Align Phosphate acetyltransferase; EC 2.3.1.8; Phosphotransacetylase (uncharacterized)
to candidate BPHYT_RS27695 BPHYT_RS27695 bifunctional enoyl-CoA hydratase/phosphate acetyltransferase
Query= curated2:Q9X448 (316 letters) >FitnessBrowser__BFirm:BPHYT_RS27695 Length = 467 Score = 317 bits (812), Expect = 4e-91 Identities = 173/315 (54%), Positives = 214/315 (67%), Gaps = 9/315 (2%) Query: 5 WPAQPS---------KYDRLIAAARAEAPAVTIVAHPCDETSLGGAIEAAEMGLITPILV 55 WP PS +Y+ I AR T + HPC ++ AIEA + GL+ P+L+ Sbjct: 148 WPCAPSTEVTLRRHDRYEAFIRQARTRPALRTAIVHPCSAEAIVAAIEARDEGLLEPVLI 207 Query: 56 APEAKIRNVAAEHRLDLGRREIVDVPHSHAAAAKAVALIREGRGELLMKGSLHTDELMHE 115 P+A+IR A +DL I V HSHAAAA+AV + G+ LMKGSLHTDEL+ Sbjct: 208 GPDARIRAAAEAANVDLAGVPIEAVEHSHAAAARAVEMGAAGQVAALMKGSLHTDELLGA 267 Query: 116 VAASATGLRTQRRISHVFVMDVPGHTDTLFITDAAINIFPDLEAKRDIVQNAIDLWVAIG 175 V A +GLRT RRISHV+ MDVP ++ L +TDA +NI P L+ KRDI QNAIDL +G Sbjct: 268 VVARNSGLRTARRISHVYAMDVPAYSKPLVVTDAVVNIAPSLDHKRDICQNAIDLLHVLG 327 Query: 176 LGEPRVAILSAVETVTAKIPSTIEAAALCKMAERGQITGGVLEGPLAFDNAIDQEAARIK 235 RVA L A+ETV +++P+T++AAAL MA RGQITG +++GPLAFDNAI AA+ K Sbjct: 328 AELARVAALGAIETVNSRMPATLDAAALTVMAARGQITGALVDGPLAFDNAISLAAAKTK 387 Query: 236 GINSPVAGHAQILVVPDLEAGNMLAKNLTFLTHADAAGLVLGARVPIVLTSRADSVRTRL 295 I+SPVAG A IL+VPDLEAGN+LAK L + ADAAGLVLGARVPI+LTSRADSVR RL Sbjct: 388 QIDSPVAGQADILLVPDLEAGNILAKQLMYFAGADAAGLVLGARVPIILTSRADSVRVRL 447 Query: 296 ASCAVAALYAARRRA 310 AS A+A L A R A Sbjct: 448 ASAALAKLVAERTLA 462 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: 358 Number of extensions: 13 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 316 Length of database: 467 Length adjustment: 30 Effective length of query: 286 Effective length of database: 437 Effective search space: 124982 Effective search space used: 124982 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