Align L-serine/homoserine O-acetyltransferase; Homoserine O-trans-acetylase; EC 2.3.1.30; EC 2.3.1.31 (characterized)
to candidate GFF5222 PS417_26740 homoserine acetyltransferase
Query= SwissProt::D2Z028 (374 letters) >FitnessBrowser__WCS417:GFF5222 Length = 379 Score = 234 bits (598), Expect = 2e-66 Identities = 137/363 (37%), Positives = 201/363 (55%), Gaps = 15/363 (4%) Query: 5 IPPASRFIELPDGFAMRRGGALYGARIAYETFGSLNAARDNAVLVLTGLSPDAHAAS--R 62 +P + F E A+ G AL + YET+G LNA NAVL+ LS HAA Sbjct: 14 VPQVAHFSE---PLALACGRALPAYDLIYETYGQLNATASNAVLICHALSGHHHAAGFHS 70 Query: 63 PDDPTPGWWEAMVGPGKPVDTDLWHVICVNSLGSCKGSTGPASTDPRTGEPYRLSFPELS 122 D+ PGWW++ +GPGKP+DT+ + V+ +N+LG C GSTGP+S +P TG+P+ FP L+ Sbjct: 71 VDERKPGWWDSCIGPGKPIDTNKFFVVSLNNLGGCNGSTGPSSINPETGKPFGADFPVLT 130 Query: 123 IEDIADAAAHTVRALGISRLACVVGASMGGMSALALLARHPELARTHISLSGAVHALPFS 182 +ED + A LGI++ A V+G S+GGM AL +P+ R ++++ A + Sbjct: 131 VEDWVHSQARLADLLGINQWAAVIGGSLGGMQALQWTITYPDRVRHCLAIASAPKLSAQN 190 Query: 183 IAVRSLQREAIRSDPGWLQGHYDE-GEGPRRGMLTARKLGMMTYRSAQEWDCRFGRTRIG 241 IA + R+AI +DP + G + E G P+RG++ AR +G +TY S +FGR Sbjct: 191 IAFNEVARQAILTDPEFHGGSFQEAGVIPKRGLMLARMVGHITYLSDDSMGEKFGRGLKS 250 Query: 242 ERRRADQGRFGPEFEVESYLDFHAQRFADRFDPNSYLYLSHAMDQFDLGDGGGG--GGGA 299 E+ D EF+VESYL + + F+ RFD N+YL ++ A+D FD Sbjct: 251 EKLNYD--FHSVEFQVESYLRYQGEEFSGRFDANTYLLMTKALDYFDPAANFDDDLAKTF 308 Query: 300 PGALSRMRVERALVMGARTDILFPLSQQQEIADGLSAGGADVSFLPVDTPAGHDAFLVDI 359 GA ++ VM TD F ++ +E+ D L A DV +L +D P GHDAFL+ I Sbjct: 309 EGATAKF-----CVMSFTTDWRFSPARSRELVDALMAARKDVCYLEIDAPQGHDAFLIPI 363 Query: 360 ERF 362 R+ Sbjct: 364 PRY 366 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: 422 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