Align 2-hydroxy-3-oxopropionate reductase; Tartronate semialdehyde reductase; TSAR; EC 1.1.1.60 (characterized)
to candidate WP_110803876.1 C8J30_RS01040 3-hydroxyisobutyrate dehydrogenase
Query= SwissProt::P0ABQ2 (294 letters) >NCBI__GCF_003217355.1:WP_110803876.1 Length = 290 Score = 147 bits (370), Expect = 4e-40 Identities = 104/298 (34%), Positives = 147/298 (49%), Gaps = 24/298 (8%) Query: 1 MKVGFIGLGIMGKPMSKNLLKAGYSLVVADRNPEAIADVIAAGAETASTAKAIAEQC--- 57 MKVGFIGLG MG PM+ NL KAG+ ++ D + A E + AK+IAE Sbjct: 1 MKVGFIGLGNMGAPMAANLAKAGHRVMGFD--------LAAPCPEGVAQAKSIAEAARGA 52 Query: 58 DVIITMLPNSPHVKEVALGENGIIEGAKPGTVLIDMSSIAPLASREISEALKAKGIDMLD 117 +V+ITMLPN ++ VA + + PG VL D S++ ++R+++ G+ LD Sbjct: 53 EVVITMLPNGAILRLVA---DEALRAMTPGAVLCDCSTVDVESARQVAAEAATAGMGALD 109 Query: 118 APVSGGEPKAIDGTLSVMVGGDKAIFDKYYDLMKAMAGSVVHTGEIGAGNVTKLANQVIV 177 APVSGG A GTL+ MVGG A F L M VH G GAG K+ N +I+ Sbjct: 110 APVSGGVGGATAGTLTFMVGGSDAAFATVKPLFDVMGQKAVHCGASGAGQAAKICNNMIL 169 Query: 178 ALNIAAMSEALTLATKAGVNPDLVYQAIRGGLAGSTVLDAKAP-------MVMDRNFKPG 230 + + A EA LA K G++ ++ + S ++A P D +KPG Sbjct: 170 GVTMIATCEAFALADKLGLDRAKMFDVVSTSSGYSWTMNAYCPAPGVGPKSPADNGYKPG 229 Query: 231 FRIDLHIKDLANALDTSHGVGAQLPL--TAAVMEMMQALRADGLGTADHSALACYYEK 286 F +L +KDL + + G A P+ AA + DG G D SA+ +EK Sbjct: 230 FAAELMLKDLRLSQQAAEGADADTPMGALAAALYARFVEEEDGKG-MDFSAMLPRFEK 286 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: 222 Number of extensions: 13 Number of successful extensions: 4 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: 290 Length adjustment: 26 Effective length of query: 268 Effective length of database: 264 Effective search space: 70752 Effective search space used: 70752 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 24 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