Align 3-hydroxyisobutyrate dehydrogenase (EC 1.1.1.31) (characterized)
to candidate WP_011937525.1 GURA_RS02990 NAD(P)-dependent oxidoreductase
Query= reanno::pseudo13_GW456_L13:PfGW456L13_5145 (295 letters) >NCBI__GCF_000016745.1:WP_011937525.1 Length = 287 Score = 145 bits (366), Expect = 1e-39 Identities = 92/292 (31%), Positives = 142/292 (48%), Gaps = 7/292 (2%) Query: 2 KIAFIGLGNMGAPMARNLIKAGHALRLVDLNKAVLAELEQLGGSISASAREAAEGAELVI 61 K F+GLG MG+ MA+NL+KAG + + + + EL LG +A+ R+ E + Sbjct: 3 KFGFLGLGIMGSAMAKNLLKAGFDVTVWNRSPEKCEELAALGARSAATPRQVVESCGITF 62 Query: 62 TMLPAAVHVRSVWLGEDGVLAGIGKGVPAVDCSTIDPQTARDVAAAAAKQGVAMADAPVS 121 ML +V G DGVL GIG G VD ST+D TA+ + AA +G +APVS Sbjct: 63 AMLSDPAADEAVCFGTDGVLEGIGAGKGYVDMSTVDATTAQKIGAAVTDKGGRFLEAPVS 122 Query: 122 GGTGGAAAGTLTFMVGATPELFATLQPVLAQMGRNIVHCGEVGTGQIAKICNNLLLGISM 181 G A GTL + L+ P +MG+ ++ GEVG G K+ N+++G M Sbjct: 123 GSRKPAEDGTLIILTAGDKSLYNEAMPAFERMGKKVLFLGEVGKGAEMKLVVNMVMGGMM 182 Query: 182 VGVSEAMALGDALGIDTKVLAGIINSSTGRCWSSEMYNPWPGIVETAPASRGYTGGFGAE 241 E +ALG G++ + ++++ ++ M+ G++ A+ +T F + Sbjct: 183 SIFCEGLALGAKAGLEVTDMLDVMDAG---AVANPMFKLKGGLI----AAGNFTTAFPLK 235 Query: 242 LMLKDLGLATEAARQAHQPVVLGAVAQQLYQAMSLRGEGGQDFSAIINGYRK 293 M KDL LA QP+ A A + ++ G G +DFSA+ K Sbjct: 236 HMQKDLRLAVGLGDWLGQPLFTAAAANEAFKRAKALGFGDEDFSALFKAIEK 287 Lambda K H 0.317 0.133 0.386 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: 218 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: 295 Length of database: 287 Length adjustment: 26 Effective length of query: 269 Effective length of database: 261 Effective search space: 70209 Effective search space used: 70209 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