Align Putative branched-chain alpha keto acid dehydrogenase E1 subunit beta (characterized, see rationale)
to candidate RR42_RS10660 RR42_RS10660 pyruvate dehydrogenase
Query= uniprot:G1UHX5 (328 letters) >FitnessBrowser__Cup4G11:RR42_RS10660 Length = 323 Score = 230 bits (587), Expect = 3e-65 Identities = 134/322 (41%), Positives = 182/322 (56%), Gaps = 2/322 (0%) Query: 1 MSEITMAKALNTALRDALRDDPRTILFGEDIGALGGVFRITDGLAAEFGDERCFDTPLAE 60 MS ++ AL ALR+AL +DPR L GED+G GG + ++ GL AEFG ER DTPL+E Sbjct: 1 MSRLSYRDALREALREALANDPRVFLMGEDVGRYGGTYAVSKGLLAEFGPERVRDTPLSE 60 Query: 61 SAILGTAVGMAMYGYRPVVEMQFDAFAYPAFEQLVSHVAKLRNRTRGAIGLPLTIRIPYG 120 G +G A+ G RP+VE+ F+ A +Q+V+ A + + G +PL +R+ G Sbjct: 61 LGFTGAGIGAALGGMRPIVEVMTVNFSLLALDQIVNTAALYHHMSGGQFSVPLVVRMATG 120 Query: 121 GGIGGVEHHSDSSEIYYMATPGLTVVTPATAADAYSLLRRSIASPDPVVFLEPKRLYWRK 180 G HS S E +Y PG+ V+ PAT DA +L ++A PDPV+ E LY + Sbjct: 121 AGRQVAAQHSHSFEGWYAGIPGVKVLAPATIEDARHMLAPALADPDPVLIFEHAALYNME 180 Query: 181 EALGLPVDTGPLGSAVIRRHGTHATLIAYGPAVTTALEAAEAAAEHGWDLEVIDLRTLMP 240 + L V + SA +RR G ++AYG + AL+AA+ A G EVIDLR L P Sbjct: 181 DELP-DVSGVDIRSAKVRREGKDVAIVAYGGTLAKALQAADTLAAKGIAAEVIDLRVLRP 239 Query: 241 LDDATVCASVRRTGRAVVVHEAHGFAGPGAEIAARITERCFYHLEAPVRRVTGFDVPYP- 299 LDDAT+ ASV + RAV+V E AE+ ARI E+ FY L+APV RV +VP P Sbjct: 240 LDDATIMASVAKCRRAVIVDEGWRSGSLAAEVMARIVEQVFYELDAPVARVCSEEVPIPY 299 Query: 300 PPLLERHYLPGVDRILDAVASL 321 +E LP +I+ AV L Sbjct: 300 ARHMEEAALPQAGKIVAAVKQL 321 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: 323 Number of extensions: 18 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: 323 Length adjustment: 28 Effective length of query: 300 Effective length of database: 295 Effective search space: 88500 Effective search space used: 88500 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