Align 3-hydroxyisobutyrate dehydrogenase (EC 1.1.1.31) (characterized)
to candidate Ac3H11_1088 2-hydroxy-3-oxopropionate reductase (EC 1.1.1.60)
Query= reanno::pseudo3_N2E3:AO353_05985 (294 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1088 Length = 322 Score = 158 bits (400), Expect = 1e-43 Identities = 107/295 (36%), Positives = 150/295 (50%), Gaps = 10/295 (3%) Query: 1 MKIAFIGLGNMGAPMARNLIKAGHSLNLVDLNKAVLAELAQLGGTISATAREAAQGAELV 60 +K+ FIGLG MGAPM +LI AGH L V V ++AQ T TAR A+ A++V Sbjct: 24 LKLGFIGLGIMGAPMCGHLIAAGHQL-YVHTRGRVAPQIAQSSATQCTTARGVAERADIV 82 Query: 61 ITMLPAAVHVRSVWLGEDGVLAGI--AKGVPAVDCSTIDPQTARDVAAAAAKQGVAMADA 118 MLP V V G DGV G+ + G VD S+I P +D AA G DA Sbjct: 83 FLMLPDTPDVEKVLFGADGVAQGLKGSVGKVVVDMSSISPVATKDFAARIEAVGAQYLDA 142 Query: 119 PVSGGTGGAAAGTLTFMVGATPELFATLQPVLAQMGRNIVHCGEVGTGQIAKICNNLLLA 178 PVSGG GA TL+ MVG +F ++P+ ++G+NI G G GQ AK+ N +++A Sbjct: 143 PVSGGELGAKNATLSIMVGGPEAVFERIRPLFERLGKNITLVGGNGDGQTAKVANQIIVA 202 Query: 179 ISMVGVSEAMALGDALGIDTQVLAGIINSSTGRCWSSEMYNPWPGIVETAPASRGYTGGF 238 +++ V+EA+ G D A + + G SS++ + R + GF Sbjct: 203 LNIEAVAEALLFAARAGADP---ARVRQALLGGFASSKILE----VHAERMIKRTFDPGF 255 Query: 239 GAELMLKDLGLATEAARQAHQPVMLGAVAQQLYQAMSQRGEGGKDFSAIINSYRK 293 L KDL LA +AR P+ A+AQ+L+ A G G D SA++ + K Sbjct: 256 RIGLHQKDLNLALSSARALGVPLPNTAMAQELFNACVAHGGQGWDHSAMVRALEK 310 Lambda K H 0.317 0.132 0.382 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: 224 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: 294 Length of database: 322 Length adjustment: 27 Effective length of query: 267 Effective length of database: 295 Effective search space: 78765 Effective search space used: 78765 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 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