Align Phosphate acetyltransferase; EC 2.3.1.8; Phosphotransacetylase (uncharacterized)
to candidate 8501910 DvMF_2625 Phosphate butyryltransferase (RefSeq)
Query= curated2:Q9X448 (316 letters) >FitnessBrowser__Miya:8501910 Length = 324 Score = 205 bits (521), Expect = 1e-57 Identities = 121/307 (39%), Positives = 178/307 (57%), Gaps = 5/307 (1%) Query: 9 PSKYDRLIAAARAEAPAVTIVAHPCDET-SLGGAIEAAEMGLITPILVAPEAKIRNVAAE 67 PS D L+A A I C E +LG ++A E G+ P+LV + +AAE Sbjct: 18 PSSLDELVARVAACGARPRIALAACAEAHALGALLDAMERGIAQPLLVGDMDQTARIAAE 77 Query: 68 HRLDLGRREIVDVPHSHAAAAKAVALIREGRGELLMKGSLHTDELMHEVAASATGLRTQR 127 D+ V P A AV ++R G ++LMKG ++TD L+ V ATGL + Sbjct: 78 LGRDISGIAAVHAPDPREAVQCAVDMVRRGEADVLMKGLVNTDVLLRRVLNRATGLPPKG 137 Query: 128 RISHVFVMDVP---GHTDTLFITDAAINIFPDLEAKRDIVQNAIDLWVAIGLGEPRVAIL 184 +SHV V ++P G T +TDAA+NI P+L+ K +IV NA+ + A+G+ PRVA+L Sbjct: 138 VLSHVAVFELPASGGTTRLAMMTDAAVNIRPNLQRKLEIVHNAVAVARALGIARPRVAML 197 Query: 185 SAVETVTAK-IPSTIEAAALCKMAERGQITGGVLEGPLAFDNAIDQEAARIKGINSPVAG 243 +A E V +P+T++A + +MAE+G+ + GP+A D A+ +AA KG++ PVAG Sbjct: 198 AATEKVILPAMPATLDAQIVARMAEQGEFGEADVAGPMALDIALSPDAAARKGVDHPVAG 257 Query: 244 HAQILVVPDLEAGNMLAKNLTFLTHADAAGLVLGARVPIVLTSRADSVRTRLASCAVAAL 303 A ILV PD+E+GN+L K+LT L AD A + G+ P+V+TSR DS R++ S A+A Sbjct: 258 CADILVAPDIESGNILYKSLTILARADMASTMAGSSAPLVVTSRGDSERSKFCSIALAGY 317 Query: 304 YAARRRA 310 A R+ Sbjct: 318 LALAARS 324 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: 221 Number of extensions: 11 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: 316 Length of database: 324 Length adjustment: 28 Effective length of query: 288 Effective length of database: 296 Effective search space: 85248 Effective search space used: 85248 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