Align serine O-acetyltransferase (EC 2.3.1.30) (characterized)
to candidate WP_011842651.1 RSPH17029_RS19145 serine acetyltransferase
Query= BRENDA::A0R4T4 (172 letters) >NCBI__GCF_000015985.1:WP_011842651.1 Length = 218 Score = 58.2 bits (139), Expect = 9e-14 Identities = 38/102 (37%), Positives = 54/102 (52%), Gaps = 7/102 (6%) Query: 73 IGPAFFIQHGVGTIVAAES-IGSHCWINQQVTIGHNT---RGR-PTLGDHVRVGAGAVVI 127 +G I H G ++ + IG +C I Q VT G T G+ P +G+ VR G G+VV+ Sbjct: 116 VGRRLEIGHQSGIVIHRHATIGHNCVIRQGVTFGVGTDWIEGKGPVIGNGVRFGVGSVVM 175 Query: 128 GPITLHDRATIGVNATVIHDVPAGATVVAPAATML--NRPAT 167 G +T+ DR T+G N + DV T+ P +L RPAT Sbjct: 176 GNVTIGDRVTVGPNCVISSDVAPDCTLFLPPPRVLPKARPAT 217 Lambda K H 0.323 0.138 0.437 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: 128 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: 172 Length of database: 218 Length adjustment: 20 Effective length of query: 152 Effective length of database: 198 Effective search space: 30096 Effective search space used: 30096 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: 44 (21.6 bits)
This GapMind analysis is from Apr 16 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