Align β-ketoadipyl-CoA thiolase (EC 2.3.1.174; EC 2.3.1.223) (characterized)
to candidate Ga0059261_0982 Ga0059261_0982 acetyl-CoA acetyltransferases
Query= metacyc::MONOMER-15952 (401 letters) >FitnessBrowser__Korea:Ga0059261_0982 Length = 390 Score = 316 bits (809), Expect = 8e-91 Identities = 183/400 (45%), Positives = 251/400 (62%), Gaps = 10/400 (2%) Query: 1 MNEALIIDAVRTPIGRYAGALASVRADDLGAIPLKALIARHPQLDWSAVDDVIYGCANQA 60 M E +I A RTP+G + GA AS A +LG I ++A + + ++ V +VI G A Sbjct: 1 MTEVVITAAKRTPVGSFLGAFASTPAHELGRIAIEAALEQ-AEVKGEEVSEVILGQVLTA 59 Query: 61 GEDNRNVARMAALLAGLPVSVPGTTLNRLCGSGLDAVGSAARALRCGEAGLMLAGGVESM 120 + +N AR A++ AG+P VP LN++CGSGL AV AA+A++ G+A +++AGG ESM Sbjct: 60 AQ-GQNPARQASMAAGVPKEVPAWGLNQVCGSGLRAVALAAQAVQTGDATIVVAGGQESM 118 Query: 121 SRAPFVMGKSEQAFGRSAEIFDTTIGWRFVNKLMQQGFGIDSMPETAENVAAQFNISRAD 180 S A A + DT I + GI TAEN+A Q+ ++R + Sbjct: 119 SLAAHAQSLRAGAKMGDVGLIDTMIKDGLTDVFNGYHMGI-----TAENLAEQYQVTRGE 173 Query: 181 QDAFALRSQHKAAAAIANGRLAKEIVAVEIAQRKGPAKIVEHDEHPRGDTTLEQLAKLGT 240 QD FA+RSQ+ A AA + GR EI V I RKG +V+ DE+ R TL+ +A L Sbjct: 174 QDEFAVRSQNLAEAARSEGRFKDEIAPVTIKGRKGDT-VVDQDEYIRAGATLDSVAGLRP 232 Query: 241 PFRQGGSVTAGNASGVNDGACALLLASSEAAQRHGLKARARVVGMATAGVEPRIMGIGPV 300 F++ G+VTAGNASG+NDGA AL++ S E A + G A + ATAGV+P IMGIGPV Sbjct: 233 AFKKDGTVTAGNASGLNDGAAALVVMSREEADKRGATVLATIKSWATAGVDPSIMGIGPV 292 Query: 301 PATRKVLELTGLALADMDVIELNEAFAAQGLAVLRELGLADDDERVNPNGGAIALGHPLG 360 PA++K LE G +AD+D+IE NEAFAAQ L+V +ELG D +VN NGGAIA+GHP+G Sbjct: 293 PASKKALEKAGWTVADLDLIEANEAFAAQALSVGKELGF--DPNKVNVNGGAIAIGHPIG 350 Query: 361 MSGARLVTTALHELEERQGRYALCTMCIGVGQGIALIIER 400 SGAR++TT L+E++ R + L T+CIG G GIA+ +ER Sbjct: 351 ASGARVLTTLLYEMQRRDAKKGLATLCIGGGMGIAMCVER 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: 396 Number of extensions: 15 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: 390 Length adjustment: 31 Effective length of query: 370 Effective length of database: 359 Effective search space: 132830 Effective search space used: 132830 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