Align Homoserine O-acetyltransferase; HAT; EC 2.3.1.31; Homoserine transacetylase; HTA (uncharacterized)
to candidate 7025621 Shewana3_2772 homoserine O-succinyltransferase (RefSeq)
Query= curated2:Q64YS9 (305 letters) >FitnessBrowser__ANA3:7025621 Length = 313 Score = 362 bits (928), Expect = e-105 Identities = 163/304 (53%), Positives = 219/304 (72%) Query: 1 MPLNLPDKLPAIELLKEENIFVIDNSRATQQDIRPLRIVILNLMPLKITTETDLVRLLSN 60 MP+ +PD LPA +L+ ENIFV+ +RA QDIRP++++ILNLMP KI TET L+RLL N Sbjct: 1 MPVKIPDHLPAAGILESENIFVMSETRAANQDIRPMKVLILNLMPNKIETETQLLRLLGN 60 Query: 61 TPLQVEISFMKIKSHTSKNTPIEHMKTFYTDFDKMREDRYDGMIITGAPVEQMDFEEVNY 120 TPLQV++ ++I SK+T I+HM TFY DF+ +R YDG+IITGAP+ Q+DFEEV Y Sbjct: 61 TPLQVDVDLLRIHDKESKHTSIDHMNTFYRDFEDVRHKNYDGLIITGAPLGQIDFEEVTY 120 Query: 121 WDEITEIFDWARTHVTSTLYICWAAQAGLYHHYGIPKYALDKKMFGIFKHRTLLPLHPIF 180 WD I EI DW++ HVTS L++CWAA AGLYH YG+ + L +K G+F HR P+ Sbjct: 121 WDHIREIIDWSQQHVTSVLFLCWAAHAGLYHLYGLNRKILQQKRSGVFVHRRTCQHFPLL 180 Query: 181 RGFDDEFYVPHSRHTEVRKEDILKVPELTLLSESDDSGVYMVVARGGREFFVTGHSEYSP 240 RGFDDEF+ PHSR E+ E++ + EL +L++SD++G Y+V++R R FV GH EY Sbjct: 181 RGFDDEFFAPHSRFAEMDIEELKQHSELQVLAQSDEAGAYLVLSRNNRNLFVMGHPEYQK 240 Query: 241 LTLDTEYRRDVSKGLPIEIPRNYYVNDDPDKGPLVRWRGHANLLFSNWLNYFVYQETPYN 300 TL+ EY RD+++GL +P+NYY NDDP + RW H +LL SNWLNY+VYQ TPY+ Sbjct: 241 STLNDEYHRDLAQGLNPNVPQNYYRNDDPKDDAIARWHSHGSLLVSNWLNYYVYQLTPYD 300 Query: 301 IEDI 304 + D+ Sbjct: 301 LSDM 304 Lambda K H 0.322 0.140 0.429 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: 365 Number of extensions: 17 Number of successful extensions: 1 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: 305 Length of database: 313 Length adjustment: 27 Effective length of query: 278 Effective length of database: 286 Effective search space: 79508 Effective search space used: 79508 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 (21.9 bits) S2: 48 (23.1 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