Align phosphate acetyltransferase; EC 2.3.1.8 (characterized)
to candidate WP_013450900.1 CALNI_RS03875 phosphate butyryltransferase
Query= CharProtDB::CH_090885 (294 letters) >NCBI__GCF_000183405.1:WP_013450900.1 Length = 494 Score = 156 bits (395), Expect = 8e-43 Identities = 100/314 (31%), Positives = 164/314 (52%), Gaps = 27/314 (8%) Query: 4 EKLVEMARGKGKKLAVAAAN------------DDHVIEAVYRAWRERVCEPVLFGPEEEI 51 E +V +GK + V AA DD + A RA E + + + Sbjct: 179 ESMVHQVKGKKMRDMVQAAKLLPRKNISLICPDDSSLGAANRAIEEGIVDKIYLVGNIAK 238 Query: 52 TRIIEELVPEWKNP------QIIDCPPEEAGRLAVEAVSKGECDFLMKGKIKTGDLMKIY 105 T + +KN + D +A R VE V +G+ +MKGKI T + +K Sbjct: 239 TEAYCKGFLNYKNHYEFVDLDVTDNYELDAARKGVEIVRRGDAHLIMKGKINTQNFVKAI 298 Query: 106 LDERYGLRTGKTMAMVSVMEIPDFPRPLIISDPG----MLISPTLEQKVDMIEHCVRVAN 161 LD+ GL G+ +++VS+ E+P R + ++DP + + LE D++++ + A Sbjct: 299 LDKEKGLNIGRRLSLVSIFELPSVDRLIFLTDPAINPSLFVDDKLESSFDILKNAIEAAR 358 Query: 162 VMGLETPKVAVVGAIEVVNPKMPITMEAAILSKMNQRGQIKGCIVDGPFALDNVVSEEAA 221 +G++ P+VA++ A EV + K+P ++ LS+M + V GP + D + ++ Sbjct: 359 SLGVDKPRVALLDANEVPSSKIPTSLLEKQLSEMKW----EDAYVYGPLSYDLALYPDSV 414 Query: 222 KKKGIQ-SPVAGKADILILPDIEAANILYKALVFLAKAKSASTILGGKVPVVLTSRADSE 280 +KKG++ +PVAGKADIL++P IE N LYKA V + A+ +LG PV+LTSR+D E Sbjct: 415 EKKGLKDNPVAGKADILVVPHIEGGNFLYKAWVMTMGVEVANLVLGAACPVILTSRSDGE 474 Query: 281 ETKFYSIALSAVFA 294 TKF +I S++F+ Sbjct: 475 MTKFLTICASSIFS 488 Lambda K H 0.319 0.136 0.386 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: 321 Number of extensions: 17 Number of successful extensions: 4 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: 294 Length of database: 494 Length adjustment: 30 Effective length of query: 264 Effective length of database: 464 Effective search space: 122496 Effective search space used: 122496 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 (21.7 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