Align Putative branched-chain alpha keto acid dehydrogenase E1 subunit beta (characterized, see rationale)
to candidate N515DRAFT_0355 N515DRAFT_0355 pyruvate dehydrogenase E1 component beta subunit
Query= uniprot:G1UHX5 (328 letters) >FitnessBrowser__Dyella79:N515DRAFT_0355 Length = 326 Score = 294 bits (752), Expect = 2e-84 Identities = 154/318 (48%), Positives = 201/318 (63%), Gaps = 1/318 (0%) Query: 1 MSEITMAKALNTALRDALRDDPRTILFGEDIGALGGVFRITDGLAAEFGDERCFDTPLAE 60 M++IT+ +A+ AL + DP ++ GED+G GGVFR T GL +FG+ R DTPL E Sbjct: 1 MAQITLIEAVTQALAYEMARDPSVVVLGEDVGVNGGVFRATQGLQEKFGELRVLDTPLDE 60 Query: 61 SAILGTAVGMAMYGYRPVVEMQFDAFAYPAFEQLVSHVAKLRNRTRGAIGLPLTIRIPYG 120 + I G VGMA G +PV E QF+ F YP EQ+ H A+LRNRTRG I +P R P+G Sbjct: 61 TTIAGVTVGMAAQGMKPVAEAQFEGFIYPMMEQIACHAARLRNRTRGRITVPAVWRAPWG 120 Query: 121 GGIGGVEHHSDSSEIYYMATPGLTVVTPATAADAYSLLRRSIASPDPVVFLEPKRLYWR- 179 GGI EHHS+++E + PGL VV P++ A AY LL +I PDPV+F EPKR+Y + Sbjct: 121 GGIRAPEHHSEANEHLFTNIPGLRVVMPSSPARAYGLLLAAIRDPDPVMFFEPKRIYRQY 180 Query: 180 KEALGLPVDTGPLGSAVIRRHGTHATLIAYGPAVTTALEAAEAAAEHGWDLEVIDLRTLM 239 KE + + PL + R GT T++ +G V ALEAA+ A G EVID+ TL Sbjct: 181 KEEVPDDGEALPLDVCFVLRDGTDVTIVTWGAQVKEALEAADELAAEGISAEVIDVATLT 240 Query: 240 PLDDATVCASVRRTGRAVVVHEAHGFAGPGAEIAARITERCFYHLEAPVRRVTGFDVPYP 299 PLD T+ SV++TGR V+VHEA AG GAEIAAR+ E C Y L APV RVTG+D P Sbjct: 241 PLDFDTIAESVQKTGRCVIVHEAPKTAGFGAEIAARVAEECLYELLAPVERVTGYDTHIP 300 Query: 300 PPLLERHYLPGVDRILDA 317 LE Y+P +R+++A Sbjct: 301 LFRLEMKYMPSTERVVEA 318 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: 309 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: 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