Align serine O-acetyltransferase (EC 2.3.1.30) (characterized)
to candidate PP_1110 PP_1110 serine acetyltransferase
Query= BRENDA::P95231 (229 letters) >FitnessBrowser__Putida:PP_1110 Length = 234 Score = 113 bits (282), Expect = 4e-30 Identities = 69/164 (42%), Positives = 93/164 (56%), Gaps = 11/164 (6%) Query: 8 DIRAARERDPAAPTALEVIF-CYPGVHAVWGHRLAHWLWQR-------GARLLARAAAEF 59 D++A +DPAA L I Y AV +RLAHW++ G + LA + Sbjct: 59 DLQAFAMKDPAAGRDLVFIAKTYTSYSAVLHYRLAHWIYNNSAATYGAGGQCLAAMISRR 118 Query: 60 TRILTGVDIHPGAVIGARVFIDHATGVVIGETAEVGDDVTIYHGVTLGGSGM---VGGKR 116 ++L+G +IH + IGAR IDH G VIGET+ +GDD + GVTLG G+ R Sbjct: 119 GKMLSGAEIHFRSRIGARFIIDHGMGTVIGETSTIGDDCYVLGGVTLGARGISDNPSSPR 178 Query: 117 HPTVGDRVIIGAGAKVLGPIKIGEDSRIGANAVVVKPVPPSAVV 160 HPT+G+RV IGA A VLG I +G+ + IG +V K VP +A V Sbjct: 179 HPTLGNRVQIGAFASVLGAIHVGDGAFIGPGCIVTKDVPAAARV 222 Lambda K H 0.321 0.141 0.443 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: 141 Number of extensions: 10 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: 229 Length of database: 234 Length adjustment: 23 Effective length of query: 206 Effective length of database: 211 Effective search space: 43466 Effective search space used: 43466 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: 46 (22.3 bits)
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.
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