Align 2-dehydro-3-deoxy-phosphogluconate aldolase; Keto-3-deoxygluconate 6-phosphate aldolase; KDGP aldolase; EC 4.1.2.14 (characterized)
to candidate WP_007678627.1 BN137_RS04055 KDGP aldolase family protein
Query= SwissProt::D0ZLR2 (247 letters) >NCBI__GCF_000319285.1:WP_007678627.1 Length = 246 Score = 216 bits (550), Expect = 3e-61 Identities = 121/244 (49%), Positives = 154/244 (63%), Gaps = 5/244 (2%) Query: 5 NFYRQRVAINVLAKDIANAKAIYEAAEGHAVIGVLSAQFATVEEGVPEVKRWMAEVPS-I 63 NFYR RV +NVLA NA A+YEAAEGH ++GVLS + V V +++ + + + + + Sbjct: 6 NFYRDRVCLNVLAGSKENASAVYEAAEGHVLVGVLSKNYPDVVSAVADMRDYASRIDNAL 65 Query: 64 SVGLGAGDPAQYYKAAMIAAHTHPAHVNQTFTGSGFAAGALAATGGEQTHINALVSPTGT 123 S+GLGAGDP Q + IA P HVNQ FTG G A+ AL G +T +N LVSP GT Sbjct: 66 SLGLGAGDPNQSAMVSAIARELQPQHVNQVFTGVG-ASRALLGQG--ETVVNGLVSPAGT 122 Query: 124 PGEVVISTGVSSSQGTPARVSCEAAVRMMQDMGAHAAKFFPMGGEKSLPELYALATTAAR 183 PG V ISTG S V E A+ +++DMG + K+FPMGG E A+A AR Sbjct: 123 PGWVKISTGPLSHAAPDGIVPVETAIALLKDMGGSSIKYFPMGGLACRDEYQAVAQACAR 182 Query: 184 HGMTLIEPTGGISLDNFGIILQTCLEAGVPRVMPHVYSSIIDPQTGNTRPEDIIRLMEIV 243 H L EPTGGI LDNF IL+ LEAGV +V+PH+YSSIID +G TRPED+ RL+ I Sbjct: 183 HDFWL-EPTGGIDLDNFADILRIALEAGVSKVIPHIYSSIIDSASGETRPEDVRRLLTIT 241 Query: 244 KALV 247 + V Sbjct: 242 REWV 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: 174 Number of extensions: 7 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: 247 Length of database: 246 Length adjustment: 24 Effective length of query: 223 Effective length of database: 222 Effective search space: 49506 Effective search space used: 49506 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