Align Phosphate acetyltransferase; EC 2.3.1.8; Phosphotransacetylase (uncharacterized)
to candidate HSERO_RS12030 HSERO_RS12030 phosphate acetyl/butaryl transferase
Query= curated2:Q9X448 (316 letters) >FitnessBrowser__HerbieS:HSERO_RS12030 Length = 484 Score = 327 bits (839), Expect = 3e-94 Identities = 168/297 (56%), Positives = 218/297 (73%), Gaps = 1/297 (0%) Query: 15 LIAAARAEAPAVTIVAHPCDETSLGGAIEAAEMGLITPILVAPEAKIRNVAAEHRLDLGR 74 L+ AR PA V HPCDE SL ++A GLI+PILVAP +++ +A H+LD+ Sbjct: 187 LLEHARKPGPAPVAVVHPCDELSLAAVLDAHAAGLISPILVAPRSRLLALAESHKLDISA 246 Query: 75 REIVDVPHSHAAAAKAVALIREGRGELLMKGSLHTDELMHEVAASATGLRTQRRISHVFV 134 + DVPHSHAAAA+A+ L+ G+ E+LMKGSLHT+E M V A GL T+RR+SH ++ Sbjct: 247 FPLEDVPHSHAAAARAIELVMHGKVEMLMKGSLHTEEFMGAVVA-CPGLHTKRRMSHCYL 305 Query: 135 MDVPGHTDTLFITDAAINIFPDLEAKRDIVQNAIDLWVAIGLGEPRVAILSAVETVTAKI 194 M P + ITDAA+NI P L K DI++NAI+L IG+ P+VAIL+AVETV ++ Sbjct: 306 MQTPSYPRPFIITDAAVNIEPGLAEKADIIRNAIELAHVIGVKTPKVAILAAVETVNPRM 365 Query: 195 PSTIEAAALCKMAERGQITGGVLEGPLAFDNAIDQEAARIKGINSPVAGHAQILVVPDLE 254 P+T++AAALCKMA+RGQITG +L+GPLAFDNA+ +AR+KGI S VAG A ILVVPDLE Sbjct: 366 PATLDAAALCKMADRGQITGAILDGPLAFDNAVSPVSARVKGIRSEVAGQADILVVPDLE 425 Query: 255 AGNMLAKNLTFLTHADAAGLVLGARVPIVLTSRADSVRTRLASCAVAALYAARRRAA 311 +GN+LAK L ++ A +AGLVLGAR+P++LTSRADS TRLASCAVA + A R+A Sbjct: 426 SGNLLAKQLEYMGGAISAGLVLGARIPLILTSRADSRETRLASCAVARMLAQHYRSA 482 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: 329 Number of extensions: 11 Number of successful extensions: 2 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: 484 Length adjustment: 31 Effective length of query: 285 Effective length of database: 453 Effective search space: 129105 Effective search space used: 129105 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: 50 (23.9 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