Align 6-phospho-5-dehydro-2-deoxy-D-gluconate aldolase; DKGP aldolase; EC 4.1.2.29 (uncharacterized)
to candidate WP_012469022.1 GLOV_RS04670 fructose-1,6-bisphosphate aldolase, class II
Query= curated2:Q5WKY5 (293 letters) >NCBI__GCF_000020385.1:WP_012469022.1 Length = 325 Score = 180 bits (456), Expect = 4e-50 Identities = 118/315 (37%), Positives = 162/315 (51%), Gaps = 31/315 (9%) Query: 1 MGFVPMAPLLADAKKDSYAIGQFNINGLQWAKAILAGAESQQSPVIAAASDRLIDYLGGF 60 +G V + A A YAI +N N L+ +AI+ SPVI S Y Sbjct: 11 LGLVNTKEMFAKAMAGKYAIPAYNFNNLEQLQAIVVACVETNSPVIIQVSKGARSYANET 70 Query: 61 QTVVAMMGA--LTDELGITVPVVLHLDHGLSIERCKKAVDAGFSSVMFDGSHYPINENID 118 MGA + ELG T+P+ LHLDHG S E CK VD+GFSSVM DGSH P +EN+ Sbjct: 71 MLRYMAMGAVQMARELGSTIPICLHLDHGDSFELCKSCVDSGFSSVMIDGSHLPYDENVA 130 Query: 119 MTKEVVAYAHAHNVSVEGEVGTVGGMEDGLMAE-IKYADVEECQRFVCETNVDALAAALG 177 + K+VV YAH +VSVEGE+G + G+ED + AE Y EE + FV +T VD+LA ++G Sbjct: 131 LCKKVVEYAHQFDVSVEGELGVLAGIEDEVSAEHSTYTKPEEVEDFVKKTGVDSLAISIG 190 Query: 178 SVHGKYKGE-----PKLGFNEMAAISAS-TNVPLVLHGAS-------------------- 211 + HG YK + P L F+ +A P+VLHGAS Sbjct: 191 TSHGAYKFKAGQPVPPLRFDILAECEKRLPGFPIVLHGASSVVQEYVELINQNGGKMEGA 250 Query: 212 -GIPDEQLQRAIKLGHAKININTECMIAWSDACRTTFAEQETAFEPRLLLQEG-LAMVQA 269 G+P+EQL++A KINI+++ +A + R F + F+PR L E +++ Sbjct: 251 VGVPEEQLRQAAASAVCKINIDSDGRLAVTAKVREYFGKDPKEFDPRKYLGEARKELIKL 310 Query: 270 TVEKKIKQFGAANKA 284 K G+A KA Sbjct: 311 IKHKNETVLGSAGKA 325 Lambda K H 0.317 0.132 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: 245 Number of extensions: 15 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: 293 Length of database: 325 Length adjustment: 27 Effective length of query: 266 Effective length of database: 298 Effective search space: 79268 Effective search space used: 79268 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: 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