Align serine O-acetyltransferase; EC 2.3.1.30 (characterized, see rationale)
to candidate CA265_RS10155 CA265_RS10155 serine acetyltransferase
Query= uniprot:Q72EB6_DESVH (323 letters) >FitnessBrowser__Pedo557:CA265_RS10155 Length = 270 Score = 196 bits (498), Expect = 5e-55 Identities = 110/264 (41%), Positives = 155/264 (58%), Gaps = 21/264 (7%) Query: 31 YEAVYHQSLHGSPMPSLEALTELMARLRAALFPGYFGASNIVLESMRYHLAANLDSIYRI 90 +E + L +P E ++ +L LFP + ++ ++A +Y I Sbjct: 6 FEQIIKNPLEQPNIPPNEVISRWAEKLIQVLFPENSPKVFSTITEVKEYIAVLELELYDI 65 Query: 91 LAEQVRRGGCFACADYATDCQNCESHSQETAMEFMRALPRIRQLLATDVKAAYEGDPAAK 150 ++ +C ++C+N A +F LP + ++L TD+ A YEGDPAA+ Sbjct: 66 ISA--------SCRLKNSECKNA-------AGQFFEELPALYRVLNTDIVAIYEGDPAAQ 110 Query: 151 SPGETIFCYPSIYAMIHHRIAHELYRLDVPVIPRIISEMAHSRTGIDIHPGATVGEEFFI 210 S E I YP YA+ +RIAH LY +P++PRI++E AHS+TGIDIHP A++GE F I Sbjct: 111 SRFEVIRTYPGFYAICFYRIAHMLYNFGIPLVPRILTEYAHSKTGIDIHPAASIGEYFHI 170 Query: 211 DHGTGVVIGETCIIGRGCRLYQGVTLGALSFPKDGGGALIKGIPRHPILQDGVTVYAGAT 270 DHGTG+VIGET IGR +LYQGVTLGALS K + G RHP ++D V +Y+GAT Sbjct: 171 DHGTGIVIGETSTIGRYVKLYQGVTLGALSVKK-----TLAGSKRHPTVEDRVVIYSGAT 225 Query: 271 ILGRVT-IGAGAIVGGNVWVTHDV 293 ILG T IG +I+GGNVW+T + Sbjct: 226 ILGGETIIGHDSIIGGNVWLTESI 249 Lambda K H 0.320 0.137 0.410 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: 303 Number of extensions: 18 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: 323 Length of database: 270 Length adjustment: 26 Effective length of query: 297 Effective length of database: 244 Effective search space: 72468 Effective search space used: 72468 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: 48 (23.1 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