Align L-serine/homoserine O-acetyltransferase; Homoserine O-trans-acetylase; EC 2.3.1.30; EC 2.3.1.31 (characterized)
to candidate WP_057687234.1 ABB28_RS15260 homoserine O-acetyltransferase
Query= SwissProt::D2Z028 (374 letters) >NCBI__GCF_001431535.1:WP_057687234.1 Length = 370 Score = 471 bits (1213), Expect = e-137 Identities = 235/370 (63%), Positives = 281/370 (75%), Gaps = 3/370 (0%) Query: 1 MREFIPPASRFIELPDGFAMRRGGALYGARIAYETFGSLNAARDNAVLVLTGLSPDAHAA 60 M EFIPP + F LP F +RGGAL R+AYET+G+L+A NA+L++TGLSPDAHAA Sbjct: 1 MTEFIPPGTLFHALPSPFPFKRGGALTAGRVAYETWGTLDADAGNAILIVTGLSPDAHAA 60 Query: 61 SRPDDPTPGWWEAMVGPGKPVDTDLWHVICVNSLGSCKGSTGPASTDPRTGEPYRLSFPE 120 S +P GWWE MVGPGKP+DTD W VICVNSLGSCKGSTGPAS D TG+PYRLSFPE Sbjct: 61 SNAANPATGWWEGMVGPGKPIDTDRWFVICVNSLGSCKGSTGPASIDAATGKPYRLSFPE 120 Query: 121 LSIEDIADAAAHTVRALGISRLACVVGASMGGMSALALLARHPELARTHISLSGAVHALP 180 LS+ED A A+ VRALGI++LAC+VG SMGGM+ALALL HP +AR+HI++SG+ ALP Sbjct: 121 LSVEDGARASVEVVRALGITQLACLVGNSMGGMTALALLLLHPGIARSHINISGSAQALP 180 Query: 181 FSIAVRSLQREAIRSDPGWLQGHYDEGEGPRRGMLTARKLGMMTYRSAQEWDCRFGRTRI 240 FSIA+RSLQREAIR DP W G YD+ P GM ARKLG++TYRSA EWD RFGR R+ Sbjct: 181 FSIAIRSLQREAIRLDPQWNGGQYDDANYPESGMRMARKLGVITYRSALEWDGRFGRVRL 240 Query: 241 GERRRADQGRFGPEFEVESYLDFHAQRFADRFDPNSYLYLSHAMDQFDLGDGGGGGGGAP 300 + +AD FG EF+VESYL+ HA+RF FDPN YLYLS +MD FDL + G G Sbjct: 241 -DSDQADDDPFGLEFQVESYLEGHARRFVRFFDPNCYLYLSRSMDWFDLAE--HGNGDVM 297 Query: 301 GALSRMRVERALVMGARTDILFPLSQQQEIADGLSAGGADVSFLPVDTPAGHDAFLVDIE 360 L+ ++VE+AL +GA TDILFP+ QQQ+IADGL AGGA+ F+ +D+P GHDAFLVD E Sbjct: 298 AGLATIKVEKALAIGANTDILFPVQQQQQIADGLRAGGAEAHFIGLDSPQGHDAFLVDFE 357 Query: 361 RFGPPVAKFL 370 RFGP V FL Sbjct: 358 RFGPAVRGFL 367 Lambda K H 0.321 0.138 0.427 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: 498 Number of extensions: 13 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: 374 Length of database: 370 Length adjustment: 30 Effective length of query: 344 Effective length of database: 340 Effective search space: 116960 Effective search space used: 116960 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 (21.8 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Apr 10 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