Align Putative branched-chain alpha keto acid dehydrogenase E1 subunit beta (characterized, see rationale)
to candidate BWI76_RS14155 BWI76_RS14155 transketolase
Query= uniprot:G1UHX5 (328 letters) >FitnessBrowser__Koxy:BWI76_RS14155 Length = 339 Score = 199 bits (507), Expect = 6e-56 Identities = 128/329 (38%), Positives = 167/329 (50%), Gaps = 15/329 (4%) Query: 5 TMAKALNTALRDALRDDPRTILFGED--------------IGALGGVFRITDGLAAEFGD 50 T +A+ AL + D R +L GED I A GGV +T GL +FG Sbjct: 5 TYREAVKEALAQEMEHDERVVLIGEDLRGGHGGNAPEEARIEAFGGVLGVTKGLWTQFGS 64 Query: 51 ERCFDTPLAESAILGTAVGMAMYGYRPVVEMQFDAFAYPAFEQLVSHVAKLRNRTRGAIG 110 +R DTP+ ESAI+G A G A G RPV E+ F F + + L + AK R G Sbjct: 65 DRVIDTPITESAIVGMAAGAAATGLRPVAELMFMDFFGVSHDALYNQAAKFRYMFGGKAK 124 Query: 111 LPLTIRIPYGGGIGGVEHHSDSSEIYYMATPGLTVVTPATAADAYSLLRRSIASPDPVVF 170 PL +R G G HS S + TPGL VV P+T D LL +SI DPVVF Sbjct: 125 APLVMRGMIGAGFSAAAQHSQSPYNIFATTPGLKVVVPSTPYDVKGLLIQSIRDDDPVVF 184 Query: 171 LEPKRLYWRKEALGLPVDTGPLGSAVIRRHGTHATLIAYGPAVTTALEAAEAAAEHGWDL 230 E K LY K + + T PLG A R G T+IA V A + A+ A G + Sbjct: 185 CEHKMLYDLKGEVPDEIYTIPLGVANYTREGEDVTIIALSAMVHKANQVADKLAREGISV 244 Query: 231 EVIDLRTLMPLDDATVCASVRRTGRAVVVHEAHGFAGPGAEIAARITERCFYHLEAPVRR 290 EV+D RT+ PLD+ + SV TGR V+V E+ G ++AA I + F+ L+AP+ Sbjct: 245 EVVDPRTISPLDEEGILESVASTGRVVIVDESAARFGFAHDVAALIASQAFHFLKAPIVL 304 Query: 291 VTGFDVPYP-PPLLERHYLPGVDRILDAV 318 VT P P P LE+ ++PGV+RI AV Sbjct: 305 VTPPHTPVPFSPALEKLWIPGVERIEAAV 333 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: 281 Number of extensions: 13 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: 339 Length adjustment: 28 Effective length of query: 300 Effective length of database: 311 Effective search space: 93300 Effective search space used: 93300 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