Align Probable 3-hydroxyisobutyrate dehydrogenase; HIBADH; EC 1.1.1.31 (uncharacterized)
to candidate Ac3H11_1664 2-hydroxy-3-oxopropionate reductase (EC 1.1.1.60)
Query= curated2:P63936 (294 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1664 Length = 294 Score = 153 bits (387), Expect = 4e-42 Identities = 111/294 (37%), Positives = 150/294 (51%), Gaps = 17/294 (5%) Query: 4 IAFLGLGNMGAPMSANLVGAGHVVRGFDPAPTAASGAAAHGVAVFRSAPEAVAEADVVIT 63 IA LG+G MG PM+ L AGH VR ++ A A +GV V + EAV +AD+VI+ Sbjct: 8 IAVLGIGMMGLPMARRLSEAGHPVRAWNRTRAKAEPLALYGVTVSNTPAEAVQDADIVIS 67 Query: 64 MLPTGEVVRRCYTDVLAAA--RPATLFIDSSTISVTDAREVHALAESHGMLQLDAPVSGG 121 +L G VV + D AA R +LFID ++I ++AR+ A G+ LDAPVSGG Sbjct: 68 LLENGPVVGQVLFDQGAARAMRRGSLFIDMASIQPSEARDHAARLGELGVAHLDAPVSGG 127 Query: 122 VKGAAAATLAFMVGGDESTLRRARPVLEPMAGKIIHCGAAGAGQAAKVCNNMVLAVQQIA 181 GA A TLA MVGG +RA PV P+ G+ H G GAGQ AK+ N M++ + A Sbjct: 128 TVGAEAGTLAIMVGGRPEDYQRALPVFAPL-GRATHVGPHGAGQLAKLANQMIVGITIGA 186 Query: 182 IAEAFVLAEKLGLSAQSLFDVITG--ATGNCWAVHTNCPVPGPVPTSPANNDFKPGFSTA 239 +AEA + A K G + + I+G A +H V DF P A Sbjct: 187 VAEALLFAAKGGADMAKVREAISGGFADSRILQLHGQRMV---------ERDFAPRGRMA 237 Query: 240 LMNKDLGLAMDAVAATGATAPLGSHAADIYAKFAADH--ADLDFSAVIHTLRAR 291 + KD+ AM TG AP+ + +YA +H DLD S + L +R Sbjct: 238 VQLKDMRNAMATAHETGFDAPITALFEALYAD-GVEHGLGDLDHSGLFVELASR 290 Lambda K H 0.319 0.131 0.382 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: 220 Number of extensions: 9 Number of successful extensions: 5 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: 294 Length adjustment: 26 Effective length of query: 268 Effective length of database: 268 Effective search space: 71824 Effective search space used: 71824 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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