Align 3-hydroxyisobutyrate dehydrogenase; HIBADH; EC 1.1.1.31 (characterized)
to candidate WP_279338484.1 HTA01S_RS01495 NAD(P)-dependent oxidoreductase
Query= SwissProt::P28811 (298 letters) >NCBI__GCF_001592305.1:WP_279338484.1 Length = 301 Score = 151 bits (381), Expect = 2e-41 Identities = 102/286 (35%), Positives = 148/286 (51%), Gaps = 12/286 (4%) Query: 3 DIAFLGLGNMGGPMAANLLKAGHRVNVFDLQPKAVLGLVEQGAQGADSALQCCEGAEVVI 62 +IA LG+G MG P+A L AG++V+ ++ P L GAQ D+ Q A++VI Sbjct: 14 NIAVLGIGMMGWPIARRLCVAGYQVSAWNRSPDKAERLRPFGAQVCDTPAQAVAQADLVI 73 Query: 63 SMLPAGQHVESLYLGDDGLLARVAGKPLLIDCSTIAPETARKVAEAAAAKGLTLLDAPVS 122 ++L G+ VE + L G + L++D S+I P AR A AA G+ LDAPVS Sbjct: 74 TLLEDGKVVEDV-LFRQGTTEGLRPGALVVDMSSIQPRQARDHAARLAAIGVHHLDAPVS 132 Query: 123 GGVGGARAGTLSFIVGGPAEGFARARPVLENMGRNIFHAGDHGAGQVAKICNNMLLGILM 182 GG GA TL+ + GG F RARPV E++GR H G HG+GQ+AK+ N M++GI + Sbjct: 133 GGTVGAEQATLAIMAGGKPADFERARPVFEHLGRPT-HVGPHGSGQLAKLANQMIVGITI 191 Query: 183 AGTAEALALGVKNGLDPAVLSEVMKQSSGGNWALNLYNPWPGVMPQAPASNGYAGGFQVR 242 AEAL L K G D A + + + + L ++ Q +A + Sbjct: 192 GAVAEALLLCEKGGADMAKVRQAITGGFADSRILQVHG-------QRMVERDFAKRGAIS 244 Query: 243 LMNKDLGLALANAQAVQASTPLGALARNLFSL---HAQADAEHEGL 285 + KD+ A+A A+ + P+ AL LF+ H AD +H L Sbjct: 245 VQLKDMRNAMATAREIGFEAPITALFEQLFAQAADHGLADLDHSAL 290 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: 269 Number of extensions: 14 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: 301 Length adjustment: 27 Effective length of query: 271 Effective length of database: 274 Effective search space: 74254 Effective search space used: 74254 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 Apr 09 2024. 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