Align Putative branched-chain alpha keto acid dehydrogenase E1 subunit beta (characterized, see rationale)
to candidate 5209455 Shew_1926 transketolase, central region (RefSeq)
Query= uniprot:G1UHX5 (328 letters) >FitnessBrowser__PV4:5209455 Length = 325 Score = 263 bits (671), Expect = 6e-75 Identities = 148/328 (45%), Positives = 201/328 (61%), Gaps = 8/328 (2%) Query: 1 MSEITMAKALNTALRDALRDDPRTILFGEDIGALGGVFRITDGLAAEFGDERCFDTPLAE 60 M++I M +A+N AL A+ D + ++FGED+G GGVFR T GL +FG +RCF+TPL E Sbjct: 1 MAKINMLQAINDALTIAMETDDKAVIFGEDVGHFGGVFRATSGLQDKFGRDRCFNTPLTE 60 Query: 61 SAILGTAVGMAMYGYRPVVEMQFDAFAYPAFEQLVSHVAKLRNRTRGAIGL-PLTIRIPY 119 I G A G+A G + E+QF + +PAF+Q+V+ AK R R+ + +T R PY Sbjct: 61 QGIAGFANGLASNGMTAIAEIQFADYIFPAFDQIVNESAKFRYRSGNEFNVGGITYRTPY 120 Query: 120 GGGIGGVEHHSDSSEIYYMATPGLTVVTPATAADAYSLLRRSIASPDPVVFLEPKRLYWR 179 GGGI G +HS S E Y+ TPGL VV P A A LL SI +PVVF EPKRLY Sbjct: 121 GGGIAGGHYHSQSPEAYFTQTPGLKVVVPRNAYQAKGLLLASIRDKNPVVFFEPKRLY-- 178 Query: 180 KEALGLPVDTG---PLGSAVIRRHGTHATLIAYGPAVTTALEAAEAAAEHGWDLEVIDLR 236 + ++G D LG A + + GT T++A+G + EAA+ AA+ G EVIDLR Sbjct: 179 RASVGEVPDEAYEIELGKAEVVQEGTDITVLAWGAQMEIVEEAAKMAAKKGISCEVIDLR 238 Query: 237 TLMPLDDATVCASVRRTGRAVVVHEAHGFAGPGAEIAARITERCFYHLEAPVRRVTGFDV 296 TL P D TV ASV++TGR V+ HEA G EIAA I + CF +LE+P+ RV G D Sbjct: 239 TLAPWDVDTVAASVKKTGRLVINHEAPLTGGFAGEIAATIQQECFLYLESPISRVCGLDT 298 Query: 297 PYPPPLLERHYLPGVDRILDAV-ASLEW 323 PY P + E+ Y+P + +A+ AS+++ Sbjct: 299 PY-PLIHEKEYMPDALKTFEAIKASMKY 325 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: 296 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: 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