Align 2-hydroxy-3-oxopropionate reductase (EC 1.1.1.60) (characterized)
to candidate 5209194 Shew_1672 3-hydroxyisobutyrate dehydrogenase (RefSeq)
Query= BRENDA::Q8ZLV8 (296 letters) >FitnessBrowser__PV4:5209194 Length = 299 Score = 168 bits (425), Expect = 2e-46 Identities = 98/294 (33%), Positives = 162/294 (55%), Gaps = 10/294 (3%) Query: 5 VGFIGLGIMGKPMSKNLLKAGYSLVVSDRNPEAIADVIAAGAETASTAKAIAEQCDVIIT 64 V FIGLG MG PM+ NL+KAGY++ D + A++ V+ GA A +A A A DV+IT Sbjct: 4 VAFIGLGNMGGPMAVNLVKAGYTVKAFDLSQTALSHVVEEGAMQAPSACAAAAAADVVIT 63 Query: 65 MLPNSPHVKEVALGEN---GIIEGAKPGTVLIDMSSIAPLASREISDALKAKGVEMLDAP 121 MLP HV+ + LG+ GII+ GT+LID S+I ++R +++ K KG+E +DAP Sbjct: 64 MLPAGKHVRSLYLGDEQNKGIIDVVADGTLLIDCSTIDAESARFVAEQAKTKGLEFIDAP 123 Query: 122 VSGGEPKAIDGTLSVMVGGDKAIFDKYYDLMKAMAGSVVHTGDIGAGNVTKLANQVIVAL 181 VSGG A GTL+ + GG F++ ++ M ++ H G GAG V K+ N +++++ Sbjct: 124 VSGGTAGAAAGTLTFICGGSDTAFEQAQGVLNVMGANIFHAGGPGAGQVAKICNNMLLSV 183 Query: 182 NIAAMSEALTLATKAGVNPDLVYQAIRGGLAGSTVLDA--KAPMVMD-----RNFKPGFR 234 + SE++ + G++P ++ + ++ G+ LD P VM+ ++ GF Sbjct: 184 LMVGTSESIQMGIDHGLDPKVLSEIMKVSSGGNWTLDKYNPCPDVMENVPSSNGYQGGFM 243 Query: 235 IDLHIKDLANALDTSHGVGAQLPLTAAVMEMMQALRADGHGNDDHSALACYYEK 288 +DL +KDL + + + + P+ A + G+G D S++ + K Sbjct: 244 VDLMVKDLGLSQEAALLSNSSTPMGALARSLYVNHARQGNGKRDFSSIFEQFNK 297 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: 219 Number of extensions: 10 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: 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