Align 3-hydroxyisobutyrate dehydrogenase (EC 1.1.1.31) (characterized)
to candidate WP_086510174.1 BZY95_RS12045 2-hydroxy-3-oxopropionate reductase
Query= reanno::pseudo3_N2E3:AO353_05985 (294 letters) >NCBI__GCF_002151265.1:WP_086510174.1 Length = 295 Score = 170 bits (430), Expect = 4e-47 Identities = 107/289 (37%), Positives = 151/289 (52%), Gaps = 7/289 (2%) Query: 2 KIAFIGLGNMGAPMARNLIKAGHSLNLVDLNKAVLAELAQLGGTISATAREAAQGAELVI 61 KI FIGLG MG PMA +L+ AGH + V+ A+ ELA G ++A + A+ AE+VI Sbjct: 3 KIGFIGLGIMGRPMAGHLLDAGHEIITVEHGSAIPRELADKGARVAANPKAVAEQAEVVI 62 Query: 62 TMLPAAVHVRSVWLGEDGVLAGIAKGVPAVDCSTIDPQTARDVAAAAAKQGVAMADAPVS 121 TM+P V V GE+GV+ G+ G +D S+I P + A + G DAPVS Sbjct: 63 TMVPDTPDVELVLFGENGVVEGLKPGTLVIDMSSIAPIATQGFAKRIHEAGGEYVDAPVS 122 Query: 122 GGTGGAAAGTLTFMVGATPELFATLQPVLAQMGRNIVHCGEVGTGQIAKICNNLLLAISM 181 GG GGA LT MVGAT E F +P+L MG+ I H G G GQ K+ N +++A+++ Sbjct: 123 GGEGGAINAALTIMVGATQEGFERARPILEVMGKTITHIGGHGAGQTCKVANQIVVALTI 182 Query: 182 VGVSEAMALGDALGIDTQVLAGIINSSTGRCWSSEMYNPWPGIVETAPASRGYTGGFGAE 241 V+E + G D +A + S G S++ + + R + GF + Sbjct: 183 EAVAEGLLFASKAGAD---VAKVRESLLGGLAQSKILD----VHGERMIKRTFDPGFKIK 235 Query: 242 LMLKDLGLATEAARQAHQPVMLGAVAQQLYQAMSQRGEGGKDFSAIINS 290 L KDL LA E AR + + A AQQL+QA G D + I+ + Sbjct: 236 LHQKDLNLALEGARSLNLALPGTANAQQLFQACVAHGGENWDHAGILRA 284 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: 204 Number of extensions: 10 Number of successful extensions: 2 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: 295 Length adjustment: 26 Effective length of query: 268 Effective length of database: 269 Effective search space: 72092 Effective search space used: 72092 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