Align Phosphate propanoyltransferase; Phosphate acyltransferase PduL; Phosphotransacylase PduL; PTAC; Propanediol utilization protein PduL; EC 2.3.1.222 (characterized)
to candidate WP_008813240.1 M988_RS11440 phosphate propanoyltransferase
Query= SwissProt::Q9XDN5 (210 letters) >NCBI__GCF_001655005.1:WP_008813240.1 Length = 216 Score = 320 bits (820), Expect = 1e-92 Identities = 162/206 (78%), Positives = 178/206 (86%) Query: 1 MDKELLQSTVRKVLDEMRQRPIPLGVSNRHIHLSAQDYERLFPGHPISEKKALLQPGQYA 60 M+K LL+ V K+LDEMR RPIPLGVSNRH+HLS QDY++LFP P+ EKKALLQPGQ+A Sbjct: 1 MEKTLLEPVVSKILDEMRLRPIPLGVSNRHLHLSVQDYQQLFPNQPLIEKKALLQPGQFA 60 Query: 61 AEQTVTLVGPKGQLKNVRLLGPLRSVSQVEISRTDARTLGIAAPLRMSGNLKGTPGIRLV 120 AEQTVTLVGPKG LKNVR+LGPLRS SQVEISRTDARTLGI APLRMSGNL TP IRLV Sbjct: 61 AEQTVTLVGPKGSLKNVRILGPLRSHSQVEISRTDARTLGIHAPLRMSGNLDQTPAIRLV 120 Query: 121 SPFAELELPSGVIVAQRHIHMSPLDALILRVSHGDMVSVAIEGDDRGLIFNNVAIRVSPD 180 SP+ ELELP GVIVAQRHIHMSPLDAL+ RV HGD V VAI+G R LI ++VAIRVSP Sbjct: 121 SPYGELELPQGVIVAQRHIHMSPLDALLYRVKHGDCVQVAIQGSGRRLILDDVAIRVSPQ 180 Query: 181 MRLEMHIDTDEANAAGADNPHAFARL 206 M+LEMHIDTDEANAAGAD+P AFA L Sbjct: 181 MKLEMHIDTDEANAAGADDPAAFATL 206 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: 250 Number of extensions: 11 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: 210 Length of database: 216 Length adjustment: 22 Effective length of query: 188 Effective length of database: 194 Effective search space: 36472 Effective search space used: 36472 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: 45 (21.9 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