Align Putative branched-chain alpha keto acid dehydrogenase E1 subunit beta (characterized, see rationale)
to candidate Synpcc7942_0143 Synpcc7942_0143 pyruvate/2-oxoglutarate dehydrogenase complex dehydrogenase (E1) component
Query= uniprot:G1UHX5 (328 letters) >FitnessBrowser__SynE:Synpcc7942_0143 Length = 326 Score = 191 bits (484), Expect = 3e-53 Identities = 117/299 (39%), Positives = 161/299 (53%), Gaps = 1/299 (0%) Query: 1 MSEITMAKALNTALRDALRDDPRTILFGEDIGALGGVFRITDGLAAEFGDERCFDTPLAE 60 M+E M AL A+ + + DP + GED+G GG +++T L ++GD R DTP+AE Sbjct: 1 MAETFMFNALRAAIDEEMARDPNVFVLGEDVGHYGGSYKVTKDLYQKYGDFRLLDTPIAE 60 Query: 61 SAILGTAVGMAMYGYRPVVEMQFDAFAYPAFEQLVSHVAKLRNRTRGAIGLPLTIRIPYG 120 + G AVG AM G RP+VE F AF Q+ ++ A LR + G +P+ R P G Sbjct: 61 NGFTGMAVGAAMTGLRPIVEGMNMGFLLLAFNQIANN-AMLRYTSGGNFTIPIVFRGPGG 119 Query: 121 GGIGGVEHHSDSSEIYYMATPGLTVVTPATAADAYSLLRRSIASPDPVVFLEPKRLYWRK 180 G HS E Y+ A PGL +V +T +A LL+ +I +PV+F E LY K Sbjct: 120 VGRQLGAEHSQRLEAYFHAVPGLKIVACSTPYNAKGLLKAAIRDNNPVLFFEHVLLYNLK 179 Query: 181 EALGLPVDTGPLGSAVIRRHGTHATLIAYGPAVTTALEAAEAAAEHGWDLEVIDLRTLMP 240 E L PL A I R G T++ Y L+A + + G+D EVIDL +L P Sbjct: 180 EDLPDEEYICPLDKAEIVRPGKDVTVLTYSRMRYHCLQAVKTLEKEGFDPEVIDLISLKP 239 Query: 241 LDDATVCASVRRTGRAVVVHEAHGFAGPGAEIAARITERCFYHLEAPVRRVTGFDVPYP 299 D + ASVR+T R V+V E G AE++A I ERCF L+APV R++ D+P P Sbjct: 240 FDFEAIEASVRKTHRVVIVEECMKTGGIAAELSAAIMERCFDELDAPVVRLSSQDIPTP 298 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: 268 Number of extensions: 17 Number of successful extensions: 3 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: 326 Length adjustment: 28 Effective length of query: 300 Effective length of database: 298 Effective search space: 89400 Effective search space used: 89400 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: 48 (23.1 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