Align Phosphate acetyltransferase; EC 2.3.1.8; Phosphotransacetylase (uncharacterized)
to candidate HSERO_RS01300 HSERO_RS01300 phosphate acetyltransferase
Query= curated2:Q9X448 (316 letters) >FitnessBrowser__HerbieS:HSERO_RS01300 Length = 319 Score = 321 bits (823), Expect = 1e-92 Identities = 174/299 (58%), Positives = 212/299 (70%) Query: 11 KYDRLIAAARAEAPAVTIVAHPCDETSLGGAIEAAEMGLITPILVAPEAKIRNVAAEHRL 70 +YD+LI A V HPC +L GA+EA + GL P+LV PE +IR +A + Sbjct: 12 RYDQLIRDALGAQAMRVAVVHPCSPEALQGALEARDEGLFDPVLVGPETRIRRIAEAADI 71 Query: 71 DLGRREIVDVPHSHAAAAKAVALIREGRGELLMKGSLHTDELMHEVAASATGLRTQRRIS 130 L IV HSHAAAA+AV + G LMKGSLH+DEL+ V A+GLRT+RRIS Sbjct: 72 SLQGLPIVPAEHSHAAAARAVEMAVAGEVGALMKGSLHSDELLGAVVGGASGLRTERRIS 131 Query: 131 HVFVMDVPGHTDTLFITDAAINIFPDLEAKRDIVQNAIDLWVAIGLGEPRVAILSAVETV 190 HV+ M +P + L ITDAAINI P L KRDI QNAIDL +G+ P VA+L+AVETV Sbjct: 132 HVYAMAIPAYPKPLIITDAAINIAPTLAHKRDICQNAIDLLHVMGVPRPHVAVLAAVETV 191 Query: 191 TAKIPSTIEAAALCKMAERGQITGGVLEGPLAFDNAIDQEAARIKGINSPVAGHAQILVV 250 +PST++AAAL MA R QITG +++GPLAFDNAI +AA +KGI SPVAG A IL+V Sbjct: 192 NPAMPSTLDAAALTVMATRHQITGALVDGPLAFDNAISLQAASVKGIVSPVAGSADILLV 251 Query: 251 PDLEAGNMLAKNLTFLTHADAAGLVLGARVPIVLTSRADSVRTRLASCAVAALYAARRR 309 PDLEAGNMLAK L +L+ ADAAGLVLGARVPI+LTSRADS+R RLAS A+A L A+R+R Sbjct: 252 PDLEAGNMLAKQLIYLSQADAAGLVLGARVPIILTSRADSLRVRLASSALARLVASRQR 310 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: 265 Number of extensions: 12 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: 319 Length adjustment: 27 Effective length of query: 289 Effective length of database: 292 Effective search space: 84388 Effective search space used: 84388 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 Sep 17 2021. 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