Align Phosphate acetyltransferase; EC 2.3.1.8; Phosphotransacetylase (uncharacterized)
to candidate RR42_RS03805 RR42_RS03805 phosphate acetyltransferase
Query= curated2:Q9X448 (316 letters) >FitnessBrowser__Cup4G11:RR42_RS03805 Length = 313 Score = 391 bits (1005), Expect = e-113 Identities = 204/308 (66%), Positives = 241/308 (78%), Gaps = 2/308 (0%) Query: 9 PSKYDRLIAAARAEAPAV-TIVAHPCDETSLGGAIEAAEMGLITPILVAPEAKIRNVAAE 67 P KY L+A + + PA+ T VAHPCD +SLGGA++AA +GLI P+L+ PEA+IR VA Sbjct: 5 PDKYSVLLARCQ-DLPAIPTAVAHPCDASSLGGALQAASLGLIVPLLIGPEARIRQVADA 63 Query: 68 HRLDLGRREIVDVPHSHAAAAKAVALIREGRGELLMKGSLHTDELMHEVAASATGLRTQR 127 + LDLG ++DVPHSHAAAA+AVA +R G ELLMKGSLHTDEL+HEV AS TGLRT R Sbjct: 64 NALDLGDSVLIDVPHSHAAAARAVAAVRAGEAELLMKGSLHTDELLHEVTASTTGLRTGR 123 Query: 128 RISHVFVMDVPGHTDTLFITDAAINIFPDLEAKRDIVQNAIDLWVAIGLGEPRVAILSAV 187 R+SHVF MDVP + LFITDAA+NIFP L K DI +NAIDL +G+ P+VAILSAV Sbjct: 124 RLSHVFAMDVPSYHKPLFITDAAVNIFPTLNDKADICRNAIDLLRVLGIERPKVAILSAV 183 Query: 188 ETVTAKIPSTIEAAALCKMAERGQITGGVLEGPLAFDNAIDQEAARIKGINSPVAGHAQI 247 ETVT KIPSTI+AAALC M+ RGQI GG+L+GPLAFDNAI EAA KGI S VAG I Sbjct: 184 ETVTDKIPSTIDAAALCMMSRRGQIEGGILDGPLAFDNAISHEAAVTKGIVSEVAGDPDI 243 Query: 248 LVVPDLEAGNMLAKNLTFLTHADAAGLVLGARVPIVLTSRADSVRTRLASCAVAALYAAR 307 L+VPDLEAGNMLAK LTFL A+AAG+VLGARVPI++TSRADSVR R+ SCA+A L A Sbjct: 244 LLVPDLEAGNMLAKQLTFLAGAEAAGIVLGARVPIIVTSRADSVRARIGSCAIAVLLAHA 303 Query: 308 RRAAQVAA 315 RR Q ++ Sbjct: 304 RRTGQASS 311 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: 287 Number of extensions: 7 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: 313 Length adjustment: 27 Effective length of query: 289 Effective length of database: 286 Effective search space: 82654 Effective search space used: 82654 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