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_012385750.1 BIND_RS14270 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase
Query= SwissProt::Q47098 (262 letters) >NCBI__GCF_000019845.1:WP_012385750.1 Length = 273 Score = 122 bits (305), Expect = 1e-32 Identities = 78/253 (30%), Positives = 122/253 (48%), Gaps = 12/253 (4%) Query: 3 NSFKAALKAGRPQIGLWLGLSSSYSAELLAGAGFDWLLIDGEHAPNNVQTVLTQLQAIAP 62 N+ + + AG+ I WL ++ ++AE++A G+D + ID +H + T LQA+ Sbjct: 4 NAIRQSFAAGKAVINGWLSIACPFTAEIMAHQGYDSITIDLQHGLVGYEVATTMLQAMQA 63 Query: 63 YPSQPVVRPSWNDPVQIKQLLDVGTQTLLVPMVQNADEAREAVRATRYPPAGIRGVGSAL 122 P+VR W DP I + LD G ++ PM+ EA + V RYPP G R G Sbjct: 64 SSVTPMVRVPWLDPGAIMKALDAGAYGVICPMINTPKEAEKLVSCVRYPPNGTRSFGPTR 123 Query: 123 ARASRWNRIPDYLQKANDQMCVLVQIETREAMKNLPQILDVEGVDGVFIGPADLSADMGY 182 + DY + A+ ++ IET +A NL I G+DG++IGPADL+ +G Sbjct: 124 VSIASG---ADYGEHADREVLCFAMIETAQAFANLDAIAATPGLDGLYIGPADLT--LGL 178 Query: 183 AG-------NPQHPEVQAAIEQAIVQIRESGKAPGILIANEQLAKRYLELGALFVAVGVD 235 G + + PE+ AAI+ + ++G + A + + G V + D Sbjct: 179 TGRQYRTGFDREEPEMVAAIKTILEAAHKAGIRACLHNGTPTYAAKAISWGFDLVTISND 238 Query: 236 TTLLARAAEALAA 248 LLA AA+A A Sbjct: 239 VRLLAGAAQASVA 251 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: 157 Number of extensions: 6 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: 273 Length adjustment: 25 Effective length of query: 237 Effective length of database: 248 Effective search space: 58776 Effective search space used: 58776 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 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