Align L-serine/homoserine O-acetyltransferase; Homoserine O-trans-acetylase; EC 2.3.1.30; EC 2.3.1.31 (characterized)
to candidate WP_011159971.1 TX73_RS22665 homoserine O-acetyltransferase
Query= SwissProt::D2Z028 (374 letters) >NCBI__GCF_000195775.1:WP_011159971.1 Length = 400 Score = 247 bits (630), Expect = 5e-70 Identities = 141/335 (42%), Positives = 188/335 (56%), Gaps = 7/335 (2%) Query: 30 RIAYETFGSLNAARDNAVLVLTGLSPDAHAAS-RPDDPTPGWWEAMVGPGKPVDTDLWHV 88 +IAY+T+G+LNA + NA+LV L+ D H A+ P PG W +VGPGKP+DTD + V Sbjct: 49 QIAYQTYGTLNADKSNAILVCHALTMDQHIANVHPITGKPGGWLTLVGPGKPIDTDRYFV 108 Query: 89 ICVNSLGSCKGSTGPASTDPRTGEPYRLSFPELSIEDIADAAAHTVRALGISRLACVVGA 148 IC N +G C GSTGPAS +P TG+ + L FP ++I D+ A A + GI +L CVVG Sbjct: 109 ICSNVIGGCMGSTGPASINPATGKAWGLDFPVITIPDMVRAQAMLIDRFGIDKLFCVVGG 168 Query: 149 SMGGMSALALLARHPELARTHISLSGAVHALPFSIAVRSLQREAIRSDPGWLQGHY-DEG 207 SMGGM L PE + ++++ A +IA L R+A+ +DP W G Y + G Sbjct: 169 SMGGMQVLQWSVAFPERVFSALAIACATRHSAQNIAFHELGRQAVMADPDWQHGRYFEHG 228 Query: 208 EGPRRGMLTARKLGMMTYRSAQEWDCRFGRTRIGERRRADQGRFGPEFEVESYLDFHAQR 267 P RG+ AR +TY S +FGR + R F +F+VESYL + Sbjct: 229 CFPHRGLAVARMAAHITYLSDAALHRKFGRKM--QDRELPTFSFDADFQVESYLRYQGSS 286 Query: 268 FADRFDPNSYLYLSHAMDQFDLGDGGGGGGGAPGALSRMRVERALVMGARTDILFPLSQQ 327 F +RFD NSYLYL+ AMD FD+ G A R R V+ +D LFP S+ Sbjct: 287 FVERFDANSYLYLTRAMDYFDI---AADHDGVLAAAFRGTQTRFCVVSFTSDWLFPTSES 343 Query: 328 QEIADGLSAGGADVSFLPVDTPAGHDAFLVDIERF 362 + I L+AGGA VSF + T GHDAFL+D F Sbjct: 344 RAIVHALNAGGARVSFAEIVTDKGHDAFLLDEPEF 378 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: 447 Number of extensions: 21 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: 400 Length adjustment: 30 Effective length of query: 344 Effective length of database: 370 Effective search space: 127280 Effective search space used: 127280 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 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