Align 3-hydroxyisobutyrate dehydrogenase (EC 1.1.1.31) (characterized)
to candidate WP_051941255.1 BS73_RS32725 NAD(P)-dependent oxidoreductase
Query= reanno::psRCH2:GFF2390 (296 letters) >NCBI__GCF_000744815.1:WP_051941255.1 Length = 324 Score = 154 bits (389), Expect = 3e-42 Identities = 105/296 (35%), Positives = 147/296 (49%), Gaps = 16/296 (5%) Query: 3 IGFIGLGNMGAPMAHNLLKAGHQLSVFDLNAAAVENLV---GAGALPVDSPTAIAQGN-- 57 +G +GLG MG MA +L +AG + V D+ A E G G ++ A A Sbjct: 14 VGLVGLGTMGLGMARSLRRAGLRPGVHDVRAEVAERFAAEGGEGGEVGEAGEAFATAGEL 73 Query: 58 ---AELIITMLPAAAHVKGVYLGVNGLIAHSRAGVMLIDCSTIDPHSAREVAKAAAEHGN 114 ++++ ++ A V+ V G G A R G + + CSTI P + E+A AE Sbjct: 74 AATVDVLVGVVVDAEQVEAVLFGEGGAAARLRPGAVYVMCSTIAPERSAELAARLAELNV 133 Query: 115 PMLDAPVSGGTGGAAAGTLTFMVGGSDPDFDHAQPILAAMGKNIVHCGA-AGNGQVAKVA 173 LDAPVSGG AAAG LT M GS + A P+L A+ + GA G G K Sbjct: 134 HYLDAPVSGGAARAAAGELTMMTSGSADAYALADPVLEALSATVYRLGAEPGLGSTVKAV 193 Query: 174 NNMLLGISMIGVAEAMALGVALGMDAKTLAGVINTSSGRCWSSDTYNPFPGVLDNVPSSR 233 N +L G+ + AEAMALGV G+ +TL VI S+G W + N VL + Sbjct: 194 NQLLAGVHIAAAAEAMALGVKAGVPPETLYEVITHSAGNSWMFE--NRMAHVL-----AG 246 Query: 234 GYSGGFGSDLMLKDLGLATEAAKQVRQPVILGALAQQLYQSFSAQGHGGLDFSAII 289 Y+ D+ +KDLG+ + A+ R P+ L A A Q++ +A G GG D SA+I Sbjct: 247 DYTPRSAVDIFVKDLGIVLDTARPQRFPLPLAATAHQMFLQAAAGGLGGEDDSAVI 302 Lambda K H 0.318 0.134 0.392 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: 270 Number of extensions: 13 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: 296 Length of database: 324 Length adjustment: 27 Effective length of query: 269 Effective length of database: 297 Effective search space: 79893 Effective search space used: 79893 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