Align acetyl-CoA C-acetyltransferase (subunit 2/2) (EC 2.3.1.9) (characterized)
to candidate WP_109969931.1 DK846_RS15640 thiolase domain-containing protein
Query= BRENDA::I3R3D1 (383 letters) >NCBI__GCF_003173355.1:WP_109969931.1 Length = 387 Score = 305 bits (782), Expect = 1e-87 Identities = 170/384 (44%), Positives = 235/384 (61%), Gaps = 6/384 (1%) Query: 1 MDRVAIIGASMTQFGQR-DAWIRELLAEAGQAALADADVSPDEIEHLYVSNMASGEFEGQ 59 M VA+IG T+FG++ ++ R L +AG AL DA++S + I+ ++V NM++G F Q Sbjct: 1 MREVAVIGVGCTKFGEKWESSFRNLFVDAGALALEDANLSGEHIDEIFVGNMSAGRFVEQ 60 Query: 60 TGVPNALAHDLAAMPAYT---ARIDQTSSSGGAGVYAAWQSVASGASDMTMLVGGEKMTH 116 + AL D A + R++ +SGG A+ +VASG SD+ + G EKMT Sbjct: 61 EHI-GALIADYAGLATENIPATRVEAACASGGLAFRQAYTAVASGMSDIVVAAGVEKMTD 119 Query: 117 RSTAEATDVIASLT-HPVEYKHGVTLPSFAGLTARLYLDTYDAPRESLGKVAVKNHKNGL 175 T TDV+A+ E G+T P + A Y+ Y RE L +VAVKNH+NG Sbjct: 120 VDTEVTTDVLAAAADREWEGIAGITFPGLYAMIATQYMHRYGLTREQLAQVAVKNHENGA 179 Query: 176 DNPHAQFRKEVDLETVLDSPVVADPLRLYDFCPITDGSAALVFCSESVAREYTDDYVVIS 235 NP+AQF+K + L+TVL S +VADPLRL+D P+TDG++A++ AR++TD + + Sbjct: 180 LNPNAQFQKPITLDTVLKSTLVADPLRLFDCSPVTDGASAVILAPLEKARQFTDTPIKVL 239 Query: 236 GIGGATDTHVVHERADPTTMGGVVNSSDIAYEMADLEPDDIDVAELHDMFTILEFLQSED 295 G G A+ + +H+R D T+ V + + A++ A LE DI E+HD FTI E ED Sbjct: 240 GCGQASSSIALHDRKDICTLDATVAAGNRAFQTAKLERKDIGFVEVHDCFTIAEICAIED 299 Query: 296 LGFFEKGEGWKAVEEGVTDRDGELPINTSGGLKSKGHPLGASGVAQVYEIYKQLIGDAGD 355 LGF +KGE K EEG T G+LPIN SGGLK+ GHP+GA+G+ QVYE+ KQL GDAG Sbjct: 300 LGFCKKGEAGKLTEEGYTALGGKLPINPSGGLKACGHPVGATGIKQVYEVVKQLRGDAGK 359 Query: 356 RQVDADIGLACNVGGFGNCVTTTI 379 RQ+DADIG+ NVGG G V I Sbjct: 360 RQLDADIGMTHNVGGTGATVVCHI 383 Lambda K H 0.315 0.132 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: 455 Number of extensions: 24 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: 383 Length of database: 387 Length adjustment: 30 Effective length of query: 353 Effective length of database: 357 Effective search space: 126021 Effective search space used: 126021 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: 42 (22.0 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