Align 2-oxoisovalerate dehydrogenase subunit beta; Branched-chain alpha-keto acid dehydrogenase E1 component beta chain; BCKDH E1-beta; EC 1.2.4.4 (characterized)
to candidate RR42_RS33050 RR42_RS33050 2-oxoisovalerate dehydrogenase
Query= SwissProt::Q5SLR3 (324 letters) >FitnessBrowser__Cup4G11:RR42_RS33050 Length = 325 Score = 317 bits (812), Expect = 3e-91 Identities = 160/323 (49%), Positives = 223/323 (69%), Gaps = 1/323 (0%) Query: 1 MALMTMVQALNRALDEEMAKDPRVVVLGEDVGKRGGVFLVTEGLLQKYGPDRVMDTPLSE 60 MA + +V+A+N+AL +A DPRVV+LGED+G GGVF T GL ++G +RV+DTPL+E Sbjct: 1 MAEINLVEAVNQALGHALAHDPRVVLLGEDIGVNGGVFRATAGLQARFGAERVIDTPLAE 60 Query: 61 AAIVGAALGMAAHGLRPVAEIQFADYIFPGFDQLVSQVAKLRYRSGGQFTAPLVVRMPSG 120 + I GAA+GMAA GL PVAEIQF +I+P D +++ +LR+R+ G+ + P+V+R P G Sbjct: 61 SGIAGAAIGMAAMGLAPVAEIQFTGFIYPAIDHIINHAGRLRHRTRGRLSCPMVLRSPYG 120 Query: 121 GGVRGGHHHSQSPEAHFVHTAGLKVVAVSTPYDAKGLLKAAIRDEDPVVFLEPKRLYRSV 180 G+ HHS+SPEA F H G++VV STP A GLL AA+RD DPVVFLEP RLYR Sbjct: 121 AGIHAPEHHSESPEAMFAHIPGIRVVIPSTPARAYGLLLAAMRDPDPVVFLEPTRLYRLF 180 Query: 181 KEEVPEEDYTLPIGKAALRREGKDLTLIGYGTVMPEVLQAAAELAKAGVSAEVLDLRTLM 240 +EEVP+ LP+ R+G D+TL+ +G ++ E AA L G++A V+D+ TL Sbjct: 181 REEVPDNGEALPLDTCFTLRDGDDITLVSWGAMLQETQAAADLLLDEGIAAAVIDVATLK 240 Query: 241 PWDYEAVMNSVAKTGRVVLVSDAPRHASFVSEVAATIAEDLLDMLLAPPIRVTGFDTPYP 300 P D + ++ SVA+TGR V+V +APR A F +E+AA +A+ L L AP RVTG+DT P Sbjct: 241 PLDMDTILESVARTGRCVIVHEAPRSAGFGAEIAANLADAGLYSLAAPVQRVTGYDTVVP 300 Query: 301 YAQ-DKLYLPTVTRILNAAKRAL 322 A+ + YLP+V RI +AA++A+ Sbjct: 301 MARLEYTYLPSVARIADAARKAM 323 Lambda K H 0.319 0.136 0.389 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: 303 Number of extensions: 13 Number of successful extensions: 1 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: 324 Length of database: 325 Length adjustment: 28 Effective length of query: 296 Effective length of database: 297 Effective search space: 87912 Effective search space used: 87912 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: 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