Align 3-methyl-2-oxobutanoate dehydrogenase subunit alpha; Branched-chain alpha-ketoacid dehydrogenase E1 component subunit alpha; BCKADH E1-alpha; EC 1.2.4.4 (characterized)
to candidate WP_011605406.1 FRAAL_RS18710 thiamine pyrophosphate-dependent dehydrogenase E1 component subunit alpha
Query= SwissProt::P9WIS3 (367 letters) >NCBI__GCF_000058485.1:WP_011605406.1 Length = 365 Score = 251 bits (641), Expect = 2e-71 Identities = 152/350 (43%), Positives = 191/350 (54%), Gaps = 11/350 (3%) Query: 20 VQLVGPDGTPTAERRYHRDLPEETLRWLYEMMVVTRELDTEFVNLQRQGELALYTPCRGQ 79 V+L+ PDGT + R+ + R Y MV+ R LD E LQRQGEL L+ P RGQ Sbjct: 13 VRLLAPDGTRVTDPRFAVLADHDLCREFYSSMVLARRLDEEATALQRQGELVLWIPLRGQ 72 Query: 80 EAAQVGAAACLRKTDWLFPQYRELGVYLVRGIPPGHVGVAWRGTWHGGLQFTTKCCAPMS 139 EAAQVG+AA +R D++FP YRE V RG+P V RG H G A + Sbjct: 73 EAAQVGSAAAVRPRDFIFPSYREHAVAWHRGVPAAEVIRLLRGVSHDGWDTAEHNMANYT 132 Query: 140 VPIGTQTLHAVG--------AAMAAQRLDEDSVTVAFLGDGATSEGDVHEALNFAAVFTT 191 + + +QTLHAVG A+ D D + +LGDGA S+GD +EA +AA F Sbjct: 133 IVLASQTLHAVGYGMGMVLDGAVGTGDPDRDGAVLVYLGDGAMSQGDANEAFVWAASFGA 192 Query: 192 PCVFYVQNNQWAISMPVSRQTAAPSIAHKAIGYGMPGIRVDGNDVLACYAVMAEAAARAR 251 P VF QNNQWAIS P RQ+ +A +A G+G PG+RVDGNDVLA +AV A AR Sbjct: 193 PVVFLCQNNQWAISTPTRRQSTM-QLARRADGFGFPGVRVDGNDVLAMHAVTTWALEHAR 251 Query: 252 AGDGPTLIEAVTYRLGPHTTADDPTRYRSQEEVDRWATLDPIPRYRTYLQDQGLWSQRLE 311 G GP LIEA TYR+ PHTT+DD TRY+ EE+ W DPI R R L + S Sbjct: 252 GGGGPVLIEANTYRMAPHTTSDDATRYQPAEELAVWRARDPIERLRLLLAAE--VSAGWF 309 Query: 312 EQVTARAKHVRSELRDAVFDAPDFDVDEVFTTVYAEITPGLQAQREQLRA 361 ++V A +LR A +F V A+ T +AQRE A Sbjct: 310 DEVREHADDAAGDLRRACLAMDPPAPVTMFGNVSADETADQRAQREWFTA 359 Lambda K H 0.320 0.134 0.413 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: 388 Number of extensions: 14 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: 367 Length of database: 365 Length adjustment: 30 Effective length of query: 337 Effective length of database: 335 Effective search space: 112895 Effective search space used: 112895 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 49 (23.5 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