Align 3-hydroxyisobutyrate dehydrogenase; HIBADH; EC 1.1.1.31 (characterized)
to candidate WP_011767085.1 AZO_RS16875 NAD(P)-dependent oxidoreductase
Query= SwissProt::P28811 (298 letters) >NCBI__GCF_000061505.1:WP_011767085.1 Length = 296 Score = 173 bits (439), Expect = 4e-48 Identities = 106/267 (39%), Positives = 150/267 (56%), Gaps = 11/267 (4%) Query: 4 IAFLGLGNMGGPMAANLLKAGHRVNVFDLQPKAVLGLVEQGA-QGAD---SALQCCEGAE 59 + F+GLG MG PMA +LLKAGH+V ++ +P A L+ G GA+ + +E Sbjct: 3 VGFVGLGVMGVPMAGHLLKAGHQVAIWARRPDAAQALIADGTLAGAELCATPAALAARSE 62 Query: 60 VVISMLPAGQHVESLYLGDDGLLARVAGKPLLIDCSTIAPETARKVAEAAAAKGLTLLDA 119 VVIS++ A VE+L GDDGL A A + +D STIAP TAR +A A +G+ +DA Sbjct: 63 VVISIITASADVEALAFGDDGLAAGFAPGAIHVDMSTIAPATARALAARYAKQGVGWVDA 122 Query: 120 PVSGGVGGARAGTLSFIVGGPAEGFARARPVLENMGRNIFHAGDHGAGQVAKICNNMLLG 179 PVSGG GAR TL+ + GG AE AR RP+ E +GR + H G GAGQVAK CN M++ Sbjct: 123 PVSGGGTGAREATLAIMAGGEAETLARVRPLFEVLGRTVVHIGPAGAGQVAKACNQMIMV 182 Query: 180 ILMAGTAEALALGVKNGLDPAVLSEVMKQSSGGNWALNLYNPWPGVMPQAPASNGYAGGF 239 + +AEA+ L +G+D L+ V + GG+ A + G M + + G Sbjct: 183 AAIQASAEAMHLANAHGVD---LAAVQRALMGGSAASRVMEVMGGRM----VARDFGAGI 235 Query: 240 QVRLMNKDLGLALANAQAVQASTPLGA 266 + RL +KD + + A + P+ A Sbjct: 236 EARLHHKDFAILMGEAVGLGVPLPVAA 262 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: 289 Number of extensions: 13 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: 298 Length of database: 296 Length adjustment: 26 Effective length of query: 272 Effective length of database: 270 Effective search space: 73440 Effective search space used: 73440 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 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