Align Putative branched-chain alpha keto acid dehydrogenase E1 subunit beta (characterized, see rationale)
to candidate AO353_19955 AO353_19955 pyruvate dehydrogenase
Query= uniprot:G1UHX5 (328 letters) >FitnessBrowser__pseudo3_N2E3:AO353_19955 Length = 326 Score = 221 bits (563), Expect = 2e-62 Identities = 135/318 (42%), Positives = 177/318 (55%), Gaps = 2/318 (0%) Query: 5 TMAKALNTALRDALRDDPRTILFGEDIGALGGVFRITDGLAAEFGDERCFDTPLAESAIL 64 T +AL ALR+AL+ DPR L GED+G GG + ++ GL FG ER D PL+E + Sbjct: 6 TYREALREALREALQRDPRVFLMGEDVGRYGGSYAVSLGLLEAFGPERIRDAPLSELGFV 65 Query: 65 GTAVGMAMYGYRPVVEMQFDAFAYPAFEQLVSHVAKLRNRTRGAIGLPLTIRIPYGGGIG 124 G +G A+ G RP+VE+ F+ A + L++ A LR+ + G +PL +R+ G G Sbjct: 66 GAGIGAALGGMRPIVEIMTVNFSLLALDPLMNTAAALRHMSGGQFSVPLVVRMATGAGRQ 125 Query: 125 GVEHHSDSSEIYYMATPGLTVVTPATAADAYSLLRRSIASPDPVVFLEPKRLYWRKEALG 184 HS S E +Y PGL ++ PAT DA +L ++ PDPV+ E +LY + G Sbjct: 126 LAAQHSHSLEGWYAHIPGLKILAPATVEDARGMLWPALLDPDPVLIFEHAQLYSLEGETG 185 Query: 185 LPVDTGPLGSAVIRRHGTHATLIAYGPAVTTALEAAEAAAEHGWDLEVIDLRTLMPLDDA 244 T + SA +RR G TLIAYG + AL AAE A G D EVIDLR L PLDD Sbjct: 186 -EWQTLDISSAKVRRAGKDLTLIAYGGTLGKALAAAEQLAGEGIDCEVIDLRVLRPLDDQ 244 Query: 245 TVCASVRRTGRAVVVHEAHGFAGPGAEIAARITERCFYHLEAPVRRVTGFDVPYP-PPLL 303 T+ ASV +T RA+VV E AEI RI E+ F+ L+AP RV +VP P P L Sbjct: 245 TIMASVCKTRRALVVDEGWRSGSLSAEIITRIVEQGFFELDAPPSRVCSAEVPIPYPRHL 304 Query: 304 ERHYLPGVDRILDAVASL 321 E LP V I+ A L Sbjct: 305 EEAALPQVSTIVAAAREL 322 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: 315 Number of extensions: 16 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: 326 Length adjustment: 28 Effective length of query: 300 Effective length of database: 298 Effective search space: 89400 Effective search space used: 89400 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