Align Homoserine O-acetyltransferase; HAT; Homoserine transacetylase; HTA; EC 2.3.1.31 (characterized)
to candidate WP_013817591.1 METME_RS04475 homoserine O-succinyltransferase
Query= SwissProt::P54167 (301 letters) >NCBI__GCF_000214665.1:WP_013817591.1 Length = 355 Score = 165 bits (418), Expect = 1e-45 Identities = 115/335 (34%), Positives = 162/335 (48%), Gaps = 42/335 (12%) Query: 2 PINIPTHLPAKQVLESEHIFVMDESRAFHQDIRPQKIIILNLMPKKI--QTETQLLRLLG 59 P+ T LP Q L E ++ RA HQ IR I +LN+MP TE Q RL+G Sbjct: 3 PLVAHTDLPTFQRLHEEGEEILTPDRASHQCIRELHIGLLNIMPDAALEATERQFFRLVG 62 Query: 60 --NSPLQVHFTFLIPSTHTPKNTAREHLDEFYTTFSNIRHKRFDGMIITGAPIEHLAFEE 117 N Q H + AR H+ +Y +F I+ D +II+GA + H ++ Sbjct: 63 ACNQIAQFHVHPFTIGGLERNSAARVHIQRYYESFEQIKQDGLDALIISGANVTHDHLQD 122 Query: 118 VSYWEELKEIMEWSKTNVTSTLHICWGAQAGLYYHYGVEKIQMPKKIFGVFEHTVLSKHE 177 ++WE L E+ EW+K NVTS L C A + YGVE+ ++P+K +GVF H V+ K Sbjct: 123 EAFWEPLTEVFEWAKQNVTSVLCSCLATHALIQSCYGVERTRLPEKRWGVFSHKVVDKQH 182 Query: 178 RLVRGFDELYYVPHSRHTDINMEQLQAVPELNILTASKEAGVCLIVSKDE-KQVFLTGHP 236 L+ + + VPHSR ++ ++ L +L AS+EAGV L VS D + VF GHP Sbjct: 183 PLMAEINTRFDVPHSRFNEVFQADMEK-HGLKVLVASEEAGVHLAVSPDGFRIVFFQGHP 241 Query: 237 EYDTNTLLQEYERDLERNLSTVEA-----PKHYF-----------------AKGSNEPVN 274 EYD +LL+EY+R++ R + A P HYF AK +P+ Sbjct: 242 EYDDISLLKEYKREVLRYYNDERADYPPFPDHYFDAGVQKMLADYAGRVILAKAKGKPLE 301 Query: 275 -------------RWKAHATLLFMNWLNYYVYQET 296 W+ A +F NWL VYQ T Sbjct: 302 PLPEAEIIPHLDITWRDSAKAVFNNWLG-KVYQIT 335 Lambda K H 0.320 0.135 0.415 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: 309 Number of extensions: 17 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: 301 Length of database: 355 Length adjustment: 28 Effective length of query: 273 Effective length of database: 327 Effective search space: 89271 Effective search space used: 89271 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: 48 (23.1 bits)
This GapMind analysis is from Apr 10 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