Align Phosphate acetyltransferase; EC 2.3.1.8; Phosphotransacetylase (uncharacterized)
to candidate WP_086510346.1 BZY95_RS12980 enoyl-CoA hydratase
Query= curated2:Q9X448 (316 letters) >NCBI__GCF_002151265.1:WP_086510346.1 Length = 472 Score = 358 bits (919), Expect = e-103 Identities = 187/306 (61%), Positives = 228/306 (74%) Query: 7 AQPSKYDRLIAAARAEAPAVTIVAHPCDETSLGGAIEAAEMGLITPILVAPEAKIRNVAA 66 A+ + +++AA AP V HP DE S+ GA+E+A GLI P+LV P+AK+ A Sbjct: 166 AERAHLHEMLSAAEHPAPVSMAVVHPVDEVSIMGAVESARQGLIRPVLVGPKAKVHAAAE 225 Query: 67 EHRLDLGRREIVDVPHSHAAAAKAVALIREGRGELLMKGSLHTDELMHEVAASATGLRTQ 126 +D+ E+VDVPHSHAAAA+AVA+ R GR E LMKG+LHTDEL+HEV TGLRT+ Sbjct: 226 AAGVDIAEFELVDVPHSHAAAAEAVAMTRAGRVEALMKGALHTDELLHEVVKRDTGLRTE 285 Query: 127 RRISHVFVMDVPGHTDTLFITDAAINIFPDLEAKRDIVQNAIDLWVAIGLGEPRVAILSA 186 R +SHV DVP + LFITDAAINI+P L K+DIVQNAIDL A+GL PRVA+LSA Sbjct: 286 RCLSHVMAFDVPTYPRPLFITDAAINIYPTLAHKKDIVQNAIDLAHAVGLDSPRVALLSA 345 Query: 187 VETVTAKIPSTIEAAALCKMAERGQITGGVLEGPLAFDNAIDQEAARIKGINSPVAGHAQ 246 VETV KI ST+EAAALCKMA+RGQI GGVL+GPLAFDNA+ + AA KGI+SPVAG A Sbjct: 346 VETVNPKIASTLEAAALCKMADRGQIRGGVLDGPLAFDNAVSEAAAAAKGIDSPVAGRAD 405 Query: 247 ILVVPDLEAGNMLAKNLTFLTHADAAGLVLGARVPIVLTSRADSVRTRLASCAVAALYAA 306 ILV PDLE+ NML K LT+L A AGLV+GARVPIVLTSRAD TR+ASCA+A L + Sbjct: 406 ILVAPDLESANMLMKQLTYLADATGAGLVVGARVPIVLTSRADDAITRMASCALALLVSE 465 Query: 307 RRRAAQ 312 +++ A+ Sbjct: 466 QQKRAR 471 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: 334 Number of extensions: 10 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: 472 Length adjustment: 30 Effective length of query: 286 Effective length of database: 442 Effective search space: 126412 Effective search space used: 126412 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