Align serine O-acetyltransferase (EC 2.3.1.30) (characterized)
to candidate WP_017547591.1 C792_RS0101075 homoserine O-succinyltransferase
Query= BRENDA::Q03BU2 (271 letters) >NCBI__GCF_000330705.1:WP_017547591.1 Length = 310 Score = 164 bits (415), Expect = 2e-45 Identities = 84/257 (32%), Positives = 137/257 (53%), Gaps = 3/257 (1%) Query: 5 PLKIGILNVMHDKADTKTRLQHVLTHTAIPVDLHFYYPMTHYAGRTVPEAVSSILDPLDI 64 PL++ ILN+M K +T+ L +L +T + +D+ F Y TH + T + + D Sbjct: 35 PLRMLILNLMPKKEETELHLLRLLGNTPLQIDVEFLYMSTHRSRNTPTSHLQKYYNSFDE 94 Query: 65 HEVATMDGFIITGSPIETLEFDQVHYIAEVRTLLKTLSQHVPNQLYLCWGGMVALNYFFG 124 DG I+TG+P+E LE++QV YI E++ ++ HV ++ ++CWG ALN++FG Sbjct: 95 IRNQKFDGMIVTGAPVEKLEYEQVDYIDELKDIINWAQTHVYSRFFICWGAQFALNHYFG 154 Query: 125 ISKLILPHKLFGVYPQTILEP-HPLLKGLKNDFKSPHARYAEMDVRGIHADPRLTINATT 183 I K LP KLFG++ + + P HPLL+G + + P +R+ +D + P L + Sbjct: 155 IGKQELPAKLFGIFEYSNIYPDHPLLRGFDDIYSVPQSRHTTVDWNALRNTPDLDVLTEH 214 Query: 184 TKGKLFMATEPTDTQTFVFSHIEYDRWGLDSEYKREVAAHPEIDYVRAKHYYHHKNDYDH 243 + + F+F H+EY+R L EY+R+++ ID +Y+ H Sbjct: 215 PEFGPDITASKERRDLFIFGHLEYERDTLKQEYERDISDGQHIDL--PHNYFPGDESSRH 272 Query: 244 PKFNWKKTQRTIFDNWI 260 P FNWK +F+NWI Sbjct: 273 PVFNWKSHGHILFNNWI 289 Lambda K H 0.322 0.138 0.433 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: 278 Number of extensions: 15 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: 271 Length of database: 310 Length adjustment: 26 Effective length of query: 245 Effective length of database: 284 Effective search space: 69580 Effective search space used: 69580 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 Jul 26 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