Align serine O-acetyltransferase (EC 2.3.1.30) (characterized)
to candidate WP_012505314.1 PAES_RS03660 homoserine O-acetyltransferase
Query= BRENDA::I1R9N5 (509 letters) >NCBI__GCF_000020625.1:WP_012505314.1 Length = 357 Score = 207 bits (528), Expect = 4e-58 Identities = 111/273 (40%), Positives = 155/273 (56%), Gaps = 15/273 (5%) Query: 95 KEPFLLDWGGILPEFNIAYETWGELNADKSNAILLHTGLSASSHAHSTETNPKPGWWEKF 154 ++PF L+ GG+LPE +AY TWG LN D+SNA+L+ L+ S+ A WW Sbjct: 17 RQPFTLESGGVLPEVTVAYRTWGRLNRDRSNAVLVCHALTGSADADE--------WWPGM 68 Query: 155 IGPGGPLDTNKYHVICTNVIGGCNGSTGPSSVDPGNGERYATRFPILTMDDMVRAQFKLL 214 G G D + VIC+NV+G C G+TGP SV+P +G Y FP +T+ DMV Q LL Sbjct: 69 FGKGCAFDPDHDFVICSNVLGSCYGTTGPLSVNPQSGRHYGPDFPAITIRDMVHLQRLLL 128 Query: 215 DHLGIDKLYASVGSSMGGMQSLAAGVQSPSRVGRIVSISGCARSHPYSIAMRHTQRQVLM 274 D LGI++L VG+S+GGMQ L G P +V ++ + R + IA QR +M Sbjct: 129 DELGIERLRLVVGASLGGMQVLEWGCLYPEKVHALMPMGISGRHSAWCIAQSEAQRSAIM 188 Query: 275 MDPNWNRGFYYGKVPPHAGMKLAREIATVTYRSGPEWEQRFGRRRADSSKPPALCPDFLI 334 D WN G+Y P G+ AR +A TYRS +++RFGR+R DS F Sbjct: 189 ADREWNDGWYDPAHQPKGGLGAARMMAMCTYRSFENFQERFGRKRKDSLL-------FQA 241 Query: 335 ETYLDHAGEKWCLNYDPNSLLYVSKAMDLFDLG 367 E+YL + GEK +D N+ + +++AMD+ DLG Sbjct: 242 ESYLHYQGEKLVRRFDANTYIALTRAMDMHDLG 274 Score = 31.2 bits (69), Expect = 6e-05 Identities = 17/64 (26%), Positives = 33/64 (51%), Gaps = 8/64 (12%) Query: 444 PTLVMGVASDILFPAWQQREVAEAIRLAGNRNVTHVELSEEMSMFGHDTFLLDLKYIGNN 503 P ++ + SDIL+P +Q E+A +L + ++ ++ +GHD FL+ + Sbjct: 290 PVAILSITSDILYPPEEQEELA---KLIPDSSIGYLR-----EPYGHDAFLILTDEVSAM 341 Query: 504 LRMF 507 +R F Sbjct: 342 VRQF 345 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: 505 Number of extensions: 25 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 509 Length of database: 357 Length adjustment: 32 Effective length of query: 477 Effective length of database: 325 Effective search space: 155025 Effective search space used: 155025 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