Align β-ketoadipyl-CoA thiolase (EC 2.3.1.174; EC 2.3.1.223) (characterized)
to candidate GFF329 PGA1_c03400 acetyl-CoA acetyltransferase PhaA
Query= metacyc::MONOMER-15952 (401 letters) >FitnessBrowser__Phaeo:GFF329 Length = 391 Score = 291 bits (744), Expect = 3e-83 Identities = 172/400 (43%), Positives = 240/400 (60%), Gaps = 10/400 (2%) Query: 1 MNEALIIDAVRTPIGRYAGALASVRADDLGAIPLKALIARHPQLDWSAVDDVIYGCANQA 60 M +I A RT +G + GA A A DLGA L+A++ R +D S V + I G A Sbjct: 1 MTNVVIASAARTAVGSFGGAFAKTPAHDLGAAVLQAVVER-AGIDKSEVSETILGQVLTA 59 Query: 61 GEDNRNVARMAALLAGLPVSVPGTTLNRLCGSGLDAVGSAARALRCGEAGLMLAGGVESM 120 + +N AR A + AGLP +LN++CGSGL AV AA+ ++ G+A ++ AGG E+M Sbjct: 60 AQ-GQNPARQAHINAGLPQESAAWSLNQVCGSGLRAVALAAQHIQLGDAAIVCAGGQENM 118 Query: 121 SRAPFVMGKSEQAFGRSAEIFDTTIGWRFVNKLMQQGFGIDSMPETAENVAAQFNISRAD 180 + +P DT I + F M +TAENVA ++ ISR Sbjct: 119 TLSPHAANLRAGHKMGDMSYIDTMI-----RDGLWDAFNGYHMGQTAENVAEKWQISREM 173 Query: 181 QDAFALRSQHKAAAAIANGRLAKEIVAVEIAQRKGPAKIVEHDEHPRGDTTLEQLAKLGT 240 QD FA+ SQ+KA AA G+ A EI A + RKG IV+ DE+ R T+E + KL Sbjct: 174 QDEFAVASQNKAEAAQKAGKFADEIAAFTVKTRKGDI-IVDQDEYIRHGATIEAMQKLRP 232 Query: 241 PFRQGGSVTAGNASGVNDGACALLLASSEAAQRHGLKARARVVGMATAGVEPRIMGIGPV 300 F + GSVTA NASG+NDGA A LL S++ A++ G++ AR+ ATAG++P IMG+GP+ Sbjct: 233 AFAKDGSVTAANASGLNDGAAATLLMSADDAEKRGIEPLARIASYATAGLDPSIMGVGPI 292 Query: 301 PATRKVLELTGLALADMDVIELNEAFAAQGLAVLRELGLADDDERVNPNGGAIALGHPLG 360 A+RK LE G ++ D+D++E NEAFAAQ AV +++G D VN NGGAIA+GHP+G Sbjct: 293 YASRKALEKAGWSVDDLDLVEANEAFAAQACAVNKDMGW--DPAIVNVNGGAIAIGHPIG 350 Query: 361 MSGARLVTTALHELEERQGRYALCTMCIGVGQGIALIIER 400 SG R++ T L E++ R + L T+CIG G G+A+ +ER Sbjct: 351 ASGCRVLNTLLFEMKRRDAKKGLATLCIGGGMGVAMCVER 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: 372 Number of extensions: 19 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: 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