Align 3-hydroxyisobutyrate dehydrogenase (EC 1.1.1.31) (characterized)
to candidate WP_063836874.1 BS73_RS00355 NAD(P)-dependent oxidoreductase
Query= reanno::psRCH2:GFF2390 (296 letters) >NCBI__GCF_000744815.1:WP_063836874.1 Length = 362 Score = 127 bits (319), Expect = 4e-34 Identities = 90/297 (30%), Positives = 145/297 (48%), Gaps = 15/297 (5%) Query: 1 MHIGFIGLGNMGAPMAHNLLKAGHQLSVFDLNAAAVENLVGAGALPVDSPTAIAQGNAEL 60 + +G+IG G MGA MA L +AGH L+V++ A E L GA DS + + ++ Sbjct: 15 LRVGWIGTGRMGAAMAERLARAGHDLAVWNRTRAKAEPLRRFGAEVRDSIAELR--DRDV 72 Query: 61 IITMLPAAAHVKGVYLGVNGLI---AHSRAG---VMLIDCSTIDPHSAREVAKAAAEHGN 114 + T + + +K V LG +GLI + AG +++DCST+ ++ V +A A G Sbjct: 73 VFTTVAGSEDLKEVLLGEDGLIHSDGQAPAGPVPAVVVDCSTVSAEASAAVREACAAAGA 132 Query: 115 PMLDAPVSGGTGGAAAGTLTFMVGGSDPDFDHAQPILAAMGKNIVHCGAAGNGQVAKVAN 174 L APVSG AG L+ +V G ++ P+L +G+ + G ++ K+A+ Sbjct: 133 DFLAAPVSGNAKVVEAGKLSLVVSGPQKAYERVSPLLHTIGRAATYAGEGDTARLVKIAH 192 Query: 175 NMLLGISMIGVAEAMALGVALGMDAKTLAGVINTSSGRCWSSDTYNPFPGVLDNVPSSRG 234 N+ LG+ +AE L G+ +N S S+ T P + + Sbjct: 193 NVFLGVVTQSLAEITVLAEKGGVPRHAFLEFLNDSV--LGSAFTRYKSPAFV-----NLD 245 Query: 235 YSGGFGSDLMLKDLGLATEAAKQVRQPVILGALAQQLYQSFSAQGHGGLDFSAIINQ 291 YS F L+ KDL L +AA+++ P+ L A QL Q+ G G DF+ +++Q Sbjct: 246 YSPTFTPPLLRKDLDLGLDAARELGVPMPLAAATAQLVQATIGGGRTGEDFAVLLDQ 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: 288 Number of extensions: 9 Number of successful extensions: 3 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: 362 Length adjustment: 28 Effective length of query: 268 Effective length of database: 334 Effective search space: 89512 Effective search space used: 89512 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