Align Phosphate acetyltransferase; EC 2.3.1.8; Phosphotransacetylase (uncharacterized)
to candidate WP_012115227.1 XAUT_RS16345 phosphate acetyltransferase
Query= curated2:Q9X448 (316 letters) >NCBI__GCF_000017645.1:WP_012115227.1 Length = 327 Score = 383 bits (984), Expect = e-111 Identities = 209/300 (69%), Positives = 229/300 (76%) Query: 11 KYDRLIAAARAEAPAVTIVAHPCDETSLGGAIEAAEMGLITPILVAPEAKIRNVAAEHRL 70 KYDRLIAAA+A VAHPCDE SLG A+EAAE+GLI PILV P KI AA RL Sbjct: 21 KYDRLIAAAQALPKLRVAVAHPCDEASLGAALEAAELGLIEPILVGPPGKIAAAAAAARL 80 Query: 71 DLGRREIVDVPHSHAAAAKAVALIREGRGELLMKGSLHTDELMHEVAASATGLRTQRRIS 130 D+ V HSH AAAKAV L+R G + LMKGSLHTDELM V A TGLRT RRIS Sbjct: 81 DISALRQVGAAHSHDAAAKAVELVRCGEADALMKGSLHTDELMSAVVARDTGLRTARRIS 140 Query: 131 HVFVMDVPGHTDTLFITDAAINIFPDLEAKRDIVQNAIDLWVAIGLGEPRVAILSAVETV 190 H FVMDVP H D L ITDAAINI P LE K IVQNAIDL A+ EPRVA+LSA+ETV Sbjct: 141 HCFVMDVPSHPDPLIITDAAINIAPSLEDKSHIVQNAIDLANALKFDEPRVAVLSAMETV 200 Query: 191 TAKIPSTIEAAALCKMAERGQITGGVLEGPLAFDNAIDQEAARIKGINSPVAGHAQILVV 250 +PSTIEAAALCKMA+RGQITGG+++GPLA DNAID +A IK I SPVAG A ILVV Sbjct: 201 NPNVPSTIEAAALCKMADRGQITGGIVDGPLALDNAIDLGSAAIKHITSPVAGRANILVV 260 Query: 251 PDLEAGNMLAKNLTFLTHADAAGLVLGARVPIVLTSRADSVRTRLASCAVAALYAARRRA 310 PDLEAGNMLAK+LTFL ADAAG+VLGARVPI+LTSRADS TRLASCAVA+L A +RA Sbjct: 261 PDLEAGNMLAKSLTFLAGADAAGIVLGARVPIILTSRADSKTTRLASCAVASLLADAQRA 320 Lambda K H 0.320 0.133 0.376 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: 314 Number of extensions: 10 Number of successful extensions: 1 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: 316 Length of database: 327 Length adjustment: 28 Effective length of query: 288 Effective length of database: 299 Effective search space: 86112 Effective search space used: 86112 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 Apr 09 2024. The underlying query database was built on Sep 17 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