Align Beta-ketoadipyl-CoA thiolase; 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized)
to candidate Dsui_0976 Dsui_0976 acetyl-CoA acetyltransferase
Query= SwissProt::Q8VPF1 (401 letters) >FitnessBrowser__PS:Dsui_0976 Length = 393 Score = 243 bits (621), Expect = 5e-69 Identities = 153/401 (38%), Positives = 226/401 (56%), Gaps = 12/401 (2%) Query: 1 MSREVYICDAVRTPIGRFGGSLAAVRADDLAAVPVKALVERNPQVDWSQLDEVYLGCANQ 60 MS + I RTP+G F G ++ A L A +KA VER + Q++EV G Q Sbjct: 1 MSDPIVIVSVARTPMGGFQGDFNSLTAPQLGATAIKAAVER-AGIKPEQVEEVVFGNVLQ 59 Query: 61 AGEDNRNVARMALLLAGLPDSVPGVTLNRLCASGMDAVGTAFRAIASGEAELVIAGGVES 120 AG + AR A L AGLP S T++++C S + +V ++ +G E+ +AGG ES Sbjct: 60 AGV-GQAPARQAALGAGLPLSAGCTTIHKVCGSALKSVMMVHDSLLAGSYEIGVAGGQES 118 Query: 121 MSRAPYVMGKADSAF--GRGQKIEDTTIGWRFINPLMKAQYGVDAMPETADNVADDYKVS 178 MS APY++ KA + G GQ ++ F + L A M A+ A+ Y + Sbjct: 119 MSNAPYLLPKARGGYRLGHGQLLDHM-----FFDGLEDAYQKGRLMGTFAEECAESYGFT 173 Query: 179 RADQDAFALRSQQLAGRAQAAGYFAEEIVPVVIKGKKGETVVDADEHLRPDTTLEALAKL 238 R QD +A++S A +A G F EI PV I GKKG+ VVD DE +E + L Sbjct: 174 REAQDEWAIQSTVRAQKAIKEGLFKWEIAPVTIAGKKGDVVVDQDEQPLK-AQIEKIPAL 232 Query: 239 KPVNGPDKTVTAGNASGVNDGSVALILASAEAVKKHGLKARAKVLGMASAGVAPRVMGIG 298 KP D TVTA N+S ++DG+ AL+L K GL AK++G + P + Sbjct: 233 KPAFKKDGTVTAANSSSISDGAAALVLMKESKAKVLGLAPIAKIVGHTTHAQEPNLFTTA 292 Query: 299 PVPAVRKLLERLNLSVADFDVIELNEAFAAQGLAVTRELGIADDDARVNPNGGAIALGHP 358 PV A+ KL+++ +VAD D+ E+NEAFA +A ++L + D A+VN +GGA ALGHP Sbjct: 293 PVFAMEKLMQKTGWNVADVDLWEINEAFAVVTMAAIKDLKL--DPAKVNVHGGACALGHP 350 Query: 359 LGASGARLVLTAVHQLEKSGGQRGLCTMCVGVGQGVALAVE 399 +GASGAR+++T + L++ G ++G+ ++C+G G+ VA+ VE Sbjct: 351 IGASGARILVTLIGALKQYGKKKGVASLCIGGGEAVAVGVE 391 Lambda K H 0.317 0.134 0.379 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: 392 Number of extensions: 16 Number of successful extensions: 5 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: 401 Length of database: 393 Length adjustment: 31 Effective length of query: 370 Effective length of database: 362 Effective search space: 133940 Effective search space used: 133940 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 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