Align Beta-ketoadipyl-CoA thiolase; 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized)
to candidate 3606642 Dshi_0074 acetyl-CoA acetyltransferase (RefSeq)
Query= SwissProt::Q8VPF1 (401 letters) >FitnessBrowser__Dino:3606642 Length = 392 Score = 280 bits (716), Expect = 5e-80 Identities = 171/403 (42%), Positives = 243/403 (60%), Gaps = 18/403 (4%) Query: 3 REVYICDAVRTPIGRFGGSLAAVRADDLAAVPVKALVERNPQVDWSQLDEVYLGCANQAG 62 R V IC A RTP+G F G + V A L + + + V +Q++E+ +GC AG Sbjct: 2 RTVAICGAARTPMGGFQGVFSDVSAAQLGGAAIAGALA-DAGVAPAQVNELLMGCVLPAG 60 Query: 63 EDNRNVARMALLLAGLPDSVPGVTLNRLCASGMDAVGTAFRAIASGEAELVIAGGVESMS 122 + + AR A AGL D+VP TLN++C SGM A A IA G+++LV+AGG+ESM+ Sbjct: 61 Q-GQAPARQAGYAAGLGDAVPATTLNKMCGSGMKAAMIACDQIALGQSDLVVAGGMESMT 119 Query: 123 RAPYVMGK--ADSAFGRGQKIEDTTIGWRFINPLMKAQYGVDAMPETADNVADDYKVSRA 180 APY++ K + G GQ I+ F++ L A M A++ A+ ++ +RA Sbjct: 120 NAPYLLDKMRGGARIGHGQVIDHM-----FLDGLEDAYDKGRLMGTFAEDCAEAFQFTRA 174 Query: 181 DQDAFALRSQQLAGRAQAAGYFAEEIVPVVIKGKKGETVVDADEH---LRPDTTLEALAK 237 QD +AL S + A A+A+ FA E+VPV + G+KGETVV DE RP E + Sbjct: 175 AQDTYALGSLENALAAEASEAFAMELVPVTVSGRKGETVVIRDEQPAAARP----EKIPH 230 Query: 238 LKPVNGPDKTVTAGNASGVNDGSVALILASAEAVKKHGLKARAKVLGMASAGVAPRVMGI 297 LKP D TVTA N+S ++DG+ AL+LA A + HGL RA+VLG AS P + Sbjct: 231 LKPAFRKDGTVTAANSSSISDGAAALVLADAGQAEAHGLPVRARVLGHASHAQKPALFPT 290 Query: 298 GPVPAVRKLLERLNLSVADFDVIELNEAFAAQGLAVTRELGIADDDARVNPNGGAIALGH 357 PVPA RKLL+RL VAD D+ E+NEAFA +A E+G+ + ++N NGGA ALGH Sbjct: 291 APVPAARKLLDRLGWCVADVDLWEVNEAFAVVPMAFMHEMGVPRE--KMNVNGGACALGH 348 Query: 358 PLGASGARLVLTAVHQLEKSGGQRGLCTMCVGVGQGVALAVER 400 P+GASGAR+++T ++ +E +RG+ +C+G G+G A+A+ER Sbjct: 349 PIGASGARILVTLLNAMEARDLKRGVAAICIGGGEGTAIALER 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: 433 Number of extensions: 24 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: 392 Length adjustment: 31 Effective length of query: 370 Effective length of database: 361 Effective search space: 133570 Effective search space used: 133570 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