Align Homoserine O-acetyltransferase; HAT; EC 2.3.1.31; Homoserine transacetylase; HTA (uncharacterized)
to candidate GFF2318 Psest_2366 Homoserine acetyltransferase
Query= curated2:Q67NS3 (383 letters) >FitnessBrowser__psRCH2:GFF2318 Length = 340 Score = 119 bits (298), Expect = 1e-31 Identities = 111/340 (32%), Positives = 151/340 (44%), Gaps = 48/340 (14%) Query: 27 LESGQRLTDVTLCYEVFGRLNPAGDNAILVCHALTGDSHVAGRYRPDDPKPGWWDDAVGP 86 LE+G+RL + LCY+V G N A DN +L+ S+ G + P G A GP Sbjct: 18 LENGERLRNARLCYQVVGTPNRARDNLVLI------PSYYGGTHWGSLPLLG----ADGP 67 Query: 87 GKALDTDRYCVICSNVLGGCQGSTGPSSVNPATGRPYGLDFPLVTVRDMVRAQARLLDLL 146 L YCV+ +N+ G ST PS+ P G DFP V++ D VRAQ LLD L Sbjct: 68 ---LAGGEYCVVLTNLFGA-GWSTSPSNAAPGQG---AADFPRVSLLDNVRAQKALLDRL 120 Query: 147 GVR--RLLAVIGGSLGAMQALEWAATYPDRMRGIIPIGGAGRFHPQGIAFNEVQRQAILN 204 +L V G S+G MQ L WA YP+R+R I+P P F E + A+ Sbjct: 121 YGEDWQLALVTGWSMGGMQTLFWAMAYPERVRAILPFCCTAHCWPHNRVFLEGVKAALCA 180 Query: 205 DPGFLGGQYYGTPGPVRGL-ATARMLGMITYRS---DESMWTQFGRNPQGEANPLHQGFA 260 D +LGG+Y + P RGL A R Y + +W + G Sbjct: 181 DAAWLGGRY--SVPPERGLRAFGRAYAGWAYSQAFYRQELWRELGFE------------- 225 Query: 261 VAYQVESYLHYQGRKLVERFDANSYLYLTRAMDLMDLGR--GRGSYEEAHARIQARVLAV 318 +E+ L Y + +E+ DAN L + D R GS EA R++AR + + Sbjct: 226 ---SLEALLDYWEQDHLEQ-DANDLLCVLHTWQSADPARSFAAGSLAEALGRVRARSILM 281 Query: 319 GIRSDLLFPTYLQRETVELVRASGGRAEYVEMDSPWGHDA 358 SDL F R L+ AE ++S WGH A Sbjct: 282 PGSSDLYFTVEDARHEAALIPG----AELRVLESDWGHCA 317 Lambda K H 0.321 0.140 0.432 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: 382 Number of extensions: 14 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: 383 Length of database: 340 Length adjustment: 29 Effective length of query: 354 Effective length of database: 311 Effective search space: 110094 Effective search space used: 110094 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 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