Align 2-keto-3-deoxy-L-rhamnonate aldolase; KDR aldolase; EC 4.1.2.53; 2-dehydro-3-deoxyrhamnonate aldolase (uncharacterized)
to candidate 3608243 Dshi_1647 2-dehydro-3-deoxyglucarate aldolase (RefSeq)
Query= curated2:B5R262 (267 letters) >FitnessBrowser__Dino:3608243 Length = 260 Score = 209 bits (532), Expect = 5e-59 Identities = 106/241 (43%), Positives = 148/241 (61%) Query: 7 NPFKEGLRKGDTQIGLWLSSTTSYMAEIAATSGYDWLLIDGEHAPNTVQDLYHQLQAIAP 66 N K+ L GD QIG+WL +AE+AA G+DW L+DGEH+PN + QL+A+ Sbjct: 6 NQLKQALLAGDVQIGIWLGFGAPAVAELAAGCGFDWCLVDGEHSPNDPAQMIDQLRAMVG 65 Query: 67 YASQPVIRPIEGSKALIKQVLDIGAQTLLIPMVDTAEQARQVVSATRYPPLGQRGVGASV 126 + P++R G ++K+ LD+G QT+++PMV+TA QA+Q+V A RYPP G RGVGA++ Sbjct: 66 QGAMPIVRVPVGEDWVLKRALDLGVQTIMVPMVETAAQAQQIVRAMRYPPDGVRGVGAAL 125 Query: 127 ARAARWGRIDNYMAQANESLCLLVQVESKVALENLDAILEVEGIDGVFIGPADLSASLGY 186 ARA+ + Y+ AN +C +VQ+ES A+ + I VEG+D +FIGPADL+A +GY Sbjct: 126 ARASGYSLDAEYVTTANAQICTIVQIESHAAVRAIPEIAAVEGVDVLFIGPADLAADMGY 185 Query: 187 PDNAGHPEVQRIIESCIYRIRAAGKAAGFLAVDPAMAQKCLAWGANFVAVGVDTMLYTEA 246 P A PEV +I + + I +GK G LA A + A GA FV VG D A Sbjct: 186 PGRADAPEVDAVICAALGEIARSGKVPGVLAFSETDAVRFAAAGARFVGVGADVTSLAVA 245 Query: 247 L 247 L Sbjct: 246 L 246 Lambda K H 0.318 0.132 0.384 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: 186 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: 267 Length of database: 260 Length adjustment: 25 Effective length of query: 242 Effective length of database: 235 Effective search space: 56870 Effective search space used: 56870 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