Align Putative branched-chain alpha keto acid dehydrogenase E1 subunit beta (characterized, see rationale)
to candidate GFF1390 Psest_1427 Pyruvate/2-oxoglutarate dehydrogenase complex, dehydrogenase (E1) component, eukaryotic type, beta subunit
Query= uniprot:G1UHX5 (328 letters) >FitnessBrowser__psRCH2:GFF1390 Length = 340 Score = 187 bits (476), Expect = 2e-52 Identities = 121/332 (36%), Positives = 177/332 (53%), Gaps = 10/332 (3%) Query: 3 EITMAKALNTALRDALRDDPRTILFGEDIGALGGVFRITDGLAAEFGDERCFDTPLAESA 62 ++T+A+A+ A+ +R DP+ + GEDIG LGGVF T GL EFG R DTP++E+A Sbjct: 9 KLTVARAMAEAVAQEMRLDPKVFVMGEDIGQLGGVFGNTRGLYEEFGKTRIRDTPISETA 68 Query: 63 ILGTAVGMAMYGYRPVVEMQFDAFAYPAFEQLVSHVAKLRNRTRGAIGLPLTIRIPYGGG 122 +G AVG A G RP+VE+ F F + + + +AK + G + +P+ + G G Sbjct: 69 FIGAAVGAASDGMRPIVELMFVDFFGVCMDAIYNLMAKNTYFSGGKVPVPMVLMASTGAG 128 Query: 123 IGGVEHHSDSSEIYYMATPGLTVVTPATAADAYSLLRRSIASPDPVVFLEPKRLY---W- 178 HS + PG+ VV P+ A DA L+ +I +PVV+L K L W Sbjct: 129 YSDAGQHSQCLYGTFAHLPGMKVVVPSNAYDAKGLMTAAIRDDNPVVYLFHKALQGMGWL 188 Query: 179 -RKEALGLPVDTGP----LGSAVIRRHGTHATLIAYGPAVTTALEAAEAAAEHGWDLEVI 233 ++ +PV P +G A R G +L++ G V AL AA + G EVI Sbjct: 189 GTEKGATVPVPEEPYIVEIGKAKTVREGRDVSLVSLGAGVHHALRAAAQLEKDGVSAEVI 248 Query: 234 DLRTLMPLDDATVCASVRRTGRAVVVHEAHGFAGPGAEIAARITERCFYHLEAPVRRVTG 293 DLR+L+PLD V ASVR+TGR +V+ E + G EI A + E L+A +RV Sbjct: 249 DLRSLVPLDREHVIASVRKTGRLIVIDEDYHSFGVSGEIIASVVEHDIGMLKARPQRVAF 308 Query: 294 FDVPYP-PPLLERHYLPGVDRILDAVASLEWE 324 D+P P P++E+ LP D+I+ A ++ E Sbjct: 309 PDIPIPFTPVMEQWALPNADKIVAAYHAMHKE 340 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: 278 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: 340 Length adjustment: 28 Effective length of query: 300 Effective length of database: 312 Effective search space: 93600 Effective search space used: 93600 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 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