Align Phosphate propanoyltransferase; Phosphate acyltransferase PduL; Phosphotransacylase PduL; PTAC; Propanediol utilization protein PduL; EC 2.3.1.222 (characterized)
to candidate WP_027458048.1 K420_RS0110665 acetate/propionate family kinase
Query= SwissProt::Q9XDN5 (210 letters) >NCBI__GCF_000519045.1:WP_027458048.1 Length = 768 Score = 180 bits (457), Expect = 6e-50 Identities = 94/175 (53%), Positives = 118/175 (67%), Gaps = 2/175 (1%) Query: 21 PIPLGVSNRHIHLSAQDYERLF-PGHPISEKKALLQPGQYAAEQTVTLVGPKGQLKNVRL 79 PIP+ +S H+HLS D E LF PGH ++ K L QPGQ+A E+ V LVGPKG++ VR+ Sbjct: 577 PIPVEISAHHVHLSQADVEALFGPGHQLTPKSELSQPGQFACEEQVHLVGPKGRIAKVRV 636 Query: 80 LGPLRSVSQVEISRTDARTLGIAAPLRMSGNLKGTPGIRLVSPFAELELPSGVIVAQRHI 139 LGP R +QVEI+ T+ LGI P+R SG+L GTPGI L P+ + GVI AQRHI Sbjct: 637 LGPTRKETQVEIAMTEQFKLGIQPPIRQSGDLTGTPGITLEGPYGSTTIERGVICAQRHI 696 Query: 140 HMSPLDALILRVSHGDMVSVAIEGDDRGLIFNNVAIRVSPDMRLEMHIDTDEANA 194 HM+P DA+ V +V V IEG +R LIF +V +RV+P RL MHIDTDE NA Sbjct: 697 HMTPEDAMRFHVRDNTVVRVRIEG-ERQLIFGDVVVRVNPAFRLAMHIDTDEGNA 750 Lambda K H 0.319 0.136 0.388 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: 418 Number of extensions: 21 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 210 Length of database: 768 Length adjustment: 31 Effective length of query: 179 Effective length of database: 737 Effective search space: 131923 Effective search space used: 131923 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 Apr 09 2024. 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