Align 2-hydroxy-3-oxopropionate reductase (EC 1.1.1.60) (characterized)
to candidate RR42_RS28555 RR42_RS28555 3-hydroxyisobutyrate dehydrogenase
Query= BRENDA::Q8ZLV8 (296 letters) >FitnessBrowser__Cup4G11:RR42_RS28555 Length = 299 Score = 189 bits (479), Expect = 9e-53 Identities = 105/292 (35%), Positives = 159/292 (54%), Gaps = 7/292 (2%) Query: 3 MKVGFIGLGIMGKPMSKNLLKAGYSLVVSDRNPEAIADVIAAGAETASTAKAIAEQCDVI 62 M + FIGLG MG PM++NLLKAG++L V D NP A++ + A GA A +A+ A + D + Sbjct: 1 MHIAFIGLGNMGAPMARNLLKAGHALTVFDLNPTALSALQADGAAVAPSARKAAAEADFV 60 Query: 63 ITMLPNSPHVKEVALGENGIIEGAKPGTVLIDMSSIAPLASREISDALKAKGVEMLDAPV 122 ITMLP + HV+ LG G++ G +PG L+D S+I P R ++ K +G + DAPV Sbjct: 61 ITMLPAATHVRATYLGPEGVLAGVRPGVPLVDSSTIDPATIRALAAEAKRQGNPIADAPV 120 Query: 123 SGGEPKAIDGTLSVMVGGDKAIFDKYYDLMKAMAGSVVHTGDIGAGNVTKLANQVIVALN 182 SGG A GTL+ MVG + +F++ ++ M ++VH GD G G V K+ N +I+ ++ Sbjct: 121 SGGTGGAQAGTLTFMVGAEPTLFEQLKPVLSCMGRNIVHCGDTGTGQVAKICNNLILGIS 180 Query: 183 IAAMSEALTLATKAGVNPDLVYQAIRGGLAGSTVLDAKAP-------MVMDRNFKPGFRI 235 + +SEA+ L K G++ ++ + D P R + GF Sbjct: 181 MIGVSEAMALGVKLGIDAGVLAGIVNTSTGRCWAADTCNPYPGVIETAPASRGYSGGFGA 240 Query: 236 DLHIKDLANALDTSHGVGAQLPLTAAVMEMMQALRADGHGNDDHSALACYYE 287 DL +KDL A D + V L L A ++ QA+ G G+ D S + Y+ Sbjct: 241 DLMLKDLGLATDAARSVRQPLFLGALAQQIYQAVSQAGDGHLDFSGVIRQYQ 292 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: 251 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: 296 Length of database: 299 Length adjustment: 26 Effective length of query: 270 Effective length of database: 273 Effective search space: 73710 Effective search space used: 73710 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