Align Homoserine O-acetyltransferase; HAT; Homoserine transacetylase; HTA; EC 2.3.1.31 (characterized)
to candidate WP_022948136.1 H035_RS0106255 homoserine O-succinyltransferase
Query= SwissProt::A5N8M0 (309 letters) >NCBI__GCF_000421465.1:WP_022948136.1 Length = 356 Score = 170 bits (430), Expect = 5e-47 Identities = 117/339 (34%), Positives = 169/339 (49%), Gaps = 41/339 (12%) Query: 1 MPIKIKDDLPAAEILNSENIFIMPENVAFHQDIRPLKIAILNLMPIKI--TTEVQLLRLI 58 MP+ + LPA E L SE ++P +A HQDIR L I LN+MP K TE Q LRL+ Sbjct: 1 MPLVAHNPLPAFERLRSEGQKVLPPEIARHQDIRALHIGFLNMMPDKALEATERQFLRLL 60 Query: 59 G--NTALQIEIELLHLKTHVCKNTSEEYLTNFYRTFDEIKNEKFDGLIITGAPIEQLEFS 116 G N +Q + ++ + + +Y +FD IK D LI++GA + E S Sbjct: 61 GACNQIVQFYVHFFTVEGLERGPEARAHFKRYYESFDRIKEAGLDALIVSGANVTHPEIS 120 Query: 117 RVNYWEELKDIMEWSKCHVYSTLHICWGAQAGLYYHYGIPKYILKEKLFGVFKHEVTEEK 176 +WE L ++ +W+K +V S L C A + Y YG+ + L K +GV+ H V E + Sbjct: 121 DEPFWEPLTEVFDWAKVNVTSILCSCLATHALVQYCYGLHRTRLPAKRWGVYSHRVVEPR 180 Query: 177 EKLVRGFDDEFYVPHSRYTEVKREDVEKVKELTILAQSKKAGVYL-ILDNKGRRIFVTGH 235 LV + F VPHSR+ E+ R D+E+V L IL +S++AGV+L + + R +F GH Sbjct: 181 HPLVSDINTRFDVPHSRFNELFRRDLERV-GLKILVESEEAGVHLAVSPDLFRVVFFQGH 239 Query: 236 SEYDPLTLKDEYMRDISK-----GEDI-KMPENYF------------------------P 265 EYD ++L EY R++ + ED PE+YF P Sbjct: 240 PEYDTISLLKEYKREVLRYHLRDREDYPPSPEHYFNAEAQAILADYRAAVQSARRRGAPP 299 Query: 266 DDNPDRKPVV----KWRSHADLLFSNWLNYYVYQETPYD 300 D P+ + WR A +F+NWL VYQ T D Sbjct: 300 PDFPESALIPLLDNTWRDTAKGVFNNWLG-LVYQITDQD 337 Lambda K H 0.320 0.139 0.420 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: 286 Number of extensions: 16 Number of successful extensions: 4 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: 309 Length of database: 356 Length adjustment: 28 Effective length of query: 281 Effective length of database: 328 Effective search space: 92168 Effective search space used: 92168 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 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