Align Amino-acid acetyltransferase; EC 2.3.1.1; N-acetylglutamate synthase; AGS; NAGS (uncharacterized)
to candidate Ac3H11_1907 Acetylglutamate kinase (EC 2.7.2.8)
Query= curated2:B7VJZ6 (445 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1907 Length = 317 Score = 112 bits (281), Expect = 1e-29 Identities = 88/288 (30%), Positives = 137/288 (47%), Gaps = 20/288 (6%) Query: 14 QSTPYVNAHRGKTMVIMLGGEAVADRNF-GNIISDIALLHSLGVKIVLVHGARPQINQLL 72 Q+ PY+ GKTMVI GG A+ D + D+ LL +G+ V+VHG PQI L Sbjct: 39 QALPYIRKFHGKTMVIKYGGNAMTDPALQADFAEDVVLLKLVGMNPVVVHGGGPQIETAL 98 Query: 73 EKQDCHTPYHKNIRVTDEYSLGVAMQA-AGQLQLAITARLSMSLNNTPMAGTQLNVMSGN 131 + + + +RVTD ++ V AG++Q I + N L G Sbjct: 99 NRLGKKGEFIQGMRVTDAETMEVVEWVLAGEVQQDIVGLI----NQAGGKAVGLTGRDGG 154 Query: 132 FITAQPLGVDDGT------DYCHSGRIRRIDIEGINRTLDQGSIVLLGPIASSVTGESFN 185 I AQ L + D D G I ID + D I ++ PI ES+N Sbjct: 155 MIRAQKLKMVDNKNPAIEHDVGQVGDIVSIDPSVVKALQDDAFIPVISPIGFGENNESYN 214 Query: 186 LLSEEVATQVAIRLKADKLIGFCSEQGVTDESGNVLAELFPKDAKQILERLTESQNPAED 245 + ++ VA+++A LKA+KL+ + GV D++GN+L +L A++I E + Sbjct: 215 INADVVASKLAEVLKAEKLMLLTNTPGVLDKAGNLLTDL---TARRIDELFADG-----T 266 Query: 246 MSTGTLRFLKGAISACRAGVPRCHLISYKVDGALIQELFSFDGIGTQV 293 +S G L + GA+ A +AGV H+I +V A++ E+ + GT + Sbjct: 267 ISGGMLPKIAGALDAAKAGVNAVHIIDGRVPHAMLLEILTEQAYGTMI 314 Lambda K H 0.321 0.137 0.391 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: 274 Number of extensions: 15 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: 445 Length of database: 317 Length adjustment: 30 Effective length of query: 415 Effective length of database: 287 Effective search space: 119105 Effective search space used: 119105 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 Apr 09 2024. The underlying query database was built on Apr 09 2024.
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