Align Putative branched-chain alpha keto acid dehydrogenase E1 subunit beta (characterized, see rationale)
to candidate WP_005456121.1 SACCYDRAFT_RS10830 alpha-ketoacid dehydrogenase subunit beta
Query= uniprot:G1UHX5 (328 letters) >NCBI__GCF_000244975.1:WP_005456121.1 Length = 330 Score = 235 bits (600), Expect = 1e-66 Identities = 142/322 (44%), Positives = 185/322 (57%), Gaps = 6/322 (1%) Query: 1 MSEITMAKALNTALRDALRDDPRTILFGEDIGALGGVFRITDGLAAEFGDERCFDTPLAE 60 M I+ +AL LR+ LR D +L GE+IG GG ++IT GL EFG++R DTP+AE Sbjct: 1 MPVISYREALRNTLREELRRDDDVLLIGEEIGVFGGSYKITSGLLEEFGEKRVRDTPIAE 60 Query: 61 SAILGTAVGMAMYGYRPVVEMQFDAFAYPAFEQLVSHVAKLRNRTRGAIGLPLTIRIPYG 120 +G AVG AM G RP+VE+ F+ A +Q+V+H AK+ G +P+ IR P G Sbjct: 61 EGFVGAAVGAAMLGLRPIVEIMTINFSLLALDQIVNHAAKIYGMFGGQTSVPMVIRTPGG 120 Query: 121 GGIGGVEHHSDSSEIYYMATPGLTVVTPATAADAYSLLRRSIASPDPVVFLEPKRLYWRK 180 GG HS + E+YY PGL VV P+T ADA +LL ++ DPV+FLE LY K Sbjct: 121 GGQQLGATHSQNIELYYAFVPGLKVVAPSTPADARALLLAAVRDDDPVLFLENLALYNTK 180 Query: 181 EALGLPVDTGP--LGSAVIRRHGTHATLIAYGPAVTTALEAAEAAA-EHGWDLEVIDLRT 237 +P D GP +G A + R GT T++ Y A+E A+ E G EVIDLR+ Sbjct: 181 GE--VPDDLGPAEIGRAAVVREGTDITIVGYSRMAAVAVEVADRLRDESGVSAEVIDLRS 238 Query: 238 LMPLDDATVCASVRRTGRAVVVHEAHGFAGPGAEIAARITERCFYHLEAPVRRVTGFDVP 297 L PLD T+ AS RRTG VV + G GAEIAA I++ F HL+APVRRV +VP Sbjct: 239 LRPLDRETLVASARRTGCVVVAEDDWLTYGVGAEIAASISDGAFDHLDAPVRRVAAAEVP 298 Query: 298 YP-PPLLERHYLPGVDRILDAV 318 P LE LP + + AV Sbjct: 299 LPYAKPLETAALPSAESLHTAV 320 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: 306 Number of extensions: 12 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: 330 Length adjustment: 28 Effective length of query: 300 Effective length of database: 302 Effective search space: 90600 Effective search space used: 90600 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: 49 (23.5 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