Align subunit of β-ketoadipyl CoA thiolase (EC 2.3.1.174; EC 2.3.1.16) (characterized)
to candidate 3609683 Dshi_3066 acetyl-CoA acetyltransferase (RefSeq)
Query= metacyc::MONOMER-3207 (400 letters) >FitnessBrowser__Dino:3609683 Length = 391 Score = 300 bits (767), Expect = 6e-86 Identities = 169/402 (42%), Positives = 244/402 (60%), Gaps = 15/402 (3%) Query: 1 MRDVFICDAIRTPIGRFGGALAGVRADDLAAVPLKALIEPNPAVQWDQVDEVFFGCANQA 60 M +V I A RT +G FGG+ A A DL + L+AL+ ++ +V E G Sbjct: 1 MTNVVIASAARTAVGSFGGSFANTPAHDLGSAVLEALVA-RAGIEKGEVSETILGQVLTG 59 Query: 61 GEDNRNVARMALLLAGLPESIPGVTLNRLCASGMDAIGTAFRAIASGEMELAIAGGVESM 120 G+ +N AR A + AGLP+ LN++C SG+ A+ + I G+ E+ AGG E+M Sbjct: 60 GQ-GQNPARQAHINAGLPQESAAWGLNQVCGSGLRAVALGAQHIQLGDAEIVCAGGQENM 118 Query: 121 SRAPFVMGKAESGYSRNMKLEDTTIG---WRFINPLMKSQYGVDSMPETADNVADDYQVS 177 + +P V +MK D+ I W N M +TA+NVA+ +Q+S Sbjct: 119 TLSPHVANLRAGQKMGDMKFIDSMIRDGLWDAFNGY--------HMGQTAENVAEKWQIS 170 Query: 178 RADQDAFALRSQQKAAAAQAAGFFAEEIVPVRIAHKKGETIVERDEHLRPETTLEALTKL 237 R QD FA+ SQ KA AAQ AG F +E+V I +KG+ +V++DE++R T+EA+ KL Sbjct: 171 REMQDEFAVASQNKAEAAQKAGKFDDEVVAFTIKTRKGDIVVDKDEYIRHGATMEAMQKL 230 Query: 238 KPVNGPDKTVTAGNASGVNDGAAALILASAEAVKKHGLTPRARVLGMASGGVAPRVMGIG 297 +P D +VTA NASG+NDGAA ++L SAE +K G+TP AR+ A+ G+ P +MG+G Sbjct: 231 RPAFTKDGSVTAANASGLNDGAAGVLLMSAENAEKRGITPMARIASYATAGLDPSIMGVG 290 Query: 298 PVPAVRKLTERLGVAVSDFDVIELNEAFASQGLAVLRELGVADDAPQVNPNGGAIALGHP 357 P+ A RK E+ G V D D++E NEAFA+Q AV +++G D VN NGGAIA+GHP Sbjct: 291 PIYASRKALEKAGWKVDDLDLVEANEAFAAQACAVNKDMGW--DPAIVNVNGGAIAIGHP 348 Query: 358 LGMSGARLVLTALHQLEKSGGRKGLATMCVGVGQGLALAIER 399 +G SGAR++ T L ++++ +KGLAT+C+G G G+AL +ER Sbjct: 349 IGASGARVLNTLLFEMQRRDAKKGLATLCIGGGMGVALCVER 390 Lambda K H 0.318 0.134 0.383 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: 395 Number of extensions: 18 Number of successful extensions: 4 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: 400 Length of database: 391 Length adjustment: 31 Effective length of query: 369 Effective length of database: 360 Effective search space: 132840 Effective search space used: 132840 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 (21.7 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