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 H281DRAFT_05314 H281DRAFT_05314 2-hydroxy-3-oxopropionate reductase
Query= BRENDA::Q9LSV0 (289 letters) >FitnessBrowser__Burk376:H281DRAFT_05314 Length = 297 Score = 150 bits (380), Expect = 3e-41 Identities = 88/284 (30%), Positives = 146/284 (51%), Gaps = 1/284 (0%) Query: 2 EVGFLGLGIMGKAMSMNLLKNGFKVTVWNRTLSKCDELVEHGASVCESPAEVIKKCKYTI 61 + GF+GLGIMGK M+ NLLKNG + + R+ D+L + GA C+SPA V + Sbjct: 3 KAGFIGLGIMGKPMAANLLKNGVTLAAFTRSAVP-DDLTQAGAQACDSPAAVAAQADVIF 61 Query: 62 AMLSDPCAALSVVFDKGGVLEQICEGKGYIDMSTVDAETSLKINEAITGKGGRFVEGPVS 121 M+ D V+F + G+ + G+ +DMS++ + + G +++ PVS Sbjct: 62 IMVPDTPDVERVLFGENGLASGLRAGQTVVDMSSISPMATRDFAARVRETGADYLDAPVS 121 Query: 122 GSKKPAEDGQLIILAAGDKALFEESIPAFDVLGKRSFYLGQVGNGAKMKLIVNMIMGSMM 181 G + A+ G L I+ G++A F+ P FD++GK +G VG G K+ +I+ + + Sbjct: 122 GGEVGAKAGSLTIMVGGEQATFDSVKPLFDMMGKNVTLIGAVGAGQVCKVANQVIVAATI 181 Query: 182 NAFSEGLVLADKSGLSSDTLLDILDLGAMTNPMFKGKGPSMNKSSYPPAFPLKHQQKDMR 241 A E L+LA K+G+ + + L G ++ + + G M K ++ P F ++ QKD+ Sbjct: 182 EAVGEALLLASKAGVDPARVREALMGGFASSRILEVHGERMTKRTFDPGFRIELHQKDLN 241 Query: 242 LALALGDENAVSMPVAAAANEAFKKARSLGLGDLDFSAVIEAVK 285 LAL VS+P A F + G D SA++ A++ Sbjct: 242 LALQTAQTLGVSLPNTATCQALFNACVAHGGKAWDHSAMVRALE 285 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: 211 Number of extensions: 6 Number of successful extensions: 2 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: 297 Length adjustment: 26 Effective length of query: 263 Effective length of database: 271 Effective search space: 71273 Effective search space used: 71273 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 Sep 17 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