Align 2-keto-3-deoxy-L-rhamnonate aldolase; KDR aldolase; EC 4.1.2.53; 2-dehydro-3-deoxyrhamnonate aldolase (uncharacterized)
to candidate RR42_RS27855 RR42_RS27855 4-hydroxy-2-oxo-heptane-1,7-dioate aldolase
Query= curated2:B5R262 (267 letters) >FitnessBrowser__Cup4G11:RR42_RS27855 Length = 267 Score = 271 bits (692), Expect = 1e-77 Identities = 135/257 (52%), Positives = 173/257 (67%) Query: 7 NPFKEGLRKGDTQIGLWLSSTTSYMAEIAATSGYDWLLIDGEHAPNTVQDLYHQLQAIAP 66 N FK L + QIGLWL + Y AE+ A +G+DWLLIDGEHAPNTV + QLQA+A Sbjct: 6 NTFKRALAANEQQIGLWLGLASPYTAEVLAGAGFDWLLIDGEHAPNTVPTILAQLQALAA 65 Query: 67 YASQPVIRPIEGSKALIKQVLDIGAQTLLIPMVDTAEQARQVVSATRYPPLGQRGVGASV 126 Y +PV+R IKQ+LD+G QTLL+PMV A +A V+ATRYPP G RGVG+++ Sbjct: 66 YPVRPVVRASWNDTVQIKQLLDLGVQTLLVPMVQDATEAAAAVAATRYPPQGVRGVGSAM 125 Query: 127 ARAARWGRIDNYMAQANESLCLLVQVESKVALENLDAILEVEGIDGVFIGPADLSASLGY 186 ARA+RW R+ Y+AQAN +C+LVQVE++ L +LDAI EG+DGVFIGPADL+A +G+ Sbjct: 126 ARASRWNRVGGYLAQANGEMCVLVQVETRAGLAHLDAIAATEGVDGVFIGPADLAADMGH 185 Query: 187 PDNAGHPEVQRIIESCIYRIRAAGKAAGFLAVDPAMAQKCLAWGANFVAVGVDTMLYTEA 246 N GHPEV+ I I RIR AGK AG L+ D A +++ +A G F AVGVD + A Sbjct: 186 LGNPGHPEVRSAIADAIVRIRRAGKGAGILSADVAQSRQYVALGTTFTAVGVDATMLARA 245 Query: 247 LDSRLAMFKSVQSVSTA 263 +S A FK S T+ Sbjct: 246 AESLAAQFKGHGSAGTS 262 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: 207 Number of extensions: 10 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: 267 Length adjustment: 25 Effective length of query: 242 Effective length of database: 242 Effective search space: 58564 Effective search space used: 58564 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