Align serine O-acetyltransferase (EC 2.3.1.30) (characterized)
to candidate WP_007472882.1 CMTB2_RS00345 homoserine O-acetyltransferase
Query= BRENDA::I1R9N5 (509 letters) >NCBI__GCF_000170735.1:WP_007472882.1 Length = 368 Score = 205 bits (522), Expect = 2e-57 Identities = 120/275 (43%), Positives = 164/275 (59%), Gaps = 5/275 (1%) Query: 96 EPFLLDWGGILPEFNIAYETWGELNADKSNAILLHTGLSASSHAHST-ETNPKPGWWEKF 154 +P L+ G IL + I YET+GELN DKSNAIL+ LS S HA + + KPGWW+ Sbjct: 12 KPLYLESGRILEPWQIIYETYGELNEDKSNAILITHALSGSHHAAGWYKGDRKPGWWDGL 71 Query: 155 IGPGGPLDTNKYHVICTNVIGGCNGSTGPSS-VDPGNGERYATRFPILTMDDMVRAQFKL 213 IG +DT KY VICTNVIG C GST P S + PG+ ERY +FP++T+ DMV+AQ L Sbjct: 72 IGDSKAIDTTKYFVICTNVIGSCFGSTSPMSPIYPGSNERYRLKFPVITIKDMVKAQKIL 131 Query: 214 LDHLGIDKLYASVGSSMGGMQSLAAGVQSPSRVGRIVSISGCARSHPYSIAMRHTQRQVL 273 LD LGI KL A VG SMGGMQ+L GV P V I+ I+ ++ PY IA+ + + + Sbjct: 132 LDSLGIKKLKAVVGGSMGGMQALRFGVDFPGFVENIIPIATTYQTRPYVIAINKSMIEAI 191 Query: 274 MMDPNWNRGFY-YGKVPPHAGMKLAREIATVTYRSGPEWEQRFGRRRADSSKPPALCPDF 332 D + G Y GK G+ +AR I + Y S ++++FGR + L F Sbjct: 192 RADCEFKNGNYEIGK--ELKGLAVARMIGYLNYISPKTFDKKFGREYVKTDGMFELFGRF 249 Query: 333 LIETYLDHAGEKWCLNYDPNSLLYVSKAMDLFDLG 367 +E+YL++ G + +D S +Y+ KA+ LFD+G Sbjct: 250 QVESYLEYNGAMFPKWFDALSYIYLLKAISLFDIG 284 Lambda K H 0.317 0.134 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: 433 Number of extensions: 25 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: 509 Length of database: 368 Length adjustment: 32 Effective length of query: 477 Effective length of database: 336 Effective search space: 160272 Effective search space used: 160272 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 51 (24.3 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