Align acetyl-CoA C-acetyltransferase (subunit 2/2) (EC 2.3.1.9) (characterized)
to candidate AZOBR_RS24680 AZOBR_RS24680 hypothetical protein
Query= BRENDA::I3RA72 (383 letters) >FitnessBrowser__azobra:AZOBR_RS24680 Length = 387 Score = 152 bits (383), Expect = 2e-41 Identities = 120/358 (33%), Positives = 176/358 (49%), Gaps = 19/358 (5%) Query: 32 LEDAGVAPASVDHLYVSNMASGEFE--GQTGVMNALAHDLGVIPAYTQRIDQTSSSGGAG 89 L+DAG+ VD L ASG++ G T + LA +G+ P Y ++ T G + Sbjct: 37 LDDAGLTLKDVDGLCA---ASGDWAEGGSTMDVVELAEYIGIAPTY---VNSTDVGGCSY 90 Query: 90 IYEAWQS---IASGVSEMTLL-VGGEKMTHKTTGESTDIIASCTHPEEYK--HGVTLPSF 143 I +A Q+ IA+G++E+ ++ + S D P +Y+ + TL S Sbjct: 91 ILQAGQAAAAIATGLAEVVVISYAACPRWWPLSSPSFDPFVFPAGPGQYEIPYAPTLIST 150 Query: 144 AGMTARNYLERFDAPRESLARVAVKNHRNGVDNPKAQFQKEIDIETALESPIIADPLRLY 203 G+ AR +++ + E LA+VAV + NP A+ +K I ++ L SP+IA PL Sbjct: 151 YGLFARRHMDLYGTTPEQLAQVAVTFREHAAKNPDARLRKPITVDDVLASPMIASPLHRL 210 Query: 204 DFCPITDGSAAMMFTTEERAQEITDEYAIVSGVGGA-TDTHVVHERDDPTVMGGVVESSK 262 D C +TDG A++ T+ ERA+++ V G G A T DD T + S Sbjct: 211 DCCVVTDGGGAVVMTSRERARDLKKPPVHVVGYGAAVARTQNSQIPDDLTTPAAL--SGP 268 Query: 263 QAYEMAGVGPDDLDVAELHDMFTILEFLQLEGIGVADHGAAWELAMDGVTAKDGGLPINT 322 +A+ MAGV P ++DVA+++D FTI L LE +G G + DG G LP NT Sbjct: 269 RAFAMAGVTPGEIDVAQIYDAFTITPMLALEDLGFCGRGESGAFVADGNLTLGGSLPTNT 328 Query: 323 SGGLKSKGHPLGASGVAQGVEIYEQLVGEAGPRQV-EADTALACNVGGFGNCVITTIM 379 GG S HP G G+ +E QL GE QV +A ALA +GG T I+ Sbjct: 329 DGGGLSSNHP-GKRGIFTLIESVRQLRGEGPGVQVPDARIALAHGLGGTFCSAATAIL 385 Lambda K H 0.314 0.131 0.379 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: 440 Number of extensions: 26 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: 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 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