Align acetyl-CoA C-acetyltransferase [EC: 2.3.1.9] (characterized)
to candidate WP_042120039.1 RHE_RS26490 thiolase family protein
Query= reanno::pseudo5_N2C3_1:AO356_21640 (393 letters) >NCBI__GCF_000092045.1:WP_042120039.1 Length = 399 Score = 266 bits (679), Expect = 1e-75 Identities = 169/394 (42%), Positives = 234/394 (59%), Gaps = 20/394 (5%) Query: 5 VIVAATRTAIGSFQGSLAAIPAPELGAAVIRRLLEQTGLSGEQVDEVILGQVLTAGSGQN 64 V+VAA RT IG GSLA + A +L A +IRR+L +TG+ + +D+V++G AG G N Sbjct: 14 VVVAAYRTPIGRAFGSLATVAAEDLLAPIIRRILAETGVGPDAIDDVLVGNA--AGGGGN 71 Query: 65 PARQASILAGLPHAVPALTLNKVCGSGLKALHLGAQAIRCGDAEVIIAGGMENMSLAPYV 124 R A++ AGLP AVP + +++ CGSGL+A+ + A+ I+ +AGG+E++S AP+ Sbjct: 72 IGRLAALTAGLPMAVPGVAIDRQCGSGLEAIIMAARLIQAKAGSCFLAGGVESVSTAPWR 131 Query: 125 L--PAARTGLRMGHAKMIDSMITDGLWDAFNDYHMGITAENLVDKYGISREEQDAFAAAS 182 + P A + + + S T G D MG+ AEN+ ++GISR+ QD FA S Sbjct: 132 VERPKANGAVPRFYGRARFSPETIG------DPEMGVAAENVARQFGISRQRQDEFALRS 185 Query: 183 QQKAVAAIEGGRFADEITPILIPQRKGDPVAFATDEQPRAGTTAESLGKLKPAFKKDGSV 242 + AVAA E G F EI I + PV + DE PR T+ E+L LKP F DGSV Sbjct: 186 HRLAVAAAEAGLFRPEIVEITTMR---GPVEW--DECPRPTTSPEALANLKPVFLADGSV 240 Query: 243 TAGNASSLNDGAAAVILMSAEKAKALGLPVLAKISAYANAGVDPAIMGIGPVSATRRCLD 302 TAGNA +NDGA V++MS A+ LG+ A AGVDP ++GIGPV+AT + + Sbjct: 241 TAGNACPVNDGACLVLVMSRGMARNLGIEKGLAFIDSAAAGVDPNLLGIGPVAATGKLMQ 300 Query: 303 K-AGWSLEQLDLIEANEAFAAQSLAVARELKWDMDKVNVNGGAIALGHPIGASGCRVLVS 361 + SL +D+IE NEAFAAQ LA +L+ + VN GGAIALGHP GASG ++ Sbjct: 301 RQPDLSLSAIDVIEFNEAFAAQVLASLDQLEIPANAVNKEGGAIALGHPFGASGAILVTR 360 Query: 362 LLHEMIKRDA----KKGLATLCIGGGQGVALALE 391 L ++I+ D GLA + IGGG G+ E Sbjct: 361 LYGQLIRGDGWTPRATGLAMIGIGGGIGLTALFE 394 Lambda K H 0.317 0.133 0.376 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: 398 Number of extensions: 17 Number of successful extensions: 6 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: 393 Length of database: 399 Length adjustment: 31 Effective length of query: 362 Effective length of database: 368 Effective search space: 133216 Effective search space used: 133216 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 (21.6 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Apr 09 2024. 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