Align Putative branched-chain alpha keto acid dehydrogenase E1 subunit beta (characterized, see rationale)
to candidate GFF1732 PGA1_c17560 pyruvate dehydrogenase E1 component subunit beta
Query= uniprot:G1UHX5 (328 letters) >FitnessBrowser__Phaeo:GFF1732 Length = 461 Score = 206 bits (524), Expect = 9e-58 Identities = 120/323 (37%), Positives = 174/323 (53%), Gaps = 2/323 (0%) Query: 3 EITMAKALNTALRDALRDDPRTILFGEDIGALGGVFRITDGLAAEFGDERCFDTPLAESA 62 + T+ +AL A+ + +R D L GE++G G ++I+ GL EFG +R DTP+ E Sbjct: 138 QTTVREALRDAMAEEMRGDEDVFLMGEEVGEYQGAYKISQGLLDEFGPKRVIDTPITEHG 197 Query: 63 ILGTAVGMAMYGYRPVVEMQFDAFAYPAFEQLVSHVAKLRNRTRGAIGLPLTIRIPYGGG 122 G A G A G RP+VE FA A + +++ AK + G +G P+ R P G Sbjct: 198 FAGIATGAAFGGLRPIVEFMTFNFAMQAIDHIINSAAKTLYMSGGQMGAPMVFRGPNGAA 257 Query: 123 IGGVEHHSDSSEIYYMATPGLTVVTPATAADAYSLLRRSIASPDPVVFLEPKRLYWRK-E 181 HS +YM PGL V P +A+DA L++ +I +PV+FLE + LY + + Sbjct: 258 ARVGAQHSQDYAAWYMQIPGLKVAMPYSASDAKGLMKTAIRDNNPVIFLENEILYGKSFD 317 Query: 182 ALGLPVDTGPLGSAVIRRHGTHATLIAYGPAVTTALEAAEAAAEHGWDLEVIDLRTLMPL 241 L T P G A I R G T++++G +T ALEAAE AE G EVIDLRTL P+ Sbjct: 318 VPKLDDYTVPFGKARIWRKGEDVTIVSFGIGMTYALEAAEKLAEDGISAEVIDLRTLRPM 377 Query: 242 DDATVCASVRRTGRAVVVHEAHGFAGPGAEIAARITERCFYHLEAPVRRVTGFDVPYP-P 300 D ++ SV +T R V V E G+ I++ + + F +L+APV TG DVP P Sbjct: 378 DTGSIIKSVMKTNRLVTVEEGWPQGSVGSYISSVVMQEAFDYLDAPVITCTGKDVPMPYA 437 Query: 301 PLLERHYLPGVDRILDAVASLEW 323 LE+H L D +++AV + + Sbjct: 438 ANLEKHALVTTDEVIEAVKQVTY 460 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: 374 Number of extensions: 17 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: 461 Length adjustment: 30 Effective length of query: 298 Effective length of database: 431 Effective search space: 128438 Effective search space used: 128438 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 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