Align β-ketoadipyl-CoA thiolase (EC 2.3.1.174; EC 2.3.1.223) (characterized)
to candidate 16332 b2224 acetyl-CoA acetyltransferase (NCBI)
Query= metacyc::MONOMER-15952 (401 letters) >FitnessBrowser__Keio:16332 Length = 394 Score = 325 bits (833), Expect = 1e-93 Identities = 193/403 (47%), Positives = 259/403 (64%), Gaps = 12/403 (2%) Query: 1 MNEALIIDAVRTPIGRYAGALASVRADDLGAIPLKALIARHPQLDWSAVDDVIYGCANQA 60 M +I+ AVRT IG + G+LAS A DLGA +KA I R ++D VD+VI G QA Sbjct: 1 MKNCVIVSAVRTAIGSFNGSLASTSAIDLGATVIKAAIER-AKIDSQHVDEVIMGNVLQA 59 Query: 61 GEDNRNVARMAALLAGLPVSVPGTTLNRLCGSGLDAVGSAARALRCGEAGLMLAGGVESM 120 G +N AR A L +GL +V G T+N++CGSGL +V AA+A++ G+A ++AGG+E+M Sbjct: 60 GL-GQNPARQALLKSGLAETVCGFTVNKVCGSGLKSVALAAQAIQAGQAQSIVAGGMENM 118 Query: 121 SRAPFVMGKSEQAFGR--SAEIFDTTIGWRFVNKLMQQGFGIDSMPETAENVAAQFNISR 178 S AP+++ ++ R +++D + + LM G M TAENVA ++ I+R Sbjct: 119 SLAPYLLDAKARSGYRLGDGQVYDVILR----DGLMCATHGYH-MGITAENVAKEYGITR 173 Query: 179 ADQDAFALRSQHKAAAAIANGRLAKEIVAVEIAQRKGPAKIVEHDEHPRGDTTLEQLAKL 238 QD AL SQ KAAAAI +G EIV V + RK + DE P+ ++T E L L Sbjct: 174 EMQDELALHSQRKAAAAIESGAFTAEIVPVNVVTRK-KTFVFSQDEFPKANSTAEALGAL 232 Query: 239 GTPFRQGGSVTAGNASGVNDGACALLLASSEAAQRHGLKARARVVGMATAGVEPRIMGIG 298 F + G+VTAGNASG+NDGA AL++ AA GL AR+ A+ GV P +MG+G Sbjct: 233 RPAFDKAGTVTAGNASGINDGAAALVIMEESAALAAGLTPLARIKSYASGGVPPALMGMG 292 Query: 299 PVPATRKVLELTGLALADMDVIELNEAFAAQGLAVLRELGLADDDERVNPNGGAIALGHP 358 PVPAT+K L+L GL LAD+D+IE NEAFAAQ LAV + LG D E+VN NGGAIALGHP Sbjct: 293 PVPATQKALQLAGLQLADIDLIEANEAFAAQFLAVGKNLGF--DSEKVNVNGGAIALGHP 350 Query: 359 LGMSGARLVTTALHELEERQGRYALCTMCIGVGQGIALIIERI 401 +G SGAR++ T LH ++ R L T+CIG GQGIA++IER+ Sbjct: 351 IGASGARILVTLLHAMQARDKTLGLATLCIGGGQGIAMVIERL 393 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: 411 Number of extensions: 16 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: 394 Length adjustment: 31 Effective length of query: 370 Effective length of database: 363 Effective search space: 134310 Effective search space used: 134310 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