Align amino-acid N-acetyltransferase (EC 2.3.1.1) (characterized)
to candidate GFF2734 PS417_13945 GNAT family acetyltransferase
Query= BRENDA::Q9I3W7 (177 letters) >FitnessBrowser__WCS417:GFF2734 Length = 170 Score = 221 bits (564), Expect = 4e-63 Identities = 112/169 (66%), Positives = 132/169 (78%), Gaps = 2/169 (1%) Query: 1 MTAESPTIRLERYSERHVEGLTALYNDPAVARQVLQMPYQSVEQRRKRLHDSADDDRLLI 60 M P I ++R++E H+EG+ ALYN+PAV RQVLQMP+QSVE R +L D++R L Sbjct: 1 MHTPEPHIVIQRFTEAHLEGVAALYNEPAVCRQVLQMPFQSVEAWRNKLVQ--DNERRLQ 58 Query: 61 LVALHQGDVIGSASLEQHPRIRRSHSGSIGMGVAVAWQGKGVGSRLLGELLDIADNWMNL 120 LVA+H G+VIG LEQ+ R+RR+H GS GMGVA AWQGKGVGSRLL LD+ADNWMNL Sbjct: 59 LVAVHGGEVIGQLGLEQYLRVRRAHVGSFGMGVATAWQGKGVGSRLLTAALDVADNWMNL 118 Query: 121 RRVELTVYTDNAPALALYRKFGFETEGEMRDYAVRDGRFVDVYSMARLR 169 RRVELTVY DN A ALYRKFGFE EG +RDYA+RDG+FVD SMARLR Sbjct: 119 RRVELTVYADNDAAQALYRKFGFEVEGVLRDYALRDGQFVDTVSMARLR 167 Lambda K H 0.320 0.136 0.394 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: 174 Number of extensions: 6 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: 177 Length of database: 170 Length adjustment: 18 Effective length of query: 159 Effective length of database: 152 Effective search space: 24168 Effective search space used: 24168 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: 44 (21.6 bits)
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 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