Align Putative branched-chain alpha keto acid dehydrogenase E1 subunit beta (characterized, see rationale)
to candidate WP_055434954.1 ASC41_RS01930 pyruvate dehydrogenase complex E1 component subunit beta
Query= uniprot:G1UHX5 (328 letters) >NCBI__GCF_001418085.1:WP_055434954.1 Length = 325 Score = 201 bits (512), Expect = 2e-56 Identities = 113/327 (34%), Positives = 178/327 (54%), Gaps = 5/327 (1%) Query: 1 MSEITMAKALNTALRDALRDDPRTILFGEDIGALGGVFRITDGLAAEFGDERCFDTPLAE 60 M I +A+ A+ + +R D L GE++ G ++ + G+ EFG +R DTP+AE Sbjct: 1 MKTIQFREAICEAMSEEMRRDESIYLMGEEVAEYNGAYKASKGMLDEFGAKRVIDTPIAE 60 Query: 61 SAILGTAVGMAMYGYRPVVEMQFDAFAYPAFEQLVSHVAKLRNRTRGAIGLPLTIRIPYG 120 G A+G M G RP+VE F+ +Q++++ AK+R + G + P+ R P G Sbjct: 61 LGFAGIAIGSTMTGNRPIVEYMTFNFSLVGIDQIINNAAKIRQMSGGQLKCPIVFRGPTG 120 Query: 121 --GGIGGVEHHSDSSEIYYMATPGLTVVTPATAADAYSLLRRSIASPDPVVFLEPKRLYW 178 G +G HS + E ++ TPGL VV P+ DA LL+ +I DPV+F+E +++Y Sbjct: 121 SAGQLGAT--HSQAFESWFANTPGLKVVVPSNPYDAKGLLKAAIRDDDPVIFMESEQMYG 178 Query: 179 RKEALGLPVDTGPLGSAVIRRHGTHATLIAYGPAVTTALEAAEAAAEHGWDLEVIDLRTL 238 K + T PLG A I+R GT T++++G + A +AA+ A+ G E+IDLRT+ Sbjct: 179 DKGEVPEGEYTIPLGVADIKREGTDVTIVSFGKIIKEAYKAADELAKEGISCEIIDLRTV 238 Query: 239 MPLDDATVCASVRRTGRAVVVHEAHGFAGPGAEIAARITERCFYHLEAPVRRVTGFDVPY 298 PLD V SV++T R VV+ EA F E+ + F +L+APV ++ D P Sbjct: 239 RPLDKEAVLKSVKKTNRLVVLEEAWPFGNVSTELTYIVQSEAFDYLDAPVVKINTADTPA 298 Query: 299 P-PPLLERHYLPGVDRILDAVASLEWE 324 P P+L +LP ++ AV + ++ Sbjct: 299 PYSPVLLAEWLPDYTEVIKAVKKVMYK 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: 251 Number of extensions: 10 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: 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 24 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