Align L-serine/homoserine O-acetyltransferase; Homoserine O-trans-acetylase; EC 2.3.1.30; EC 2.3.1.31 (characterized)
to candidate WP_004325782.1 C665_RS18165 homoserine O-acetyltransferase
Query= SwissProt::D2Z028 (374 letters) >NCBI__GCF_000310185.1:WP_004325782.1 Length = 375 Score = 226 bits (575), Expect = 1e-63 Identities = 137/353 (38%), Positives = 192/353 (54%), Gaps = 9/353 (2%) Query: 13 ELPDGFAMRRGGALYGARIAYETFGSLNAARDNAVLVLTGLSPDAHAASRPDDP--TPGW 70 E A+R GG L + YET+G+LNA R NAVLV LS H A D GW Sbjct: 16 EFTTPLALRSGGTLNNYHLVYETYGTLNADRSNAVLVCHALSGSHHVAGTYADAPHNVGW 75 Query: 71 WEAMVGPGKPVDTDLWHVICVNSLGSCKGSTGPASTDPRTGEPYRLSFPELSIEDIADAA 130 W+ ++GPGKP+DT + VI VN+LG C GS+GP +P TG+ + FP +++ED ++ Sbjct: 76 WDNLIGPGKPLDTRKFFVIGVNNLGGCYGSSGPNQINPATGKLWGADFPFVTVEDWVESQ 135 Query: 131 AHTVRALGISRLACVVGASMGGMSALALLARHPELARTHISLSGAVHALPFSIAVRSLQR 190 A LGI R A VVG S+GGM A++ ++P+ ++ A +IA + R Sbjct: 136 ARLADRLGIERFAAVVGGSLGGMQAMSWALQYPDRVGHVAVIAAAPKLTAQNIAFNEVAR 195 Query: 191 EAIRSDPGWLQGH-YDEGEGPRRGMLTARKLGMMTYRSAQEWDCRFGRTRIGERRRADQG 249 +AI SDP + GH Y G P RG+ AR +G +TY S +FGR+ R + Sbjct: 196 QAILSDPEFHGGHYYAHGVVPTRGLKLARMVGHITYLSDDSMAEKFGRSL---RHGRNTY 252 Query: 250 RFGPEFEVESYLDFHAQRFADRFDPNSYLYLSHAMDQFDLGDGGGGGGGAPGALSRMRVE 309 + EFE+ESYL + +FA FD N+YL + A+D FD GG P AL+R + Sbjct: 253 SYDVEFEIESYLRYQGDKFAGYFDANTYLLTTKALDYFD--PAFEYGGHLPAALARASAD 310 Query: 310 RALVMGARTDILFPLSQQQEIADGLSAGGADVSFLPVDTPAGHDAFLVDIERF 362 LV+ TD F + +EI L +VS+ +D PAGHD+FL+D R+ Sbjct: 311 -FLVISFTTDWRFSPERSREIVYALLHNKRNVSYAEIDCPAGHDSFLLDETRY 362 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: 411 Number of extensions: 20 Number of successful extensions: 5 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: 375 Length adjustment: 30 Effective length of query: 344 Effective length of database: 345 Effective search space: 118680 Effective search space used: 118680 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: 50 (23.9 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