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_011939652.1 GURA_RS14275 NAD(P)-dependent oxidoreductase
Query= BRENDA::Q9LSV0 (289 letters) >NCBI__GCF_000016745.1:WP_011939652.1 Length = 288 Score = 170 bits (431), Expect = 3e-47 Identities = 89/284 (31%), Positives = 160/284 (56%) Query: 2 EVGFLGLGIMGKAMSMNLLKNGFKVTVWNRTLSKCDELVEHGASVCESPAEVIKKCKYTI 61 ++GF+GLG +G+ M+ NL K+ + +TV++ ++LV+ GA +P+E K I Sbjct: 4 KIGFIGLGTVGRHMAANLTKSDYDLTVYDDDAEPLNDLVKLGAKAAATPSEAAKGKDMVI 63 Query: 62 AMLSDPCAALSVVFDKGGVLEQICEGKGYIDMSTVDAETSLKINEAITGKGGRFVEGPVS 121 +L + + VF K GVLE + G +DM T ET+LK+ + + F+E PV Sbjct: 64 VILPESHGLETFVFGKDGVLEGLDPGTILVDMGTHSLETTLKLADEAIKRRVMFLEAPVW 123 Query: 122 GSKKPAEDGQLIILAAGDKALFEESIPAFDVLGKRSFYLGQVGNGAKMKLIVNMIMGSMM 181 G+K+ A +G + ILA GD +L AF G ++G++G+ KMK IVN++ +M Sbjct: 124 GTKEHAANGLVTILAGGDPSLLGRCREAFSYFGLNIIHIGKIGDATKMKFIVNLVQAELM 183 Query: 182 NAFSEGLVLADKSGLSSDTLLDILDLGAMTNPMFKGKGPSMNKSSYPPAFPLKHQQKDMR 241 + +EG+V +K G ++D +L++LD G + +P+F KG S+ + + LK+ + + Sbjct: 184 QSLAEGIVFGEKLGFNADKILEVLDSGGVASPLFHSKGRSIARGDFSRNLALKYVHEQLL 243 Query: 242 LALALGDENAVSMPVAAAANEAFKKARSLGLGDLDFSAVIEAVK 285 L + + + +P A + +++A G G+ D+SAV++ ++ Sbjct: 244 LVMDAAKKVNLDLPGVEVACKLYEQAVKDGRGEEDYSAVVKVLR 287 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: 179 Number of extensions: 9 Number of successful extensions: 1 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: 288 Length adjustment: 26 Effective length of query: 263 Effective length of database: 262 Effective search space: 68906 Effective search space used: 68906 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