Align Putative branched-chain alpha keto acid dehydrogenase E1 subunit beta (characterized, see rationale)
to candidate 201484 SO2340 alpha keto acid dehydrogenase complex, E1 component, beta subunit (NCBI ptt file)
Query= uniprot:G1UHX5 (328 letters) >FitnessBrowser__MR1:201484 Length = 325 Score = 257 bits (657), Expect = 2e-73 Identities = 147/323 (45%), Positives = 194/323 (60%), Gaps = 9/323 (2%) Query: 1 MSEITMAKALNTALRDALRDDPRTILFGEDIGALGGVFRITDGLAAEFGDERCFDTPLAE 60 M+E+ M +A+N AL A++ D R ++FGED+G GGVFR T GL +FG RCF+TPL E Sbjct: 1 MAEMNMLQAVNEALSIAMQADERMVVFGEDVGHFGGVFRATSGLQEKFGRARCFNTPLTE 60 Query: 61 SAILGTAVGMAMYGYRPVVEMQFDAFAYPAFEQLVSHVAKLRNRTRGAIGL-PLTIRIPY 119 I G A G+A G V E+QF + +PAF+Q+V+ AK R R+ + L R PY Sbjct: 61 QGIAGFANGLASNGMTAVAEIQFADYIFPAFDQIVNESAKFRYRSGNEFNVGSLVFRTPY 120 Query: 120 GGGIGGVEHHSDSSEIYYMATPGLTVVTPATAADAYSLLRRSIASPDPVVFLEPKRLYWR 179 GGGI G +HS S E Y+ TPGL VV P A A LL SI +PVVF EPKRLY Sbjct: 121 GGGIAGGHYHSQSPEAYFTQTPGLKVVVPRNPAQAKGLLLASIRDKNPVVFFEPKRLY-- 178 Query: 180 KEALGLPVDTG----PLGSAVIRRHGTHATLIAYGPAVTTALEAAEAAAEHGWDLEVIDL 235 + ++G V G LG A + R G TL+A+G + +AA+ AA+ G E+IDL Sbjct: 179 RASVG-DVPAGDYEIELGKAEVLREGKDITLVAWGAQMEIIEKAADMAAKEGISCEIIDL 237 Query: 236 RTLMPLDDATVCASVRRTGRAVVVHEAHGFAGPGAEIAARITERCFYHLEAPVRRVTGFD 295 RTL P D TV SV++TGR +V HEA G EIAA I + CF +LE+P+ RV G D Sbjct: 238 RTLAPWDVNTVADSVKKTGRLLVNHEAPLTGGFAGEIAATIQQECFLYLESPISRVCGLD 297 Query: 296 VPYPPPLLERHYLPGVDRILDAV 318 PY P + E+ Y+P + +A+ Sbjct: 298 TPY-PLVHEKEYMPDALKTFEAI 319 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: 282 Number of extensions: 11 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: 328 Length of database: 325 Length adjustment: 28 Effective length of query: 300 Effective length of database: 297 Effective search space: 89100 Effective search space used: 89100 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: 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