Align glyoxylate reductase (EC 1.1.1.26); 4-hydroxybutyrate dehydrogenase (EC 1.1.1.61); glyoxylate reductase (NADP+) (EC 1.1.1.79) (characterized)
to candidate WP_279338484.1 HTA01S_RS01495 NAD(P)-dependent oxidoreductase
Query= BRENDA::Q9LSV0 (289 letters) >NCBI__GCF_001592305.1:WP_279338484.1 Length = 301 Score = 132 bits (333), Expect = 7e-36 Identities = 85/278 (30%), Positives = 135/278 (48%), Gaps = 2/278 (0%) Query: 3 VGFLGLGIMGKAMSMNLLKNGFKVTVWNRTLSKCDELVEHGASVCESPAEVIKKCKYTIA 62 + LG+G+MG ++ L G++V+ WNR+ K + L GA VC++PA+ + + I Sbjct: 15 IAVLGIGMMGWPIARRLCVAGYQVSAWNRSPDKAERLRPFGAQVCDTPAQAVAQADLVIT 74 Query: 63 MLSDPCAALSVVFDKGGVLEQICEGKGYIDMSTVDAETSLKINEAITGKGGRFVEGPVSG 122 +L D V+F + G E + G +DMS++ + + G ++ PVSG Sbjct: 75 LLEDGKVVEDVLF-RQGTTEGLRPGALVVDMSSIQPRQARDHAARLAAIGVHHLDAPVSG 133 Query: 123 SKKPAEDGQLIILAAGDKALFEESIPAFDVLGKRSFYLGQVGNGAKMKLIVNMIMGSMMN 182 AE L I+A G A FE + P F+ LG R ++G G+G KL MI+G + Sbjct: 134 GTVGAEQATLAIMAGGKPADFERARPVFEHLG-RPTHVGPHGSGQLAKLANQMIVGITIG 192 Query: 183 AFSEGLVLADKSGLSSDTLLDILDLGAMTNPMFKGKGPSMNKSSYPPAFPLKHQQKDMRL 242 A +E L+L +K G + + G + + + G M + + + Q KDMR Sbjct: 193 AVAEALLLCEKGGADMAKVRQAITGGFADSRILQVHGQRMVERDFAKRGAISVQLKDMRN 252 Query: 243 ALALGDENAVSMPVAAAANEAFKKARSLGLGDLDFSAV 280 A+A E P+ A + F +A GL DLD SA+ Sbjct: 253 AMATAREIGFEAPITALFEQLFAQAADHGLADLDHSAL 290 Lambda K H 0.317 0.134 0.379 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: 176 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: 289 Length of database: 301 Length adjustment: 26 Effective length of query: 263 Effective length of database: 275 Effective search space: 72325 Effective search space used: 72325 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 (21.6 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Apr 09 2024. 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