Align 2-hydroxy-3-oxopropionate reductase; Tartronate semialdehyde reductase; TSAR; EC 1.1.1.60 (characterized)
to candidate PP_4666 PP_4666 3-hydroxyisobutyrate dehydrogenase
Query= SwissProt::P0ABQ2 (294 letters) >FitnessBrowser__Putida:PP_4666 Length = 295 Score = 186 bits (471), Expect = 7e-52 Identities = 100/293 (34%), Positives = 161/293 (54%), Gaps = 7/293 (2%) Query: 1 MKVGFIGLGIMGKPMSKNLLKAGYSLVVADRNPEAIADVIAAGAETASTAKAIAEQCDVI 60 M++ FIGLG MG PM++NL+KAG+ L + D N +A++ G + + + K A +++ Sbjct: 1 MRIAFIGLGNMGAPMARNLIKAGHQLNLFDLNKAVLAELAELGGQISPSPKDAAANSELV 60 Query: 61 ITMLPNSPHVKEVALGENGIIEGAKPGTVLIDMSSIAPLASREISEALKAKGIDMLDAPV 120 ITMLP + HV+ V L E+G++ G +PGT +D S+I P +R++S+A AKG+DM DAPV Sbjct: 61 ITMLPAAAHVRSVYLNEDGVLAGIRPGTPTVDCSTIDPQTARDVSKAAAAKGVDMGDAPV 120 Query: 121 SGGEPKAIDGTLSVMVGGDKAIFDKYYDLMKAMAGSVVHTGEIGAGNVTKLANQVIVALN 180 SGG A GTL+ MVG +F +++ M ++VH GE+G G + K+ N +++ ++ Sbjct: 121 SGGTGGAAAGTLTFMVGASTELFASLKPVLEQMGRNIVHCGEVGTGQIAKICNNLLLGIS 180 Query: 181 IAAMSEALTLATKAGVNPDLVYQAIRGGLAGSTVLDAKAP-------MVMDRNFKPGFRI 233 + +SEA+ L G++ ++ I D P R + GF Sbjct: 181 MIGVSEAMALGNALGIDTKVLAGIINSSTGRCWSSDTYNPWPGIIETAPASRGYTGGFGA 240 Query: 234 DLHIKDLANALDTSHGVGAQLPLTAAVMEMMQALRADGLGTADHSALACYYEK 286 +L +KDL A + + + L A ++ QA+ G G D SA+ Y K Sbjct: 241 ELMLKDLGLATEAARQAHQPVILGAVAQQLYQAMSLRGEGGKDFSAIVEGYRK 293 Lambda K H 0.316 0.133 0.366 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: 230 Number of extensions: 8 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: 294 Length of database: 295 Length adjustment: 26 Effective length of query: 268 Effective length of database: 269 Effective search space: 72092 Effective search space used: 72092 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