Align Putative branched-chain alpha keto acid dehydrogenase E1 subunit beta (characterized, see rationale)
to candidate WP_067911130.1 AQZ52_RS12405 pyruvate dehydrogenase complex E1 component subunit beta
Query= uniprot:G1UHX5 (328 letters) >NCBI__GCF_001519075.1:WP_067911130.1 Length = 454 Score = 204 bits (519), Expect = 3e-57 Identities = 124/320 (38%), Positives = 167/320 (52%), Gaps = 2/320 (0%) Query: 1 MSEITMAKALNTALRDALRDDPRTILFGEDIGALGGVFRITDGLAAEFGDERCFDTPLAE 60 M T+ +AL A+ + +R D R + GE++ G +++T GL EFG R DTP+ E Sbjct: 129 MVATTVREALRDAMAEEMRADDRVFVMGEEVAEYQGAYKVTQGLLEEFGPRRVIDTPITE 188 Query: 61 SAILGTAVGMAMYGYRPVVEMQFDAFAYPAFEQLVSHVAKLRNRTRGAIGLPLTIRIPYG 120 G G AM G RP+VE FA A + +++ AK + G + P+ R P G Sbjct: 189 YGFAGIGTGAAMGGLRPIVEFMTFNFAMQAIDHIINSAAKTNYMSGGQMRCPIVFRGPNG 248 Query: 121 GGIGGVEHHSDSSEIYYMATPGLTVVTPATAADAYSLLRRSIASPDPVVFLEPKRLYWRK 180 HS + +Y + PGL V+ P AADA LL+ +I S DPVVFLE + +Y R Sbjct: 249 AASRVGAQHSQNYAPWYASVPGLVVIAPYDAADAKGLLKSAIRSEDPVVFLENELVYGRT 308 Query: 181 -EALGLPVDTGPLGSAVIRRHGTHATLIAYGPAVTTALEAAEAAAEHGWDLEVIDLRTLM 239 + L T P+G A R G T+++Y + ALEAAE A G + EVIDLRTL Sbjct: 309 FDVPALDDYTVPIGKARTMRAGRDVTIVSYSIGIALALEAAEKLAAEGIEAEVIDLRTLR 368 Query: 240 PLDDATVCASVRRTGRAVVVHEAHGFAGPGAEIAARITERCFYHLEAPVRRVTGFDVPYP 299 PLD V S+ RT R VVV E +EI + + E F HL+APV RV DVP P Sbjct: 369 PLDKDAVLESLARTNRMVVVEEGFPVCSIASEIISLVMEEGFDHLDAPVLRVCNEDVPLP 428 Query: 300 -PPLLERHYLPGVDRILDAV 318 LE+ L R++ AV Sbjct: 429 YAANLEKLALVDTARVIAAV 448 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: 429 Number of extensions: 29 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: 454 Length adjustment: 30 Effective length of query: 298 Effective length of database: 424 Effective search space: 126352 Effective search space used: 126352 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: 50 (23.9 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