Align Serine acetyltransferase; SAT; EC 2.3.1.30 (characterized)
to candidate WP_069664896.1 BCR25_RS17495 gamma carbonic anhydrase family protein
Query= SwissProt::Q06750 (217 letters) >NCBI__GCF_001730305.1:WP_069664896.1 Length = 163 Score = 43.1 bits (100), Expect = 3e-09 Identities = 37/122 (30%), Positives = 54/122 (44%), Gaps = 21/122 (17%) Query: 50 FYFLARLISQVSRFFTGIEIHPGATIGRRFFIDHGMGVVIGETCEIGNNVTVFQGVTLGG 109 F + R + V R TG + G I +D V IGE NVT+ L G Sbjct: 27 FQAVIRGDNNVVRIGTGSNVQDGTII----HVDSDAPVSIGE------NVTIGHQCILHG 76 Query: 110 TGKEKGKRHPTIKDDALIATGAKVLGSITVGEGSKIGAGSVVLH--DVPDFSTVVGIPGR 167 T++D ALI G+ +L +G+ S IGAGS+V ++P+ G P + Sbjct: 77 C---------TVEDGALIGMGSTILNHAKIGKNSLIGAGSLVTEGVEIPENVLAFGRPAK 127 Query: 168 VV 169 V+ Sbjct: 128 VI 129 Lambda K H 0.323 0.141 0.413 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: 104 Number of extensions: 11 Number of successful extensions: 1 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: 217 Length of database: 163 Length adjustment: 20 Effective length of query: 197 Effective length of database: 143 Effective search space: 28171 Effective search space used: 28171 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 Jul 26 2024. The underlying query database was built on Jul 25 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