Align 2-hydroxy-3-oxopropionate reductase (EC 1.1.1.60) (characterized)
to candidate HSERO_RS15390 HSERO_RS15390 3-hydroxyisobutyrate dehydrogenase
Query= BRENDA::Q8ZLV8 (296 letters) >FitnessBrowser__HerbieS:HSERO_RS15390 Length = 297 Score = 188 bits (478), Expect = 1e-52 Identities = 104/289 (35%), Positives = 167/289 (57%), Gaps = 7/289 (2%) Query: 1 MTMKVGFIGLGIMGKPMSKNLLKAGYSLVVSDRNPEAIADVIAAGAETASTAKAIAEQCD 60 M+ + FIGLG MG PM++NL+KAG+S+ D ++ ++ G +T + + A + D Sbjct: 1 MSANIVFIGLGNMGLPMAQNLVKAGFSVSGHDLVKASVDKLVEVGGKTEADSMAAVAKAD 60 Query: 61 VIITMLPNSPHVKEVALGENGIIEGAKPGTVLIDMSSIAPLASREISDALKAKGVEMLDA 120 V+ITMLP S HV+ + LGE G++ AKPGT+LID S+IAP A+R+++ A KA+G EMLDA Sbjct: 61 VVITMLPASRHVESLYLGEAGVLASAKPGTLLIDCSTIAPEAARKVAAAAKARGFEMLDA 120 Query: 121 PVSGGEPKAIDGTLSVMVGGDKAIFDKYYDLMKAMAGSVVHTGDIGAGNVTKLANQVIVA 180 PVSGG A GTL+ MVGG K F+ ++ M ++ H G+ G+G K+ N +++ Sbjct: 121 PVSGGTNGATAGTLTFMVGGSKEAFEAAQPYLQKMGKAIYHAGESGSGQTVKVCNNMLLG 180 Query: 181 LNIAAMSEALTLATKAGVNPDLVYQAIRGGLAGSTVLDA--KAPMVMD-----RNFKPGF 233 + + SEA+ L G++P ++ + + + L+ P VM+ + + GF Sbjct: 181 ILMIGTSEAIRLGMANGMDPKVLSEIMSKSSGRNWTLEVYNPCPGVMETAPASKGYAGGF 240 Query: 234 RIDLHIKDLANALDTSHGVGAQLPLTAAVMEMMQALRADGHGNDDHSAL 282 +DL +KDL A++ + +PL A + +G G D S++ Sbjct: 241 GVDLMLKDLGLAVENALATNCAIPLGATARNLYDIHSMNGAGKLDFSSI 289 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: 226 Number of extensions: 11 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: 297 Length adjustment: 26 Effective length of query: 270 Effective length of database: 271 Effective search space: 73170 Effective search space used: 73170 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