Align Phosphate acetyltransferase; EC 2.3.1.8; Phosphotransacetylase (uncharacterized)
to candidate WP_097031787.1 CRO07_RS16700 bifunctional enoyl-CoA hydratase/phosphate acetyltransferase
Query= curated2:Q9X448 (316 letters) >NCBI__GCF_900207575.1:WP_097031787.1 Length = 464 Score = 316 bits (809), Expect = 8e-91 Identities = 169/298 (56%), Positives = 212/298 (71%) Query: 11 KYDRLIAAARAEAPAVTIVAHPCDETSLGGAIEAAEMGLITPILVAPEAKIRNVAAEHRL 70 ++ + ARA P V HPC ++++ GAIE + GL+ PIL+ P AKIR AAE + Sbjct: 162 RWQGFVEEARALPPVRAAVVHPCSKSAILGAIEVRDEGLLDPILIGPGAKIRAAAAEAGV 221 Query: 71 DLGRREIVDVPHSHAAAAKAVALIREGRGELLMKGSLHTDELMHEVAASATGLRTQRRIS 130 L I + HSHAAAA+AV L G ++L+KGSLH+DEL+ V + + GLRT+RRIS Sbjct: 222 SLDGFRIEETEHSHAAAARAVELAACGNVQVLVKGSLHSDELLAAVVSKSGGLRTERRIS 281 Query: 131 HVFVMDVPGHTDTLFITDAAINIFPDLEAKRDIVQNAIDLWVAIGLGEPRVAILSAVETV 190 HV+ MDVP + + +TDAAINI P LE KRDI QNA+DL +G +P+VA+L+AVETV Sbjct: 282 HVYAMDVPAYRKPVIVTDAAINIAPTLEHKRDICQNAVDLMRLLGRDQPKVAVLAAVETV 341 Query: 191 TAKIPSTIEAAALCKMAERGQITGGVLEGPLAFDNAIDQEAARIKGINSPVAGHAQILVV 250 A +P+T++AAAL MA RGQITG +++GPLAFDNAI EA KGI S VAG A ILVV Sbjct: 342 NATMPATLDAAALTVMAARGQITGALVDGPLAFDNAISPEAVATKGIVSQVAGEADILVV 401 Query: 251 PDLEAGNMLAKNLTFLTHADAAGLVLGARVPIVLTSRADSVRTRLASCAVAALYAARR 308 PDLEAGNMLAK L + A AAGLVLGARVPIVLTSRAD + R+AS A+A L A R+ Sbjct: 402 PDLEAGNMLAKQLIYFAGATAAGLVLGARVPIVLTSRADPLSARIASAALAKLVAVRK 459 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: 331 Number of extensions: 12 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: 464 Length adjustment: 30 Effective length of query: 286 Effective length of database: 434 Effective search space: 124124 Effective search space used: 124124 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