Align Putative branched-chain alpha keto acid dehydrogenase E1 subunit beta (characterized, see rationale)
to candidate Ga0059261_2272 Ga0059261_2272 Pyruvate/2-oxoglutarate dehydrogenase complex, dehydrogenase (E1) component, eukaryotic type, beta subunit
Query= uniprot:G1UHX5 (328 letters) >FitnessBrowser__Korea:Ga0059261_2272 Length = 353 Score = 276 bits (707), Expect = 4e-79 Identities = 161/337 (47%), Positives = 198/337 (58%), Gaps = 21/337 (6%) Query: 2 SEITMAKALNTALRDALRDDPRTILFGEDIGALGGVFRITDGLAAEFGDERCFDTPLAES 61 + + M +A+N+AL + DP I+ GED+G GGVFR T GL A+ G R FDTP+ E Sbjct: 18 TRMNMIQAINSALDVMMARDPDVIVMGEDVGYFGGVFRATAGLQAKHGKTRVFDTPITEC 77 Query: 62 AILGTAVGMAMYGYRPVVEMQFDAFAYPAFEQLVSHVAKLRNRTRGAIGLPLTIRIPYGG 121 I+G A+GM YG RPV E+QF + YPA +QLVS A+LR R+ G PLTIR PYGG Sbjct: 78 GIVGVAIGMGAYGLRPVPEIQFADYIYPALDQLVSEAARLRYRSGGQFTAPLTIRSPYGG 137 Query: 122 GIGGVEHHSDSSEIYYMATPGLTVVTPATAADAYSLLRRSIASPDPVVFLEPKRLY---- 177 GI G + HS S E + G+ V P+T DA LL SI DPV+F EPKR+Y Sbjct: 138 GIFGGQTHSQSPEGIFTHVSGVKTVIPSTPYDAKGLLIASIEDNDPVIFFEPKRIYNGPF 197 Query: 178 ---WRKEALGLPVDTG----------PLGSAVIRRHGTHATLIAYGPAVTTALEAAEAAA 224 W + A G LG A I R G T++AYG V E Sbjct: 198 NGHWDRPAENWSKHPGGEVPEGYYRVELGKAAIVRPGEALTVLAYGTMVHVVKATVE--- 254 Query: 225 EHGWDLEVIDLRTLMPLDDATVCASVRRTGRAVVVHEAHGFAGPGAEIAARITERCFYHL 284 E G D E+IDLRTL+PLD T+ SVR+TGR +VVHEA +G GAE+A+ + ERCFYHL Sbjct: 255 EMGIDAEIIDLRTLVPLDIETIEESVRKTGRCMVVHEATRTSGFGAELASLVQERCFYHL 314 Query: 285 EAPVRRVTGFDVPYPPPLLERHYLPGVDRILDAVASL 321 EAPV RVTGFD PYP LE Y PG RI A+ + Sbjct: 315 EAPVERVTGFDTPYPHS-LEWAYFPGPVRIGQALKKI 350 Lambda K H 0.322 0.138 0.418 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: 359 Number of extensions: 12 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: 328 Length of database: 353 Length adjustment: 28 Effective length of query: 300 Effective length of database: 325 Effective search space: 97500 Effective search space used: 97500 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 (21.9 bits) S2: 49 (23.5 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