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 GFF3489 PS417_17865 2-keto-3-deoxy-L-rhamnonate aldolase
Query= SwissProt::Q47098 (262 letters) >FitnessBrowser__WCS417:GFF3489 Length = 266 Score = 339 bits (870), Expect = 3e-98 Identities = 173/258 (67%), Positives = 200/258 (77%) Query: 3 NSFKAALKAGRPQIGLWLGLSSSYSAELLAGAGFDWLLIDGEHAPNNVQTVLTQLQAIAP 62 N FK L+ G QIGLWLGL+ +Y AEL A AGFDWLLIDGEHAPN++Q +L QLQA+AP Sbjct: 6 NRFKQRLRNGEVQIGLWLGLADAYCAELAANAGFDWLLIDGEHAPNHLQGMLAQLQAVAP 65 Query: 63 YPSQPVVRPSWNDPVQIKQLLDVGTQTLLVPMVQNADEAREAVRATRYPPAGIRGVGSAL 122 YPSQ ++RP D IKQLLD+G QTLLVPMV++A +ARE VRA RYPP GIRGVGSAL Sbjct: 66 YPSQALIRPVIGDSALIKQLLDIGAQTLLVPMVESAAQARELVRAMRYPPEGIRGVGSAL 125 Query: 123 ARASRWNRIPDYLQKANDQMCVLVQIETREAMKNLPQILDVEGVDGVFIGPADLSADMGY 182 ARASRWN I YL +A+DQMC+LVQIE E + NL +I VEGVDGVFIGPADLSA MG+ Sbjct: 126 ARASRWNSIQGYLDQADDQMCLLVQIENLEGLANLDEIAAVEGVDGVFIGPADLSASMGH 185 Query: 183 AGNPQHPEVQAAIEQAIVQIRESGKAPGILIANEQLAKRYLELGALFVAVGVDTTLLARA 242 GNP HPEVQ AIE AI +I +SGKA GIL A+E LA+RY+ELGA FVAVGVDTT+L R Sbjct: 186 RGNPGHPEVQVAIEDAIGRIVQSGKAAGILSADENLARRYIELGATFVAVGVDTTVLMRG 245 Query: 243 AEALAARFGAQATAVKPG 260 +ALA +F T G Sbjct: 246 LQALAGKFKGVPTPTHAG 263 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: 260 Number of extensions: 7 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: 266 Length adjustment: 25 Effective length of query: 237 Effective length of database: 241 Effective search space: 57117 Effective search space used: 57117 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