Align L-serine/homoserine O-acetyltransferase; Homoserine O-trans-acetylase; EC 2.3.1.30; EC 2.3.1.31 (characterized)
to candidate PP_5097 PP_5097 homoserine O-acetyltransferase
Query= SwissProt::D2Z028 (374 letters) >FitnessBrowser__Putida:PP_5097 Length = 379 Score = 242 bits (617), Expect = 1e-68 Identities = 138/373 (36%), Positives = 208/373 (55%), Gaps = 11/373 (2%) Query: 5 IPPASRFIELPDGFAMRRGGALYGARIAYETFGSLNAARDNAVLVLTGLSPDAHAAS--R 62 +P +RF E A+ G +L + YET+G+LNA+ NAVL+ LS HAA Sbjct: 14 VPQTARFDE---PLALACGRSLASYELVYETYGTLNASASNAVLICHALSGHHHAAGYHA 70 Query: 63 PDDPTPGWWEAMVGPGKPVDTDLWHVICVNSLGSCKGSTGPASTDPRTGEPYRLSFPELS 122 D PGWW++ +GPGKP+DT+ + V+ +N+LG C GSTGP+S +P TG+PY FP L+ Sbjct: 71 ATDRKPGWWDSCIGPGKPIDTNRFFVVSLNNLGGCNGSTGPSSVNPATGKPYGADFPVLT 130 Query: 123 IEDIADAAAHTVRALGISRLACVVGASMGGMSALALLARHPELARTHISLSGAVHALPFS 182 +ED + LGI + A VVG S+GGM AL +PE R + ++ A + Sbjct: 131 VEDWVHSQVRLGERLGIQQWAAVVGGSLGGMQALQWTISYPERVRHCVDIASAPKLSAQN 190 Query: 183 IAVRSLQREAIRSDPGWLQGHY-DEGEGPRRGMLTARKLGMMTYRSAQEWDCRFGRTRIG 241 IA + R+AI +DP + G + D+G P+RG++ AR +G +TY S +FGR Sbjct: 191 IAFNEVARQAILTDPEFHGGSFQDQGVIPKRGLMLARMVGHITYLSDDSMGEKFGRELKS 250 Query: 242 ERRRADQGRFGPEFEVESYLDFHAQRFADRFDPNSYLYLSHAMDQFDLGDGGGGGGGAPG 301 ++ D EF+VESYL + + F+ RFD N+YL ++ A+D FD GG Sbjct: 251 DKLNYD--FHSVEFQVESYLRYQGEEFSGRFDANTYLLMTKALDYFD--PAATHGGDLAA 306 Query: 302 ALSRMRVERALVMGARTDILFPLSQQQEIADGLSAGGADVSFLPVDTPAGHDAFLVDIER 361 L+ + + +M TD F ++ +EI D L A +V +L +D+P GHDAFL+ R Sbjct: 307 TLAHVTADYC-IMSFTTDWRFSPARSREIVDALMAARKNVCYLEIDSPYGHDAFLIPTPR 365 Query: 362 FGPPVAKFLAIVA 374 + + ++ +A Sbjct: 366 YMQGFSNYMNRIA 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: 418 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: 379 Length adjustment: 30 Effective length of query: 344 Effective length of database: 349 Effective search space: 120056 Effective search space used: 120056 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