Align Putative branched-chain alpha keto acid dehydrogenase E1 subunit beta (characterized, see rationale)
to candidate SM_b20020 SM_b20020 pyruvate dehydrogenase E1 component, subunits alpha and beta
Query= uniprot:G1UHX5 (328 letters) >FitnessBrowser__Smeli:SM_b20020 Length = 692 Score = 204 bits (518), Expect = 7e-57 Identities = 127/322 (39%), Positives = 171/322 (53%), Gaps = 10/322 (3%) Query: 4 ITMAKALNTALRDALRDDPRTILFGEDIGALGGVFRITDGLAAEFGDERCFDTPLAESAI 63 I M A+ L + + R +LFGEDIG GGV +T GL +FG R FDT L+E I Sbjct: 374 INMVTAIRRTLDHEMTVNQRVVLFGEDIGPKGGVHAVTLGLQEKFGTARVFDTSLSEEGI 433 Query: 64 LGTAVGMAMYGYRPVVEMQFDAFAYPAFEQLVSHVAKLRNRTRGAIGLPLTIRIPYGGGI 123 +G AVGMA+ G PV E+QF +A PA EQL + +R RT P+ +R+ G Sbjct: 434 IGRAVGMALAGLVPVPEIQFRKYAEPAIEQL-NDCGTIRWRTSNRFAAPIVVRMAGGFLK 492 Query: 124 GGVEHHSDSSEIYYMATPGLTVVTPATAADAYSLLRRSIASPDPVVFLEPKRLY---WRK 180 G HS ++E+ ++ PG + P+ A DA LLR ++ DPV+F E + + W + Sbjct: 493 CGDPWHSQTNEVAFVHQPGWKIAVPSNAEDAVGLLRTALRGNDPVIFFEHRAMLDHPWAR 552 Query: 181 EALGLPVDTGPLGSAVIRRHGTHATLIAYGPAVTTALEAAEAAAEHGWDLEVIDLRTLMP 240 P G A R G T++ +G V EAAE G +VIDLRTLMP Sbjct: 553 RPYPGDAFALPFGKAKFTREGRDITIVTWGAMVPRCEEAAE-----GISADVIDLRTLMP 607 Query: 241 LDDATVCASVRRTGRAVVVHEAHGFAGPGAEIAARITERCFYHLEAPVRRVTGFDVPYP- 299 D V ASVRRT R ++VHE AG GAEIAA + + F L+AP+ R+T D+P P Sbjct: 608 WDRKAVIASVRRTRRCLIVHEDLATAGFGAEIAAAVADEAFIDLDAPISRLTMPDIPSPH 667 Query: 300 PPLLERHYLPGVDRILDAVASL 321 P L +P +RI + L Sbjct: 668 NPALLDWAVPSTERIRRKIIDL 689 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: 609 Number of extensions: 28 Number of successful extensions: 4 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: 692 Length adjustment: 33 Effective length of query: 295 Effective length of database: 659 Effective search space: 194405 Effective search space used: 194405 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: 51 (24.3 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