Align 3-hydroxyisobutyrate dehydrogenase (EC 1.1.1.31) (characterized)
to candidate WP_086510800.1 BZY95_RS15295 NAD(P)-dependent oxidoreductase
Query= reanno::pseudo13_GW456_L13:PfGW456L13_5145 (295 letters) >NCBI__GCF_002151265.1:WP_086510800.1 Length = 291 Score = 154 bits (389), Expect = 2e-42 Identities = 98/291 (33%), Positives = 151/291 (51%), Gaps = 8/291 (2%) Query: 3 IAFIGLGNMGAPMARNLIKAGHALRLVDLNKA-VLAELEQLGGSISASAREAAEGAELVI 61 +AFIGLG MG PMA +L AG +R+ + ++ A +EQ GGS A+ EAA+GA+LV+ Sbjct: 4 VAFIGLGVMGYPMAGHLAHAGLTVRVYNRSEGKAKAWVEQFGGSHHATPAEAAQGADLVL 63 Query: 62 TMLPAAVHVRSVWLGEDGVLAGIGKGVPAVDCSTIDPQTARDVAAAAAKQGVAMADAPVS 121 + VR V +GE G L+G+ G VD +T A+++ AA ++ + DAPVS Sbjct: 64 VCVGNDDDVRQVTVGERGALSGMHAGSLLVDHTTASADLAQELDAACRERAIGFIDAPVS 123 Query: 122 GGTGGAAAGTLTFMVGATPELFATLQPVLAQMGRNIVHCGEVGTGQIAKICNNLLLGISM 181 GG GA G LT M G T FA + LA R + G G+GQ+ K+ N + + + Sbjct: 124 GGQQGAENGALTIMCGGTEADFARAETTLAHYARAVTLMGPAGSGQLTKMVNQICIAGLV 183 Query: 182 VGVSEAMALGDALGIDTKVLAGIINSSTGRCWSSEMYNPWPGIVETAPASRGYTGGFGAE 241 G++E + + G+D + + +I+ W E + +T A Y GF + Sbjct: 184 QGLAEGLHFAERAGLDQQRVIDVISKGAAGSWQMENRH------KTMIADE-YEHGFAVD 236 Query: 242 LMLKDLGLATEAARQAHQPVVLGAVAQQLYQAMSLRGEGGQDFSAIINGYR 292 M KDLG+ E AR+ + + A+ Q Y + + G G D S+++ R Sbjct: 237 WMRKDLGICLEQARRLQARLPVTALVDQFYGDVQVMGGGRWDTSSLLRRLR 287 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: 160 Number of extensions: 6 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 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