Align 2-keto-3-deoxy-L-rhamnonate aldolase; KDR aldolase; EC 4.1.2.53; 2-dehydro-3-deoxyrhamnonate aldolase (uncharacterized)
to candidate BPHYT_RS01515 BPHYT_RS01515 2-dehydro-3-deoxyglucarate aldolase
Query= curated2:B5R262 (267 letters) >FitnessBrowser__BFirm:BPHYT_RS01515 Length = 260 Score = 172 bits (437), Expect = 5e-48 Identities = 101/257 (39%), Positives = 149/257 (57%), Gaps = 7/257 (2%) Query: 6 SNPFKEGLRKGDTQIGLWLSSTTSYMAEIAATSGYDWLLIDGEHAPNTVQDLYHQLQAIA 65 +NP K L++ D GLWLS + AE A +GYDWLLID EH+PN D+ QL+AIA Sbjct: 5 TNPLKSRLKETDPLFGLWLSLGSDAAAEALAHAGYDWLLIDMEHSPNDSGDVTSQLRAIA 64 Query: 66 P--YASQPVIRPIEGSKALIKQVLDIGAQTLLIPMVDTAEQARQVVSATRYPPLG----Q 119 S+PV+R L+K+VLD GA+TL+ P +++A++A + V T+YP G + Sbjct: 65 AAHLPSEPVVRVPSSEAWLVKRVLDAGARTLMFPNIESADEAARAVRLTQYPSAGALDGE 124 Query: 120 RGVGASVARAARWGRIDNYMAQANESLCLLVQVESKVALENLDAILEVEGIDGVFIGPAD 179 RGV +V RAA +G +Y+ AN + +VQ+ES L+ ++ I G+D +F+GPAD Sbjct: 125 RGVAGAV-RAAGYGMRRDYVQTANAQIATIVQIESARGLQEVEKIAATPGVDCLFVGPAD 183 Query: 180 LSASLGYPDNAGHPEVQRIIESCIYRIRAAGKAAGFLAVDPAMAQKCLAWGANFVAVGVD 239 L+ASLG+ ++ H +VQ + + AG AAG A+D A A++ G F+A+ D Sbjct: 184 LAASLGHLGDSKHADVQAAMARIVSAADKAGIAAGIFAMDVASAKQHRDAGFRFIALAAD 243 Query: 240 TMLYTEALDSRLAMFKS 256 M A L +S Sbjct: 244 VMWMLRATRQALQEVRS 260 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: 166 Number of extensions: 8 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: 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