Align 2-hydroxy-3-oxopropionate reductase (EC 1.1.1.60) (characterized)
to candidate WP_011937525.1 GURA_RS02990 NAD(P)-dependent oxidoreductase
Query= BRENDA::Q8ZLV8 (296 letters) >NCBI__GCF_000016745.1:WP_011937525.1 Length = 287 Score = 163 bits (413), Expect = 4e-45 Identities = 93/285 (32%), Positives = 149/285 (52%) Query: 4 KVGFIGLGIMGKPMSKNLLKAGYSLVVSDRNPEAIADVIAAGAETASTAKAIAEQCDVII 63 K GF+GLGIMG M+KNLLKAG+ + V +R+PE ++ A GA +A+T + + E C + Sbjct: 3 KFGFLGLGIMGSAMAKNLLKAGFDVTVWNRSPEKCEELAALGARSAATPRQVVESCGITF 62 Query: 64 TMLPNSPHVKEVALGENGIIEGAKPGTVLIDMSSIAPLASREISDALKAKGVEMLDAPVS 123 ML + + V G +G++EG G +DMS++ +++I A+ KG L+APVS Sbjct: 63 AMLSDPAADEAVCFGTDGVLEGIGAGKGYVDMSTVDATTAQKIGAAVTDKGGRFLEAPVS 122 Query: 124 GGEPKAIDGTLSVMVGGDKAIFDKYYDLMKAMAGSVVHTGDIGAGNVTKLANQVIVALNI 183 G A DGTL ++ GDK+++++ + M V+ G++G G KL +++ + Sbjct: 123 GSRKPAEDGTLIILTAGDKSLYNEAMPAFERMGKKVLFLGEVGKGAEMKLVVNMVMGGMM 182 Query: 184 AAMSEALTLATKAGVNPDLVYQAIRGGLAGSTVLDAKAPMVMDRNFKPGFRIDLHIKDLA 243 + E L L KAG+ + + G + + K ++ NF F + KDL Sbjct: 183 SIFCEGLALGAKAGLEVTDMLDVMDAGAVANPMFKLKGGLIAAGNFTTAFPLKHMQKDLR 242 Query: 244 NALDTSHGVGAQLPLTAAVMEMMQALRADGHGNDDHSALACYYEK 288 A+ +G L AA E + +A G G++D SAL EK Sbjct: 243 LAVGLGDWLGQPLFTAAAANEAFKRAKALGFGDEDFSALFKAIEK 287 Lambda K H 0.316 0.132 0.367 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: 227 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: 296 Length of database: 287 Length adjustment: 26 Effective length of query: 270 Effective length of database: 261 Effective search space: 70470 Effective search space used: 70470 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