Align 4-hydroxy-2-oxo-heptane-1,7-dioate aldolase; 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase; HHED aldolase; 4-hydroxy-2-ketoheptane-1,7-dioate aldolase; HKHD aldolase; EC 4.1.2.52 (characterized)
to candidate WP_011842612.1 RSPH17029_RS18910 aldolase
Query= SwissProt::Q47098 (262 letters) >NCBI__GCF_000015985.1:WP_011842612.1 Length = 250 Score = 114 bits (284), Expect = 3e-30 Identities = 80/247 (32%), Positives = 125/247 (50%), Gaps = 7/247 (2%) Query: 5 FKAALKAGRPQIGLWLGLSSSYSAELLAGAGFDWLLIDGEHAPNNVQTVLTQLQAIAPYP 64 F+A L+A P +G +L + S+ AE+LA GFD+++ID EHAP N +T L A + Sbjct: 8 FRARLRAPEPILGTFLKIPSTQPAEILATLGFDFVVIDEEHAPFNPETTDAILLACRAHG 67 Query: 65 SQPVVRPSWNDPVQIKQLLDVGTQTLLVPMVQNADEAREAVRATRYPPAGIRGVGSAL-A 123 +VR P I ++LD G +LVP V + + AREAV RY +G RG+ A A Sbjct: 68 MAGLVRV--RQPADILRVLDCGADGVLVPHVASPEAAREAVALARY--SGARGLSPATRA 123 Query: 124 RASRWNRIPDYLQKANDQMCVLVQIETREAMKNLPQILDVEGVDGVFIGPADLSADMGYA 183 A + ++ + + + V+ +E E + L IL +G+D +FIG ADL+A MG A Sbjct: 124 GAFGATDVAQHMTRQDRRCAVIAMMEDMECLDRLDGILATDGLDAIFIGRADLAASMGPA 183 Query: 184 GNPQHPEVQAAIEQAIVQIRESGKAPGILIANEQLAKRYLELGALFVAVGVDTTLLARAA 243 ++ A++ + R++G +L +N A+ + GA D L A Sbjct: 184 A--ADGGIERAVDLVLASARDAGMPALVLTSNRSEAEEFRSRGATGFLSMSDQGFLREQA 241 Query: 244 EALAARF 250 + A F Sbjct: 242 ARIRAIF 248 Lambda K H 0.317 0.133 0.387 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: 139 Number of extensions: 10 Number of successful extensions: 3 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: 262 Length of database: 250 Length adjustment: 24 Effective length of query: 238 Effective length of database: 226 Effective search space: 53788 Effective search space used: 53788 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: 47 (22.7 bits)
This GapMind analysis is from Apr 10 2024. 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