Align 3-hydroxyisobutyrate dehydrogenase; HIBADH; EC 1.1.1.31 (characterized)
to candidate 3610835 Dshi_4221 2-hydroxy-3-oxopropionate reductase (RefSeq)
Query= SwissProt::P28811 (298 letters) >FitnessBrowser__Dino:3610835 Length = 293 Score = 148 bits (373), Expect = 2e-40 Identities = 103/296 (34%), Positives = 152/296 (51%), Gaps = 17/296 (5%) Query: 1 MTDIAFLGLGNMGGPMAANLLKAGHRVNVFDLQPKAVLGLVEQGAQGADSALQCCEGAEV 60 M+D+A +GLG+MG MA +LL+AG RV D+ P+ + +G A E ++ Sbjct: 1 MSDVAIIGLGSMGYGMAQSLLRAGLRVYGADIAPEPMARFRAEGGLAARP-----EAVDI 55 Query: 61 -VISMLPAGQHVESLYLGDDGLLARVAGKPLLIDCSTIAPETARKVAEAAAAKGLTLLDA 119 VI++L A Q E++ G +G ++ + ++I C+T+ P AR +A A G+ LDA Sbjct: 56 LVIAVLNAAQ-TEAVLFGAEGWISTLRKGGVVIACATVPPRFARDMAARCAEAGVQYLDA 114 Query: 120 PVSGGVGGARAGTLSFIVGGPAEGFARARPVLENMGRNIFHAGD-HGAGQVAKICNNMLL 178 P+SGG A G LS + G AE FA A P L+ M +F GD GAG K N ML Sbjct: 115 PISGGAAKAAQGRLSIMASGGAEAFAAAAPALDAMAETVFELGDAPGAGSAMKAINQMLA 174 Query: 179 GILMAGTAEALALGVKNGLDPAVLSEVMKQSSGGNWALNLYNPWPGVMPQAPASNGYAGG 238 G +A AEA+ G+ G+DPA EV+ + +G +W N P ++ Y Sbjct: 175 GTHIAAMAEAVTFGMTQGVDPAKTVEVISRCAGTSWMFE--NRAPHIV-----EGDYTPR 227 Query: 239 FQVRLMNKDLGLALANAQAVQASTPLGALARNLFSLHAQADAEHEGLDFSSIQKLY 294 V + KDLG+ L A + + PL A A F A A + G D +++ K+Y Sbjct: 228 SSVNIWPKDLGIVLDIAAEAKFAAPLTAAALQQFM--AAAGSGLGGEDDAAVAKVY 281 Lambda K H 0.317 0.135 0.395 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: 233 Number of extensions: 16 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: 298 Length of database: 293 Length adjustment: 26 Effective length of query: 272 Effective length of database: 267 Effective search space: 72624 Effective search space used: 72624 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 (21.7 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