Align 2-hydroxy-3-oxopropionate reductase (EC 1.1.1.60) (characterized)
to candidate GFF2390 Psest_2438 3-hydroxyisobutyrate dehydrogenase
Query= BRENDA::Q8ZLV8 (296 letters) >FitnessBrowser__psRCH2:GFF2390 Length = 296 Score = 190 bits (483), Expect = 3e-53 Identities = 116/294 (39%), Positives = 166/294 (56%), Gaps = 8/294 (2%) Query: 3 MKVGFIGLGIMGKPMSKNLLKAGYSLVVSDRNPEAIADVIAAGAETASTAKAIAE-QCDV 61 M +GFIGLG MG PM+ NLLKAG+ L V D N A+ +++ AGA + AIA+ ++ Sbjct: 1 MHIGFIGLGNMGAPMAHNLLKAGHQLSVFDLNAAAVENLVGAGALPVDSPTAIAQGNAEL 60 Query: 62 IITMLPNSPHVKEVALGENGIIEGAKPGTVLIDMSSIAPLASREISDALKAKGVEMLDAP 121 IITMLP + HVK V LG NG+I ++ G +LID S+I P ++RE++ A G MLDAP Sbjct: 61 IITMLPAAAHVKGVYLGVNGLIAHSRAGVMLIDCSTIDPHSAREVAKAAAEHGNPMLDAP 120 Query: 122 VSGGEPKAIDGTLSVMVGGDKAIFDKYYDLMKAMAGSVVHTGDIGAGNVTKLANQVIVAL 181 VSGG A GTL+ MVGG FD ++ AM ++VH G G G V K+AN +++ + Sbjct: 121 VSGGTGGAAAGTLTFMVGGSDPDFDHAQPILAAMGKNIVHCGAAGNGQVAKVANNMLLGI 180 Query: 182 NIAAMSEALTLATKAGVNPDLVYQAIR--GGLAGSTVLDAKAPMVMD-----RNFKPGFR 234 ++ ++EA+ L G++ + I G S+ P V+D R + GF Sbjct: 181 SMIGVAEAMALGVALGMDAKTLAGVINTSSGRCWSSDTYNPFPGVLDNVPSSRGYSGGFG 240 Query: 235 IDLHIKDLANALDTSHGVGAQLPLTAAVMEMMQALRADGHGNDDHSALACYYEK 288 DL +KDL A + + V + L A ++ Q+ A GHG D SA+ Y K Sbjct: 241 SDLMLKDLGLATEAAKQVRQPVILGALAQQLYQSFSAQGHGGLDFSAIINQYRK 294 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: 247 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: 296 Length of database: 296 Length adjustment: 26 Effective length of query: 270 Effective length of database: 270 Effective search space: 72900 Effective search space used: 72900 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