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 BWI76_RS19980 BWI76_RS19980 2-keto-3-deoxy-L-rhamnonate aldolase
Query= SwissProt::Q47098 (262 letters) >FitnessBrowser__Koxy:BWI76_RS19980 Length = 267 Score = 294 bits (752), Expect = 1e-84 Identities = 143/250 (57%), Positives = 185/250 (74%) Query: 1 MENSFKAALKAGRPQIGLWLGLSSSYSAELLAGAGFDWLLIDGEHAPNNVQTVLTQLQAI 60 + N FKA L G QIGLWL +SSY AE+ A +G+DWLLIDGEHAPN +Q + QLQAI Sbjct: 5 LSNPFKAGLLQGEAQIGLWLSSTSSYMAEIAATSGYDWLLIDGEHAPNTIQDLYHQLQAI 64 Query: 61 APYPSQPVVRPSWNDPVQIKQLLDVGTQTLLVPMVQNADEAREAVRATRYPPAGIRGVGS 120 APY SQPV+RP + IKQ+LD+G +TLL+PMV A++ARE V ATRYPP G RGVG+ Sbjct: 65 APYVSQPVIRPVEGNRSLIKQVLDIGARTLLIPMVDTAEQAREIVSATRYPPVGTRGVGA 124 Query: 121 ALARASRWNRIPDYLQKANDQMCVLVQIETREAMKNLPQILDVEGVDGVFIGPADLSADM 180 +ARA+RW R+ +Y+ +AND++C+L+Q+E++ A+ NL IL+VEG+DGVFIGPADLSA + Sbjct: 125 GVARAARWGRVENYMAQANDELCLLIQVESKTALDNLDAILEVEGIDGVFIGPADLSASL 184 Query: 181 GYAGNPQHPEVQAAIEQAIVQIRESGKAPGILIANEQLAKRYLELGALFVAVGVDTTLLA 240 GY N HP+VQ IEQ+I +IR +GKA G L + ++A + L GA FVAVGVDT L Sbjct: 185 GYPDNAGHPDVQRIIEQSIRRIRAAGKAAGFLAVDPEMAHKALAWGANFVAVGVDTNLYT 244 Query: 241 RAAEALAARF 250 RA + A F Sbjct: 245 RALDKRLAMF 254 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: 216 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: 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