Align serine O-acetyltransferase; EC 2.3.1.30 (characterized, see rationale)
to candidate 352783 BT3256 serine acetyltransferase (NCBI ptt file)
Query= uniprot:B8DIT5_DESVM (317 letters) >FitnessBrowser__Btheta:352783 Length = 300 Score = 328 bits (842), Expect = 8e-95 Identities = 157/293 (53%), Positives = 214/293 (73%), Gaps = 6/293 (2%) Query: 18 LERIVDEMCAPESYEAVYHRSLHDAPMPSLEALAEMVSRLRAALLPGFFGAATVHMESMR 77 L + VDE+ ESY+ ++H+ P+PS + L E++ RA L PG++G +T++ ++ Sbjct: 10 LTQAVDELSESESYKGLFHQHKDGEPLPSAKVLYEIIELSRAILFPGYYGNSTINSRTIN 69 Query: 78 YHLAANLDSIYRILSEQIRRGACFTCADFARECGSCELHSRDKAIQ----FLQRLPEIRR 133 YH+ N++ ++ +L+EQI G CF+ A+ +C C R++A + F+ +LP +RR Sbjct: 70 YHIGVNIEKLFDLLTEQILAGLCFSTAE--GDCNVCSESRREEAARLAANFISKLPAMRR 127 Query: 134 MLASDVKAAYEGDPAAKSPGETVFCYPSIAAMINHRIAHELYRMEVPLIPRIISEMAHSR 193 +LA+DV+AAY GDPAAKS GE +FCYP+I A+ N+RIAHEL + VPLIPR+I+EMAHS Sbjct: 128 ILATDVEAAYNGDPAAKSYGEVIFCYPAIKAISNYRIAHELLELGVPLIPRMITEMAHSE 187 Query: 194 TGIDIHPGARIDEEFFIDHGTGVVIGETCIIGRGCRIYQGVTLGALSFPKDGDGVLIKGN 253 TGIDIHPGA+I F IDHGTGVVIG T IIG ++YQGVTLGA SFP D DG IKG Sbjct: 188 TGIDIHPGAKIGSHFTIDHGTGVVIGATSIIGNNVKLYQGVTLGAKSFPLDADGKPIKGI 247 Query: 254 PRHPILEDNVTVYAGATILGRVTIGAGSMIGGNVWVTHDVPPGSKIVQQRSAK 306 PRHPILEDNV VY+ ATILGR+TIG+ + +GGN+WVT ++P G+KIVQ ++ K Sbjct: 248 PRHPILEDNVIVYSNATILGRITIGSDATVGGNIWVTENIPAGAKIVQTKAKK 300 Lambda K H 0.322 0.138 0.417 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: 290 Number of extensions: 11 Number of successful extensions: 3 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: 317 Length of database: 300 Length adjustment: 27 Effective length of query: 290 Effective length of database: 273 Effective search space: 79170 Effective search space used: 79170 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: 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