Align Phosphate propanoyltransferase; Phosphate acyltransferase PduL; Phosphotransacylase PduL; PTAC; Propanediol utilization protein PduL; EC 2.3.1.222 (characterized)
to candidate WP_092346798.1 BLU87_RS08565 phosphate propanoyltransferase
Query= SwissProt::Q9XDN5 (210 letters) >NCBI__GCF_900107645.1:WP_092346798.1 Length = 455 Score = 162 bits (409), Expect = 1e-44 Identities = 87/198 (43%), Positives = 127/198 (64%), Gaps = 4/198 (2%) Query: 1 MDKELLQSTVRKVLDEMR--QRPIPLGVSNRHIHLSAQDYERLFPGHPISEKKALLQPGQ 58 MD ++ V KV+ + + IP+ +S RH+HLS ++LF G ++ + L QPGQ Sbjct: 246 MDNPVVDEIVAKVMAQFTDVKGDIPVELSARHVHLSPAAVQKLF-GKELTPVRELSQPGQ 304 Query: 59 YAAEQTVTLVGPKGQLKNVRLLGPLRSVSQVEISRTDARTLGIAAPLRMSGNLKGTPGIR 118 Y ++ V LVGP G L+N+ +LGP R +QVEIS TDAR LG++ P+R SG+++G+ G++ Sbjct: 305 YLCQERVRLVGPAGTLENIAVLGPARGATQVEISATDARILGLSPPIRQSGDIQGSTGLK 364 Query: 119 LVSPFAELELPSGVIVAQRHIHMSPLDALILRVSHGDMVSVAIEGDDRGLIFNNVAIRVS 178 +V+ L + G+IVA RH+HM DA+ L V D+V V I GD R ++F + IRV+ Sbjct: 365 IVTDIDTLTIDEGLIVAARHLHMHQDDAVRLGVKDKDLVRVRI-GDVRSVVFEKILIRVN 423 Query: 179 PDMRLEMHIDTDEANAAG 196 + RL MHID DE NA G Sbjct: 424 ENYRLAMHIDFDEGNACG 441 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: 267 Number of extensions: 21 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: 210 Length of database: 455 Length adjustment: 27 Effective length of query: 183 Effective length of database: 428 Effective search space: 78324 Effective search space used: 78324 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: 48 (23.1 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