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 RR42_RS26640 RR42_RS26640 2-keto-3-deoxy-L-rhamnonate aldolase
Query= SwissProt::Q47098 (262 letters) >FitnessBrowser__Cup4G11:RR42_RS26640 Length = 267 Score = 298 bits (762), Expect = 1e-85 Identities = 157/259 (60%), Positives = 189/259 (72%) Query: 2 ENSFKAALKAGRPQIGLWLGLSSSYSAELLAGAGFDWLLIDGEHAPNNVQTVLTQLQAIA 61 +N+FKAAL A +PQIGLWL ++S Y AE+ A AGFDWLLIDGEHAPN+++ L LQAIA Sbjct: 4 QNAFKAALAASQPQIGLWLSMASPYLAEVSATAGFDWLLIDGEHAPNDLRGTLNALQAIA 63 Query: 62 PYPSQPVVRPSWNDPVQIKQLLDVGTQTLLVPMVQNADEAREAVRATRYPPAGIRGVGSA 121 PY SQPVVR + IKQLLD+G + LLVPMV A++A V ATRYPP GIRGVGSA Sbjct: 64 PYRSQPVVRCVAGEVPLIKQLLDIGAKNLLVPMVDTAEQAAALVCATRYPPQGIRGVGSA 123 Query: 122 LARASRWNRIPDYLQKANDQMCVLVQIETREAMKNLPQILDVEGVDGVFIGPADLSADMG 181 + RAS+W+ DYL A+D++C+LVQ ET +A+ NL I V+GVDGVFIGPADL+A MG Sbjct: 124 VGRASQWSARADYLDVADDEICLLVQAETVKALANLDAICAVDGVDGVFIGPADLAASMG 183 Query: 182 YAGNPQHPEVQAAIEQAIVQIRESGKAPGILIANEQLAKRYLELGALFVAVGVDTTLLAR 241 + GNP HPEVQAAIE A+ I SGKA G L ++ +LA+RYL+LG FVA GVD L A Sbjct: 184 HRGNPGHPEVQAAIEGAMRTIAASGKAAGTLTSDPKLARRYLDLGCTFVATGVDVLLYAS 243 Query: 242 AAEALAARFGAQATAVKPG 260 AA LAA F TA G Sbjct: 244 AARRLAADFIGTGTAPAAG 262 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: 242 Number of extensions: 6 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: 262 Length of database: 267 Length adjustment: 25 Effective length of query: 237 Effective length of database: 242 Effective search space: 57354 Effective search space used: 57354 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 Sep 17 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