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 N515DRAFT_0355 N515DRAFT_0355 pyruvate dehydrogenase E1 component beta subunit
Query= SwissProt::Q5SLR3 (324 letters) >FitnessBrowser__Dyella79:N515DRAFT_0355 Length = 326 Score = 317 bits (812), Expect = 3e-91 Identities = 162/323 (50%), Positives = 222/323 (68%), Gaps = 1/323 (0%) Query: 1 MALMTMVQALNRALDEEMAKDPRVVVLGEDVGKRGGVFLVTEGLLQKYGPDRVMDTPLSE 60 MA +T+++A+ +AL EMA+DP VVVLGEDVG GGVF T+GL +K+G RV+DTPL E Sbjct: 1 MAQITLIEAVTQALAYEMARDPSVVVLGEDVGVNGGVFRATQGLQEKFGELRVLDTPLDE 60 Query: 61 AAIVGAALGMAAHGLRPVAEIQFADYIFPGFDQLVSQVAKLRYRSGGQFTAPLVVRMPSG 120 I G +GMAA G++PVAE QF +I+P +Q+ A+LR R+ G+ T P V R P G Sbjct: 61 TTIAGVTVGMAAQGMKPVAEAQFEGFIYPMMEQIACHAARLRNRTRGRITVPAVWRAPWG 120 Query: 121 GGVRGGHHHSQSPEAHFVHTAGLKVVAVSTPYDAKGLLKAAIRDEDPVVFLEPKRLYRSV 180 GG+R HHS++ E F + GL+VV S+P A GLL AAIRD DPV+F EPKR+YR Sbjct: 121 GGIRAPEHHSEANEHLFTNIPGLRVVMPSSPARAYGLLLAAIRDPDPVMFFEPKRIYRQY 180 Query: 181 KEEVPEEDYTLPIGKAALRREGKDLTLIGYGTVMPEVLQAAAELAKAGVSAEVLDLRTLM 240 KEEVP++ LP+ + R+G D+T++ +G + E L+AA ELA G+SAEV+D+ TL Sbjct: 181 KEEVPDDGEALPLDVCFVLRDGTDVTIVTWGAQVKEALEAADELAAEGISAEVIDVATLT 240 Query: 241 PWDYEAVMNSVAKTGRVVLVSDAPRHASFVSEVAATIAEDLLDMLLAPPIRVTGFDTPYP 300 P D++ + SV KTGR V+V +AP+ A F +E+AA +AE+ L LLAP RVTG+DT P Sbjct: 241 PLDFDTIAESVQKTGRCVIVHEAPKTAGFGAEIAARVAEECLYELLAPVERVTGYDTHIP 300 Query: 301 -YAQDKLYLPTVTRILNAAKRAL 322 + + Y+P+ R++ AAKR L Sbjct: 301 LFRLEMKYMPSTERVVEAAKRTL 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: 294 Number of extensions: 8 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: 324 Length of database: 326 Length adjustment: 28 Effective length of query: 296 Effective length of database: 298 Effective search space: 88208 Effective search space used: 88208 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