Align Phosphate acetyltransferase; EC 2.3.1.8; Phosphotransacetylase (uncharacterized)
to candidate WP_011384937.1 AMB_RS12865 bifunctional enoyl-CoA hydratase/phosphate acetyltransferase
Query= curated2:Q9X448 (316 letters) >NCBI__GCF_000009985.1:WP_011384937.1 Length = 469 Score = 385 bits (989), Expect = e-111 Identities = 204/304 (67%), Positives = 235/304 (77%) Query: 12 YDRLIAAARAEAPAVTIVAHPCDETSLGGAIEAAEMGLITPILVAPEAKIRNVAAEHRLD 71 ++ +IA AP V HPCD+ SL G +EAA++GLI PIL+ PEAKIR+VA E LD Sbjct: 164 FEDIIARCHTLAPISVAVCHPCDQVSLEGPVEAAKLGLIDPILIGPEAKIRSVAKEFNLD 223 Query: 72 LGRREIVDVPHSHAAAAKAVALIREGRGELLMKGSLHTDELMHEVAASATGLRTQRRISH 131 + IVD HSH +A KAVA+ R G E LMKGSLHTDE+MHEVA+ GLRT RRISH Sbjct: 224 IEGLRIVDTQHSHESAEKAVAMCRSGEAEALMKGSLHTDEMMHEVASRDKGLRTARRISH 283 Query: 132 VFVMDVPGHTDTLFITDAAINIFPDLEAKRDIVQNAIDLWVAIGLGEPRVAILSAVETVT 191 VFVMDVP + TL ITDAAINI+P LE K DI+QNAI+L +G+ P+VAILSAVETV Sbjct: 284 VFVMDVPTYPRTLLITDAAINIYPTLEDKADILQNAIELAHVLGVELPKVAILSAVETVY 343 Query: 192 AKIPSTIEAAALCKMAERGQITGGVLEGPLAFDNAIDQEAARIKGINSPVAGHAQILVVP 251 KI STIEAAALCKMA+RGQITG L+GPLAFDNAI +EAA+IK INSPVAG A IL+VP Sbjct: 344 PKINSTIEAAALCKMADRGQITGAQLDGPLAFDNAISEEAAKIKKINSPVAGRADILLVP 403 Query: 252 DLEAGNMLAKNLTFLTHADAAGLVLGARVPIVLTSRADSVRTRLASCAVAALYAARRRAA 311 DLEAGNMLAK L++L ADAAG+VLGARVPIVLTSRADS + RLASCAVA L+A RRA Sbjct: 404 DLEAGNMLAKQLSYLADADAAGIVLGARVPIVLTSRADSAKARLASCAVAVLFAHARRAK 463 Query: 312 QVAA 315 A Sbjct: 464 SAVA 467 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: 337 Number of extensions: 8 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: 469 Length adjustment: 30 Effective length of query: 286 Effective length of database: 439 Effective search space: 125554 Effective search space used: 125554 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