Align 2-keto-3-deoxy-L-rhamnonate aldolase; KDR aldolase; EC 4.1.2.53; 2-dehydro-3-deoxyrhamnonate aldolase (uncharacterized)
to candidate RR42_RS27275 RR42_RS27275 alpha-dehydro-beta-deoxy-D-glucarate aldolase
Query= curated2:B5R262 (267 letters) >FitnessBrowser__Cup4G11:RR42_RS27275 Length = 255 Score = 213 bits (541), Expect = 4e-60 Identities = 117/252 (46%), Positives = 156/252 (61%), Gaps = 2/252 (0%) Query: 7 NPFKEGLRKGDTQIGLWLSSTTSYMAEIAATSGYDWLLIDGEHAPNTVQDLYHQLQAIAP 66 N FK+ + QIGLW S ++ + E+ A S +DWLL+D EHAPN + L+ QL A Sbjct: 6 NAFKQAILADQPQIGLWCSLSSYQVVELVARSQFDWLLLDMEHAPNDISTLHTQLMATEG 65 Query: 67 YASQPVIRPIEGSKALIKQVLDIGAQTLLIPMVDTAEQARQVVSATRYPPLGQRGVGASV 126 S PV+RP IK+ LDIGAQ+LL+P V AE+A V+ +R+P G RGV AS Sbjct: 66 ARSHPVVRPPWNDMLWIKRCLDIGAQSLLLPYVQNAEEAANAVAWSRFPKGGMRGV-ASG 124 Query: 127 ARAARWGRIDNYMAQANESLCLLVQVESKVALENLDAILEVEGIDGVFIGPADLSASLGY 186 RA +GRI +++ E C+LVQ+ES A+ N+DAI ++G+DGVFIGP+DLSA + + Sbjct: 125 TRAGGFGRIKDFLHNVQEQTCVLVQLESMEAIRNVDAICALDGVDGVFIGPSDLSADMNH 184 Query: 187 PDNAGHPEVQRIIESCIYRIRAAGKAAGFLAVDPAMAQKCLAWGANFVAVGVDTMLYTEA 246 + HPEVQ I + I RIRA GKAAG L + A Q+ + GA FVAVG D L A Sbjct: 185 LGDIQHPEVQETIAAAIRRIRANGKAAGILTTE-AQGQQYIDMGARFVAVGTDMTLLRLA 243 Query: 247 LDSRLAMFKSVQ 258 D+ A F+ Q Sbjct: 244 TDALAARFRQAQ 255 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: 159 Number of extensions: 5 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: 267 Length of database: 255 Length adjustment: 25 Effective length of query: 242 Effective length of database: 230 Effective search space: 55660 Effective search space used: 55660 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