Align 3-ketoacyl-CoA thiolase [isoleucine degradation] (EC 2.3.1.16) (characterized)
to candidate WP_004512526.1 GMET_RS16550 acetyl-CoA C-acyltransferase
Query= reanno::MR1:200842 (396 letters) >NCBI__GCF_000012925.1:WP_004512526.1 Length = 391 Score = 390 bits (1003), Expect = e-113 Identities = 204/387 (52%), Positives = 261/387 (67%) Query: 9 EIVIVAAKRTPMGSFQGSLSGITSLSLAATAIKALLADTQVAPDKVDEVLMGCVLPAGLG 68 EI +V A RTP GSF G L+ + + LAAT +K LLA +APD V+EV++G VL G G Sbjct: 3 EIFVVDALRTPFGSFSGMLADVDAPKLAATVMKELLAKAGLAPDTVNEVIVGQVLSGGCG 62 Query: 69 QAPARQATLGAGLPLSVGATTVNKVCGSGMKTVMLAHDLIKAGSAKVVIAGGMESMSQAP 128 QAPARQA GAG+P + A TVNKVCGSG+K +ML D I+ G +++VIAGGME+MS AP Sbjct: 63 QAPARQAMRGAGIPDTAHALTVNKVCGSGLKAIMLGADSIRLGESQIVIAGGMENMSLAP 122 Query: 129 YLLDKARAGIRMGHGKVLDHMFLDGLEDAYTGGAMGTFAQKTADEFGITREQMDAFALSS 188 + L KARAG RMGH ++LD + DGL+D YTG MG + +A+ ++RE+ DAFA S Sbjct: 123 FFLKKARAGYRMGHSELLDLLIYDGLQDPYTGRHMGEIGEASAERGNLSREEQDAFARRS 182 Query: 189 LEKANAAINSGAFKTEIVPVTVSDRRGDVTIDTDEQPGNARPEKIPTLRPAFAKDGTITA 248 E A AA+ F EIVPV ++GD TI TDE+P P K+P+LR AF KDGTITA Sbjct: 183 YELAQAAVTGRIFADEIVPVVKKGKKGDETIGTDEEPFKGDPSKLPSLRAAFKKDGTITA 242 Query: 249 ANSSSISDGAAALMLTTRANAEQLGLTVLATIKGHTTHAQEPALFTTAPVGAMAKLLSNV 308 N+S+I+DGAA +LT ++ LT A I T ++ P F AP+GA+ K + Sbjct: 243 GNASTINDGAALALLTDADGLKKYNLTPKARIVASATESRHPDNFPEAPIGAIEKACAKA 302 Query: 309 GWSKDEVDLFEINEAFAMVTMLAVSELGLDMTKVNVNGGACALGHPIGCSGARLLVTLIH 368 G + ++DLFEINEAFA V +LAV LGL + KVNVNGGACA+GHPIG SG RL T+I Sbjct: 303 GLTVSDIDLFEINEAFASVALLAVKGLGLPLDKVNVNGGACAIGHPIGASGGRLAATVIR 362 Query: 369 ALKARGLKRGVASLCIGGGEATAMAIE 395 L R + G+A+LCIGGGEA A+ E Sbjct: 363 ELHRRQKRYGLATLCIGGGEAVAVIFE 389 Lambda K H 0.316 0.131 0.364 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: 464 Number of extensions: 14 Number of successful extensions: 1 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: 396 Length of database: 391 Length adjustment: 31 Effective length of query: 365 Effective length of database: 360 Effective search space: 131400 Effective search space used: 131400 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Sep 24 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