Align Homoserine O-acetyltransferase; HAT; EC 2.3.1.31; Homoserine transacetylase; HTA (uncharacterized)
to candidate 6937204 Sama_1374 homoserine O-succinyltransferase (RefSeq)
Query= curated2:Q64YS9 (305 letters) >FitnessBrowser__SB2B:6937204 Length = 316 Score = 364 bits (934), Expect = e-105 Identities = 163/304 (53%), Positives = 218/304 (71%) Query: 1 MPLNLPDKLPAIELLKEENIFVIDNSRATQQDIRPLRIVILNLMPLKITTETDLVRLLSN 60 MP+ +PD LPA E+L ENIFV+ +RA QDIRP++++ILNLMP KI TET L+RLL N Sbjct: 1 MPVKIPDNLPAAEILSAENIFVMSETRAAHQDIRPMKVLILNLMPNKIETETQLLRLLGN 60 Query: 61 TPLQVEISFMKIKSHTSKNTPIEHMKTFYTDFDKMREDRYDGMIITGAPVEQMDFEEVNY 120 TPLQV++ ++I S++T ++HM TFY DF+ +R YDG+IITGAP+ Q+DFEEV Y Sbjct: 61 TPLQVDVDLLRIHDKESRHTSLDHMNTFYRDFEDVRHKNYDGLIITGAPLGQLDFEEVTY 120 Query: 121 WDEITEIFDWARTHVTSTLYICWAAQAGLYHHYGIPKYALDKKMFGIFKHRTLLPLHPIF 180 WD I EI DW+++HVTS L++CWAA AGLYH YG+ + L K G+F H HP+ Sbjct: 121 WDHIREIIDWSQSHVTSVLFLCWAAHAGLYHLYGLKRELLKTKRSGVFVHSRSCDHHPLL 180 Query: 181 RGFDDEFYVPHSRHTEVRKEDILKVPELTLLSESDDSGVYMVVARGGREFFVTGHSEYSP 240 RGFD+EF+ PHSR+ E+ I P L +L+ESD++G Y+V++R R FV GH EY Sbjct: 181 RGFDEEFFAPHSRYAEIPVAQIHAHPALQVLAESDEAGAYLVLSRNSRNLFVIGHPEYQK 240 Query: 241 LTLDTEYRRDVSKGLPIEIPRNYYVNDDPDKGPLVRWRGHANLLFSNWLNYFVYQETPYN 300 TL EY RD++ G+ EIP+NY+ NDDP + P+ RW H +LL SNWLNY+VYQ TPY+ Sbjct: 241 STLSDEYHRDLAAGINPEIPQNYFRNDDPAQPPVARWHSHGSLLVSNWLNYYVYQLTPYD 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: 361 Number of extensions: 15 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: 316 Length adjustment: 27 Effective length of query: 278 Effective length of database: 289 Effective search space: 80342 Effective search space used: 80342 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