Align Putative branched-chain alpha keto acid dehydrogenase E1 subunit beta (characterized, see rationale)
to candidate CA265_RS18860 CA265_RS18860 alpha-ketoacid dehydrogenase subunit beta
Query= uniprot:G1UHX5 (328 letters) >FitnessBrowser__Pedo557:CA265_RS18860 Length = 328 Score = 206 bits (523), Expect = 8e-58 Identities = 119/320 (37%), Positives = 175/320 (54%), Gaps = 2/320 (0%) Query: 1 MSEITMAKALNTALRDALRDDPRTILFGEDIGALGGVFRITDGLAAEFGDERCFDTPLAE 60 M EI +AL A+ + +R D R L GE++ G ++++ G+ EFG +R DTP+AE Sbjct: 1 MREIQFREALREAMSEEMRKDDRVFLLGEEVAEYNGAYKVSQGMLDEFGAKRIIDTPIAE 60 Query: 61 SAILGTAVGMAMYGYRPVVEMQFDAFAYPAFEQLVSHVAKLRNRTRGAIGLPLTIRIPYG 120 G A G A G P+VE F+ A +Q+++ AK+ + + G P+ R P G Sbjct: 61 LGFAGIATGAATAGLIPIVEFMTFNFSLVAIDQIINGAAKILSMSGGQFSCPMVFRGPTG 120 Query: 121 GGIGGVEHHSDSSEIYYMATPGLTVVTPATAADAYSLLRRSIASPDPVVFLEPKRLYWRK 180 HS + E ++ TPGL VV PAT DA LL++SI DPV+F+E + +Y K Sbjct: 121 NAGQLGAQHSQNFENWFANTPGLKVVVPATPYDAKGLLKQSIIDQDPVIFMESEVMYGDK 180 Query: 181 EALGLPVDTGPLGSAVIRRHGTHATLIAYGPAVTTALE-AAEAAAEHGWDLEVIDLRTLM 239 + LG A + + GT T++ +G +T + A E + G ++EVIDLRT+ Sbjct: 181 GDVPAEEYYIELGKANVTKQGTDVTIVTFGKMLTRVVNPAVEELTKEGINVEVIDLRTVR 240 Query: 240 PLDDATVCASVRRTGRAVVVHEAHGFAGPGAEIAARITERCFYHLEAPVRRVTGFDVPYP 299 P+D T+ ASV++T R VVV EA A EIA + + F +L+APV R+T DVP P Sbjct: 241 PIDYDTIIASVKKTNRLVVVEEAWPLASLSGEIAFMVQKHAFDYLDAPVLRITCADVPLP 300 Query: 300 -PPLLERHYLPGVDRILDAV 318 P L LP +R++ AV Sbjct: 301 YSPTLIAASLPNAERVVKAV 320 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: 260 Number of extensions: 10 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: 328 Length adjustment: 28 Effective length of query: 300 Effective length of database: 300 Effective search space: 90000 Effective search space used: 90000 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