Align 3-hydroxyisobutyrate dehydrogenase (EC 1.1.1.31) (characterized)
to candidate SMc00274 SMc00274 oxidoreductase
Query= reanno::pseudo13_GW456_L13:PfGW456L13_5145 (295 letters) >FitnessBrowser__Smeli:SMc00274 Length = 295 Score = 185 bits (469), Expect = 1e-51 Identities = 109/293 (37%), Positives = 157/293 (53%), Gaps = 9/293 (3%) Query: 2 KIAFIGLGNMGAPMARNLIKAGHALRLVDLNKAVLAELEQLGGSISASAREAAEGAELVI 61 ++AF+GLG+MG PMA NLI+AGHA+R D+ A + L GG SA+ EA GA++++ Sbjct: 6 RVAFVGLGSMGLPMAENLIRAGHAVRGFDVRAAAMETLAATGGIRSANPAEACSGADVLV 65 Query: 62 TMLPAAVHVRSVWLGEDGVLAGIGKGVPAVDCSTIDPQTARDVAAAAAKQGVAMADAPVS 121 M+ A RSV L E G L+ + +G +T P + +A G + D PVS Sbjct: 66 LMVVNAEQARSVLL-ESGALSSLPQGAHICLMATCPPDEVKRLADEVEASGRVLVDCPVS 124 Query: 122 GGTGGAAAGTLTFMVGATPELFATLQPVLAQMGRNIVHCG-EVGTGQIAKICNNLLLGIS 180 GG GA AG LT MVGA + + + PVL MG + HCG E G G + K N LL G+ Sbjct: 125 GGVVGAKAGALTIMVGAPEKAYHAVVPVLQAMGDKVFHCGPEQGQGAVVKAINQLLCGVH 184 Query: 181 MVGVSEAMALGDALGIDTKVLAGIINSSTGRCWSSEMYNPWPGIVETAPASRGYTGGFGA 240 + +EA+ALG+ G+D L I+++S W + P I +T P + Sbjct: 185 LATAAEALALGEKAGVDAATLLEIVSNSAASSWMLKDRGP-RMITKTPPVTS------AV 237 Query: 241 ELMLKDLGLATEAARQAHQPVVLGAVAQQLYQAMSLRGEGGQDFSAIINGYRK 293 ++ +KDLG+A R + L A A Q++ A S G G +D S +I YR+ Sbjct: 238 DIFVKDLGIALATGRSVSMALPLAAAAHQMFLAESGSGNGLEDDSQVIAAYRR 290 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: 185 Number of extensions: 7 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: 295 Length of database: 295 Length adjustment: 26 Effective length of query: 269 Effective length of database: 269 Effective search space: 72361 Effective search space used: 72361 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