Align β-ketoadipyl-CoA thiolase (EC 2.3.1.174; EC 2.3.1.223) (characterized)
to candidate 3609683 Dshi_3066 acetyl-CoA acetyltransferase (RefSeq)
Query= metacyc::MONOMER-15952 (401 letters) >FitnessBrowser__Dino:3609683 Length = 391 Score = 291 bits (745), Expect = 2e-83 Identities = 172/405 (42%), Positives = 247/405 (60%), Gaps = 20/405 (4%) Query: 1 MNEALIIDAVRTPIGRYAGALASVRADDLGAIPLKALIARHPQLDWSAVDDVIYGCANQA 60 M +I A RT +G + G+ A+ A DLG+ L+AL+AR ++ V + I G Sbjct: 1 MTNVVIASAARTAVGSFGGSFANTPAHDLGSAVLEALVAR-AGIEKGEVSETILGQVLTG 59 Query: 61 GEDNRNVARMAALLAGLPVSVPGTTLNRLCGSGLDAVGSAARALRCGEAGLMLAGGVESM 120 G+ +N AR A + AGLP LN++CGSGL AV A+ ++ G+A ++ AGG E+M Sbjct: 60 GQ-GQNPARQAHINAGLPQESAAWGLNQVCGSGLRAVALGAQHIQLGDAEIVCAGGQENM 118 Query: 121 SRAPFVMG-KSEQAFGRSAEIFDTTIGWRFVNKLMQQG----FGIDSMPETAENVAAQFN 175 + +P V ++ Q G +F++ +++ G F M +TAENVA ++ Sbjct: 119 TLSPHVANLRAGQKMG----------DMKFIDSMIRDGLWDAFNGYHMGQTAENVAEKWQ 168 Query: 176 ISRADQDAFALRSQHKAAAAIANGRLAKEIVAVEIAQRKGPAKIVEHDEHPRGDTTLEQL 235 ISR QD FA+ SQ+KA AA G+ E+VA I RKG +V+ DE+ R T+E + Sbjct: 169 ISREMQDEFAVASQNKAEAAQKAGKFDDEVVAFTIKTRKGDI-VVDKDEYIRHGATMEAM 227 Query: 236 AKLGTPFRQGGSVTAGNASGVNDGACALLLASSEAAQRHGLKARARVVGMATAGVEPRIM 295 KL F + GSVTA NASG+NDGA +LL S+E A++ G+ AR+ ATAG++P IM Sbjct: 228 QKLRPAFTKDGSVTAANASGLNDGAAGVLLMSAENAEKRGITPMARIASYATAGLDPSIM 287 Query: 296 GIGPVPATRKVLELTGLALADMDVIELNEAFAAQGLAVLRELGLADDDERVNPNGGAIAL 355 G+GP+ A+RK LE G + D+D++E NEAFAAQ AV +++G D VN NGGAIA+ Sbjct: 288 GVGPIYASRKALEKAGWKVDDLDLVEANEAFAAQACAVNKDMGW--DPAIVNVNGGAIAI 345 Query: 356 GHPLGMSGARLVTTALHELEERQGRYALCTMCIGVGQGIALIIER 400 GHP+G SGAR++ T L E++ R + L T+CIG G G+AL +ER Sbjct: 346 GHPIGASGARVLNTLLFEMQRRDAKKGLATLCIGGGMGVALCVER 390 Lambda K H 0.319 0.134 0.384 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: 384 Number of extensions: 19 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: 391 Length adjustment: 31 Effective length of query: 370 Effective length of database: 360 Effective search space: 133200 Effective search space used: 133200 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 (21.8 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