGGSENLVLDAAHDGVRGMAIRFAPSVHGHGDWGFVRF 172 Query: 174 LMNIAKAAGKSGYVGQGTNAWAAVHRLDTAPLFRLVLEKGKTGQVYHCVGEQGIPFKDIA 233 L +IA G SGY+ +GT W+AVHR D A L RL +E +G H V EQ I + IA Sbjct: 173 LADIAVERGVSGYIDEGTTLWSAVHRHDAARLIRLGIEIAPSGARLHAVAEQEISTRAIA 232 Query: 234 RVIGEILNVPVASIPVDDAESHFGFLTCFVTRDGPVSSEGTRKELGWQPQQIGLLEDIRA 293 +G L+VP+ SI DDA+ HFGF+ F +S TR GW+P Q L++DIR+ Sbjct: 233 EALGSALDVPIVSIAGDDADQHFGFMAEFFGSSMTGTSATTRSLTGWEPTQPRLIDDIRS 292 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: 249 Number of extensions: 8 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: 301 Length adjustment: 27 Effective length of query: 271 Effective length of database: 274 Effective search space: 74254 Effective search space used: 74254 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