Align Homoserine O-acetyltransferase; HAT; EC 2.3.1.31; Homoserine transacetylase; HTA (uncharacterized)
to candidate WP_018947109.1 B1A74_RS01550 homoserine O-succinyltransferase
Query= curated2:C4Z0T6 (310 letters) >NCBI__GCF_001995255.1:WP_018947109.1 Length = 356 Score = 169 bits (429), Expect = 7e-47 Identities = 115/344 (33%), Positives = 169/344 (49%), Gaps = 41/344 (11%) Query: 1 MPIKIQSDLPAKAELEEENIFVMDENRAISQNIRPLEIIVLNLMP--IKQDTELQLLR-- 56 MP+ S LP L E V+ + A Q IR L I +LN+MP TE Q R Sbjct: 1 MPLVAHSGLPTFERLRSEGESVLPNDFARQQEIRALHIGLLNMMPDAALAATERQFFRLI 60 Query: 57 GLSNTPLQIDVTFLQMSSHVSKNTSASHIKKFYQTFEEIKNNNYDGMIITGAPVEKLDFE 116 G SN Q + + H++ +Y+ FE++K D +IITGA V + D Sbjct: 61 GESNQIAQFYIHPFTLPQLKRGRKGREHVENYYEDFEQLKEEGLDALIITGANVTQPDLA 120 Query: 117 EVNYWDELITVMEWSNKHVTSTIHICWGAQAGLYYHYGIKKELLPKKLSGVYKHRVMNRK 176 +W+ L V++W+ +VTST+ C A L HYG ++ + +KL GV+ HRV++R+ Sbjct: 121 LEPFWEPLAEVVDWAWDNVTSTLCSCLATHAVLQSHYGEHRQHMGEKLWGVFPHRVVDRR 180 Query: 177 EPLVRGFDDVFMAPHSRYTQASRQQILDNPRLKVLADSDEAGIYI-VLGDGGKEIFVMGH 235 PLV G + F PHSRY + +R Q ++ L+VL +S+EAGI++ DG + +F GH Sbjct: 181 HPLVTGVNTRFDVPHSRYNKVTRDQ-FEHHGLRVLVESEEAGIHLGASPDGFRMVFFQGH 239 Query: 236 PEYDRLTLDQEYKRDIDKGIE------PDLPVNYYPD-----------------DDCNRK 272 PEYD ++L +EYKR++ + IE P LP NY + C Sbjct: 240 PEYDSISLLKEYKREVVRYIEGDRKAYPPLPENYLMPQAAAILDEHREHVEAALEHCTEI 299 Query: 273 PLL-----------SWRSHANNLYTNWLNYYVYQITPYDLNESY 305 P L +W A + NWL VYQ+T D + + Sbjct: 300 PALPEALLLDRLDNTWHDTALAVINNWLG-NVYQLTNLDRRKPF 342 Lambda K H 0.318 0.137 0.413 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: 322 Number of extensions: 13 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: 310 Length of database: 356 Length adjustment: 28 Effective length of query: 282 Effective length of database: 328 Effective search space: 92496 Effective search space used: 92496 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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