Align acetylglutamate kinase (EC 2.7.2.8) (characterized)
to candidate BPHYT_RS35280 BPHYT_RS35280 acetyltransferase
Query= BRENDA::Q8P8J7 (203 letters) >FitnessBrowser__BFirm:BPHYT_RS35280 Length = 245 Score = 69.7 bits (169), Expect = 4e-17 Identities = 54/180 (30%), Positives = 83/180 (46%), Gaps = 4/180 (2%) Query: 16 LRGQHVTLEPLRAA-HADGLRAAVADGALSRLW-YTSVPSAAQVDDYIAAALAAQADGTA 73 L G++ +EP+ HA+ L A R W Y V + Y A A Sbjct: 30 LIGRYCRIEPVDVERHAEDLYDAYNSATDGRDWTYLGVGPFESLAAYREHLTRAAASADP 89 Query: 74 LPFVVRD-AAGEIAGSTRYYALDASVPKLSIGYTWYAPRVQRTGLNTEAKRLLLGHAFET 132 L V D A G+ G+ +D + + +G+ Y+PR++RT + TEA LL+ F+ Sbjct: 90 LHHAVIDLATGKAVGTLALMRIDRANGVIEVGHVTYSPRLKRTRIATEAMFLLMTQVFDK 149 Query: 133 LGCLSVVFETSWFNHTSRAAIARLGAKQDGVLRNHTRHADGTPRDTVVFSIINAEWAGVK 192 LG ++ N SRAA R G +G+ R + + RDT FSII++EW ++ Sbjct: 150 LGYRRFEWKCDSLNAPSRAAALRYGFTFEGIFRQAIVYRERN-RDTAWFSIIDSEWPALR 208 Lambda K H 0.321 0.131 0.398 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: 127 Number of extensions: 10 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: 203 Length of database: 245 Length adjustment: 22 Effective length of query: 181 Effective length of database: 223 Effective search space: 40363 Effective search space used: 40363 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 (21.9 bits) S2: 46 (22.3 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