Align acetyl-CoA C-acetyltransferase (subunit 2/2) (EC 2.3.1.9) (characterized)
to candidate WP_011023935.1 MA_RS21100 thiolase domain-containing protein
Query= BRENDA::I3R3D1 (383 letters) >NCBI__GCF_000007345.1:WP_011023935.1 Length = 390 Score = 289 bits (740), Expect = 8e-83 Identities = 167/390 (42%), Positives = 228/390 (58%), Gaps = 8/390 (2%) Query: 1 MDRVAIIGASMTQFGQR-DAWIRELLAEAGQAALADADVSPDEIEHLYVSNMASGEFEGQ 59 M VAIIG T+FG+ D +R+++ EA L DADVS EI+ LY+ NM+ G F Q Sbjct: 1 MRDVAIIGVKNTKFGELWDRSLRDIIVEAAIGVLDDADVSGKEIDALYLGNMSGGRFVDQ 60 Query: 60 TGVPNALAHDLAAMPAY----TARIDQTSSSGGAGVYAAWQSVASGASDMTMLVGGEKMT 115 + AL D + + R++ +SGG + A +VASG S++ + G EKMT Sbjct: 61 EHI-GALIADYSGLSKNLHIPATRVEAACASGGLALRQAIMAVASGYSNIVVAAGAEKMT 119 Query: 116 HRSTAEATDVIASLT-HPVEYKHGVTLPSFAGLTARLYLDTYDAPRESLGKVAVKNHKNG 174 T EA+ +A+ E G T P + A+L++ Y E L +VAVKNHKNG Sbjct: 120 DVGTEEASSALAAAADREWEGMAGATFPGLYAMIAKLHMHRYGTTSEQLAEVAVKNHKNG 179 Query: 175 LDNPHAQFRKEVDLETVLDSPVVADPLRLYDFCPITDGSAALVFCSESVAREYTDDYVVI 234 NP AQ++ E+ ++ VL S +VADPL ++D PITDG++ALV +A +YTD + I Sbjct: 180 SLNPIAQYKNEISVDDVLKSIMVADPLHIFDCSPITDGASALVVAPADIAHKYTDTPIYI 239 Query: 235 SGIGGATDTHVVHERADPTTMGGVVNSSDIAYEMADLEPDDIDVAELHDMFTILEFLQSE 294 A+DT +H+R D TT+ V ++ AY MA L P+DID+ E+HD FTI E E Sbjct: 240 KATAQASDTIALHDRRDITTLDSTVMAAKRAYSMAKLTPEDIDLVEVHDCFTIAEICAIE 299 Query: 295 DLGFFEKGEGWKAVEEGVTDRDGELPINTSGGLKSKGHPLGASGVAQVYEIYKQLIGDAG 354 DLGF EKG+G E G T G +P+NTSGGLK+ GHP+GA+G+ Q EI QL GDAG Sbjct: 300 DLGFAEKGKGGIVTENGETAIGGRIPVNTSGGLKACGHPVGATGIKQAVEIVTQLRGDAG 359 Query: 355 DRQV-DADIGLACNVGGFGNCVTTTIMESQ 383 RQV A+ G+ NVGG G I+ + Sbjct: 360 KRQVAGAEYGMTHNVGGSGATAVIHILSRE 389 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: 436 Number of extensions: 20 Number of successful extensions: 3 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: 390 Length adjustment: 30 Effective length of query: 353 Effective length of database: 360 Effective search space: 127080 Effective search space used: 127080 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