Align 3-hydroxyisobutyrate dehydrogenase (EC 1.1.1.31) (characterized)
to candidate 6937834 Sama_1975 2-hydroxy-3-oxopropionate reductase (RefSeq)
Query= reanno::pseudo13_GW456_L13:PfGW456L13_5145 (295 letters) >FitnessBrowser__SB2B:6937834 Length = 291 Score = 160 bits (404), Expect = 4e-44 Identities = 98/290 (33%), Positives = 149/290 (51%), Gaps = 12/290 (4%) Query: 2 KIAFIGLGNMGAPMARNLIKAGHALRLVDLNKAVL-AELEQLGGSISASAREAAEGAELV 60 K+AF+GLG MG PMA +L+KAGH + + + A A ++Q GG+++ S + AAE ++V Sbjct: 3 KVAFLGLGVMGYPMAGHLVKAGHQVTVYNRTTAKAEAWVKQFGGAMALSPKLAAEDQDIV 62 Query: 61 ITMLPAAVHVRSVWLGEDGVLAGIGKGVPAVDCSTIDPQTARDVAAAAAKQGVAMADAPV 120 T + + V LGEDGV+ G+ G VD +T AR++ AA QG DAPV Sbjct: 63 FTCVGNDKDLHQVVLGEDGVIHGLNAGAVLVDHTTASADIAREIGAALNAQGFGFVDAPV 122 Query: 121 SGGTGGAAAGTLTFMVGATPELFATLQPVLAQMGRNIVHCGEVGTGQIAKICNNLLLGIS 180 SGG GA G LT M G +F ++ V+ R GE G GQ+ K+ N + + Sbjct: 123 SGGQAGAENGVLTVMAGGDEAVFNQVKDVIMSYARCAERLGETGAGQLTKMVNQICIAGV 182 Query: 181 MVGVSEAMALGDALGIDTKVLAGIINSSTGRCWSSE--MYNPWPGIVETAPASRGYTGGF 238 + G++EA+ + G+D + + +I+ + W E + W G Y GF Sbjct: 183 VQGLAEALHFARSAGLDGEKVVEVISKGAAQSWQMENRYKSMWAG---------EYNFGF 233 Query: 239 GAELMLKDLGLATEAARQAHQPVVLGAVAQQLYQAMSLRGEGGQDFSAII 288 + M KDLG+A E AR+ + L A+ Q Y + G D S+++ Sbjct: 234 AIDWMRKDLGIALEEARRNGSHLPLTALVDQFYSEVQGMGGNRWDTSSLM 283 Lambda K H 0.317 0.133 0.386 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: 196 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: 295 Length of database: 291 Length adjustment: 26 Effective length of query: 269 Effective length of database: 265 Effective search space: 71285 Effective search space used: 71285 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