Align 2-dehydro-3-deoxy-phosphogluconate aldolase; Keto-3-deoxygluconate 6-phosphate aldolase; KDGP aldolase; EC 4.1.2.14 (characterized)
to candidate WP_009140812.1 HMPREF9452_RS03910 KDGP aldolase family protein
Query= SwissProt::D0ZLR2 (247 letters) >NCBI__GCF_000225705.1:WP_009140812.1 Length = 245 Score = 214 bits (546), Expect = 1e-60 Identities = 120/249 (48%), Positives = 164/249 (65%), Gaps = 6/249 (2%) Query: 1 MQQINFYRQRVAINVLAKDIANAKAIYEAAEGHAVIGVLSAQFATVEEGVPEVKRWMAEV 60 M IN+Y RV +NVLA + NA+ IY+AAEGH +GVL+A + VE V ++ ++M + Sbjct: 1 MTNINYYNDRVCLNVLAGCLENARDIYKAAEGHVEVGVLTANYPDVETCVEDMAKYMEVL 60 Query: 61 P-SISVGLGAGDPAQYYKAAMIAAHTHPAHVNQTFTGSGFAAGALAATGGEQTHINALVS 119 ++SVGLG G+PAQ+ A +A H NQ F+ G+ A G +++HINALVS Sbjct: 61 EGNLSVGLGGGNPAQWRAVADVAKTIKANHFNQVFSAVGWTR---ANVGNDESHINALVS 117 Query: 120 PTGTPGEVVISTG-VSSSQGTPARVSCEAAVRMMQDMGAHAAKFFPMGGEKSLPELYALA 178 PTGTPG+V ISTG +S PA VS + A+ M+++MG ++ KFFPMGG K EL A+A Sbjct: 118 PTGTPGKVKISTGPLSKDCADPATVSVDTAITMIKEMGGNSLKFFPMGGLKVRDELKAVA 177 Query: 179 TTAARHGMTLIEPTGGISLDNFGIILQTCLEAGVPRVMPHVYSSIIDPQTGNTRPEDIIR 238 AR L EPTGGI LDNF I++ ++AGV R++PHVYSSIID TG T+ E + + Sbjct: 178 EACAREDFCL-EPTGGIDLDNFEEIMRIIIDAGVKRIIPHVYSSIIDKSTGCTKIECVEQ 236 Query: 239 LMEIVKALV 247 L+ +VK LV Sbjct: 237 LLNMVKTLV 245 Lambda K H 0.317 0.131 0.378 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: 189 Number of extensions: 10 Number of successful extensions: 5 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: 247 Length of database: 245 Length adjustment: 24 Effective length of query: 223 Effective length of database: 221 Effective search space: 49283 Effective search space used: 49283 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 46 (22.3 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