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 BPHYT_RS28905 BPHYT_RS28905 alpha-dehydro-beta-deoxy-D-glucarate aldolase
Query= SwissProt::Q47098 (262 letters) >FitnessBrowser__BFirm:BPHYT_RS28905 Length = 267 Score = 299 bits (766), Expect = 4e-86 Identities = 152/253 (60%), Positives = 183/253 (72%) Query: 3 NSFKAALKAGRPQIGLWLGLSSSYSAELLAGAGFDWLLIDGEHAPNNVQTVLTQLQAIAP 62 N+FK AL G+PQ GLW L+ +Y ELLA AGFDWLLID EHAPN+V++ L QLQA+A Sbjct: 6 NNFKRALAEGKPQFGLWAALADAYVTELLATAGFDWLLIDNEHAPNDVRSTLAQLQAVAA 65 Query: 63 YPSQPVVRPSWNDPVQIKQLLDVGTQTLLVPMVQNADEAREAVRATRYPPAGIRGVGSAL 122 Y S PVVRP +D IKQLLD+G QTLL+PM+ A++A +AV ATRYPP GIRGVGSAL Sbjct: 66 YASHPVVRPVRSDSALIKQLLDIGAQTLLLPMIDTAEQAADAVAATRYPPQGIRGVGSAL 125 Query: 123 ARASRWNRIPDYLQKANDQMCVLVQIETREAMKNLPQILDVEGVDGVFIGPADLSADMGY 182 ARASRWNRIPDYL A D++CVLVQ+E+ + M+NL I V+GVDGVF GP+DLSA MG Sbjct: 126 ARASRWNRIPDYLNTAADELCVLVQVESVQGMENLSAIAAVDGVDGVFFGPSDLSASMGL 185 Query: 183 AGNPQHPEVQAAIEQAIVQIRESGKAPGILIANEQLAKRYLELGALFVAVGVDTTLLARA 242 G P V+ AI I + +GKA G+L + +A YLE GA FVAVG DT LL+RA Sbjct: 186 LGKPGDASVREAIRNGIQTVLRAGKAAGVLAPDPAIAADYLEAGATFVAVGTDTGLLSRA 245 Query: 243 AEALAARFGAQAT 255 A LAA + AT Sbjct: 246 AADLAASYKKTAT 258 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: 248 Number of extensions: 3 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