Align amino-acid N-acetyltransferase (EC 2.3.1.1) (characterized)
to candidate Dsui_1309 Dsui_1309 acetylglutamate kinase
Query= BRENDA::Q87EL2 (421 letters) >FitnessBrowser__PS:Dsui_1309 Length = 293 Score = 110 bits (276), Expect = 4e-29 Identities = 91/285 (31%), Positives = 138/285 (48%), Gaps = 27/285 (9%) Query: 6 EISQYLKRFSQLDAKRFAVVKVGGAVLRDD--VDALTSSLSFLQEVGLTPIVLHGAGPQL 63 E Y+KRF R VVK GG + D+ + L+ VG+ +V+HG GPQ+ Sbjct: 15 EALPYIKRFHG----RTIVVKYGGNAMTDEHLKQCFARDVVLLKLVGMNVVVVHGGGPQI 70 Query: 64 DEELTAVGIQKKTVNGFRVTLPETMAIVRKVFHA-TNLQLIEALQRNGARATSITG---G 119 + L VG + + + G RVT ETM +V V N ++ + R G +A +TG G Sbjct: 71 ENMLGRVGKKGEFIQGMRVTDAETMEVVEMVLGGQVNKDVVNLINRAGGKAVGLTGKDGG 130 Query: 120 VFEAHYL---------DQETYGLVGGISAVNIAPIEASLRAASIPVIASLGETPSGQILN 170 + A L D G VG I ++ + I A IPVIA +G G+ N Sbjct: 131 MIRAKKLLLPNKENPDDLIDVGQVGDIVQIDPSLIGNLEGAGFIPVIAPIGVGKDGETYN 190 Query: 171 INADVAANELVHVLQPYKIIFLTGTGGLLDADGKIINSINLSTEYEQLIQQPWVYGGMKL 230 INADV A ++ VL+ K++ LT T G+LD G++I I + + +++ + GGM Sbjct: 191 INADVVAGKVAEVLKAEKLVLLTNTPGVLDKAGQLITGIT-PKQIDDMVEDGTLSGGM-- 247 Query: 231 KIEQIKHLLD--RLPLESSVSITRPAD--LAKELFTHKGSGTLIR 271 + +I LD R ++S I + L E+ T G GT+I+ Sbjct: 248 -LPKISSALDAARNGVKSVHIIDGRVEHALLLEILTDHGVGTMIK 291 Lambda K H 0.320 0.136 0.399 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: 284 Number of extensions: 15 Number of successful extensions: 2 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: 421 Length of database: 293 Length adjustment: 29 Effective length of query: 392 Effective length of database: 264 Effective search space: 103488 Effective search space used: 103488 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: 49 (23.5 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