Align Phosphate acetyltransferase; EC 2.3.1.8; Phosphotransacetylase (uncharacterized)
to candidate WP_097031062.1 CRO07_RS12695 bifunctional enoyl-CoA hydratase/phosphate acetyltransferase
Query= curated2:Q9X448 (316 letters) >NCBI__GCF_900207575.1:WP_097031062.1 Length = 473 Score = 338 bits (868), Expect = 1e-97 Identities = 184/305 (60%), Positives = 217/305 (71%) Query: 10 SKYDRLIAAARAEAPAVTIVAHPCDETSLGGAIEAAEMGLITPILVAPEAKIRNVAAEHR 69 +++ LI AARA P T V HPCD+ SL GAI+A G+I P V P+AKI AA Sbjct: 168 ARFSGLIQAARAFPPMPTAVVHPCDDLSLLGAIQAEAAGIIAPWWVGPKAKILATAAAAS 227 Query: 70 LDLGRREIVDVPHSHAAAAKAVALIREGRGELLMKGSLHTDELMHEVAASATGLRTQRRI 129 + L I+D PHSHAAA AV L+R+GR LMKG LHTDEL+ V GLRT+RR+ Sbjct: 228 VTLDEARIIDAPHSHAAAEIAVDLVRDGRAAALMKGKLHTDELLSAVLCRDKGLRTERRL 287 Query: 130 SHVFVMDVPGHTDTLFITDAAINIFPDLEAKRDIVQNAIDLWVAIGLGEPRVAILSAVET 189 SHVF +DVPG LFITDAAINI PDLE RDIVQNAIDL A+G+ PR A+LSAVET Sbjct: 288 SHVFALDVPGMDRLLFITDAAINIAPDLETMRDIVQNAIDLVRALGIDCPRTALLSAVET 347 Query: 190 VTAKIPSTIEAAALCKMAERGQITGGVLEGPLAFDNAIDQEAARIKGINSPVAGHAQILV 249 VT KIPST+ AA++CKM +RGQI GG+++GPLA+DNAI EAA KGI S VAG A ILV Sbjct: 348 VTGKIPSTLLAASICKMHDRGQIVGGMVDGPLAYDNAISVEAAVAKGIRSDVAGRADILV 407 Query: 250 VPDLEAGNMLAKNLTFLTHADAAGLVLGARVPIVLTSRADSVRTRLASCAVAALYAARRR 309 P+LE+GNM+AK L L A+AAGLV+GARVPI+LTSRADS RL S A+A L A R Sbjct: 408 APNLESGNMIAKQLIHLGGAEAAGLVIGARVPIILTSRADSASARLTSAALARLQAEARP 467 Query: 310 AAQVA 314 VA Sbjct: 468 TKPVA 472 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: 363 Number of extensions: 12 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: 473 Length adjustment: 30 Effective length of query: 286 Effective length of database: 443 Effective search space: 126698 Effective search space used: 126698 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 24 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