Align 3-hydroxyisobutyrate dehydrogenase (EC 1.1.1.31) (characterized)
to candidate BPHYT_RS31915 BPHYT_RS31915 hypothetical protein
Query= reanno::psRCH2:GFF2390 (296 letters) >FitnessBrowser__BFirm:BPHYT_RS31915 Length = 276 Score = 189 bits (480), Expect = 6e-53 Identities = 106/276 (38%), Positives = 155/276 (56%), Gaps = 2/276 (0%) Query: 1 MHIGFIGLGNMGAPMAHNLLKAGHQLSVFDLNAAAVENLVGAGALPVDSPTAIAQGNAEL 60 M IGFIG G MG M NLLK H + V D A + + GA + + G ++ Sbjct: 1 MKIGFIGAGRMGHRMISNLLKGSHAVLVLDGARDARDRVASLGATLAMNLADLVTGQ-DI 59 Query: 61 IITMLPAAAHVKGVYLGVNGLIAHSRAGVMLIDCSTIDPHSAREVAKAAAEHGNPMLDAP 120 +ITMLP VY G GL + + +L++CST+D + + + A G ++DAP Sbjct: 60 VITMLPTPDVSLSVYEGAGGLFSITPPETLLLECSTVDVKTIERLGEGARASGTQLIDAP 119 Query: 121 VSGGTGGAAAGTLTFMVGGSDPDFDHAQPILAAMGKNIVHCGAAGNGQVAKVANNMLLGI 180 ++GG GAA TLTFMVGGS+ ++A+P L +MG IVH G G+G K+ NNM+ Sbjct: 120 LTGGIEGAALATLTFMVGGSEEQLEYARPALQSMGSRIVHAGRFGSGTKLKLVNNMICAT 179 Query: 181 SMIGVAEAMALGVALGMDAKTLAGVINTSSGRCWSSDTYNPFPGVLDNVPSSRGY-SGGF 239 +++ +EA+ LG+ LG+DA+ + VI +G W +TY P PGV+D PSSRG+ F Sbjct: 180 NLMVASEALTLGLKLGLDAQPMYDVIANGTGASWVLNTYYPLPGVVDGAPSSRGFRMPTF 239 Query: 240 GSDLMLKDLGLATEAAKQVRQPVILGALAQQLYQSF 275 + M KD+ A EAA+ V L +A+ L + + Sbjct: 240 PATGMAKDMRCALEAARSVEAVTPLHNVAESLLKLY 275 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: 201 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: 276 Length adjustment: 26 Effective length of query: 270 Effective length of database: 250 Effective search space: 67500 Effective search space used: 67500 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: 47 (22.7 bits)
This GapMind analysis is from Sep 17 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