Align Phosphate propanoyltransferase; Phosphate acyltransferase PduL; Phosphotransacylase PduL; PTAC; Propanediol utilization protein PduL; EC 2.3.1.222 (characterized)
to candidate WP_066921191.1 ACG33_RS11040 acetate/propionate family kinase
Query= SwissProt::Q9XDN5 (210 letters) >NCBI__GCF_001579945.1:WP_066921191.1 Length = 611 Score = 190 bits (482), Expect = 6e-53 Identities = 97/181 (53%), Positives = 127/181 (70%), Gaps = 1/181 (0%) Query: 17 MRQRPIPLGVSNRHIHLSAQDYERLF-PGHPISEKKALLQPGQYAAEQTVTLVGPKGQLK 75 M IP+ +S RH HLS +RLF PG+ + ++ AL QPGQ+AA+++V L+GP G++ Sbjct: 408 MASARIPVAISARHAHLSQATIDRLFGPGYVLRQRAALSQPGQFAAQESVALIGPGGRID 467 Query: 76 NVRLLGPLRSVSQVEISRTDARTLGIAAPLRMSGNLKGTPGIRLVSPFAELELPSGVIVA 135 VR+LGP R Q+EISRTD TLG+ AP+R+SG+L TPGI L P + LP+G+I A Sbjct: 468 GVRVLGPPRVHDQIEISRTDEFTLGVDAPVRISGDLLNTPGITLEGPRGRVTLPNGLISA 527 Query: 136 QRHIHMSPLDALILRVSHGDMVSVAIEGDDRGLIFNNVAIRVSPDMRLEMHIDTDEANAA 195 +RHIHMSP DA + V D V V ++ D R LIF +V +RVSPD LEMH+DTDEANAA Sbjct: 528 RRHIHMSPEDAALFGVRDCDTVQVKLDTDGRDLIFGDVMVRVSPDFNLEMHLDTDEANAA 587 Query: 196 G 196 G Sbjct: 588 G 588 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: 348 Number of extensions: 20 Number of successful extensions: 2 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: 210 Length of database: 611 Length adjustment: 29 Effective length of query: 181 Effective length of database: 582 Effective search space: 105342 Effective search space used: 105342 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: 49 (23.5 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