Align 3-hydroxyisobutyrate dehydrogenase (EC 1.1.1.31) (characterized)
to candidate GFF1376 HP15_1343 2-hydroxy-3-oxopropionate reductase
Query= reanno::pseudo3_N2E3:AO353_05985 (294 letters) >FitnessBrowser__Marino:GFF1376 Length = 290 Score = 165 bits (418), Expect = 1e-45 Identities = 103/287 (35%), Positives = 159/287 (55%), Gaps = 10/287 (3%) Query: 3 IAFIGLGNMGAPMARNLIKAGHSLNLVDLNKAVLAE--LAQLGGTISATAREAAQGAELV 60 +AFIGLG MG+ MA NL+ G +NL+ N++ AE L G ++ +A +A + A++V Sbjct: 5 LAFIGLGIMGSRMAANLLDKG-DVNLIVFNRSTEAEKSLKDKGAKVADSAADAVRQADVV 63 Query: 61 ITMLPAAVHVRSVWLGEDGVLAGIAKGVPAVDCSTIDPQTARDVAAAAAKQGVAMADAPV 120 +ML + V+ + LGEDG ++ +A+ VDCST++P A QG+ DAPV Sbjct: 64 FSMLASPPVVQDMALGEDGFVSAMAENALWVDCSTVNPSFTEYAGEVARAQGIRFMDAPV 123 Query: 121 SGGTGGAAAGTLTFMVGATPELFATLQPVLAQMGRNIVHCGEVGTGQIAKICNNLLLAIS 180 +G AA+G LTF+VGA E F +++P+L MG+ IVH G+VG G K+ N +LA S Sbjct: 124 AGTREPAASGELTFLVGADDEDFQSVEPLLQTMGKKIVHVGQVGRGTAFKMLVNAMLAQS 183 Query: 181 MVGVSEAMALGDALGIDTQVLAGIINSSTGRCWSSEMYNPWPGIVETAPASRGYTGGFGA 240 M+ +E LG+ LG L + + + P+ G + + F Sbjct: 184 MLAFAETTLLGEKLGFSRDFLMDTLP-------NLPVTPPFIGGKAELIRNGDFDAQFPL 236 Query: 241 ELMLKDLGLATEAARQAHQPVMLGAVAQQLYQAMSQRGEGGKDFSAI 287 ELM KDL L + A + QP+ L +A+++Y + S G G KDF+++ Sbjct: 237 ELMHKDLHLLEQTAYEVGQPLYLANLAKEVYGSASSSGWGRKDFASV 283 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: 181 Number of extensions: 8 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: 294 Length of database: 290 Length adjustment: 26 Effective length of query: 268 Effective length of database: 264 Effective search space: 70752 Effective search space used: 70752 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