Align 2-keto-3-deoxy-L-rhamnonate aldolase; KDR aldolase; EC 4.1.2.53; 2-dehydro-3-deoxyrhamnonate aldolase (uncharacterized)
to candidate GFF1907 PGA1_c19370 4-hydroxy-2-oxovalerate aldolase BphF
Query= curated2:B5R262 (267 letters) >FitnessBrowser__Phaeo:GFF1907 Length = 254 Score = 193 bits (491), Expect = 3e-54 Identities = 101/244 (41%), Positives = 150/244 (61%), Gaps = 2/244 (0%) Query: 7 NPFKEGLRKGDTQIGLWLSSTTSYMAEIAATSGYDWLLIDGEHAPNTVQDLYHQLQAIAP 66 N FK + G Q+G+W + + + E+ +G++W+L+D EHA ++ LQAI Sbjct: 6 NRFKSAIANGTRQLGVWNTIGGNTVPELLGGAGFEWVLVDCEHAAIETIEVLPALQAIGQ 65 Query: 67 YA-SQPVIRPIEGSKALIKQVLDIGAQTLLIPMVDTAEQARQVVSATRYPPLGQRGVGAS 125 + V+R L K+VLD+GAQ +++P V TA +A V A RY P G RG+ A Sbjct: 66 NPDTSAVVRVAANDATLFKRVLDMGAQNVMVPYVQTAREAAAAVHAMRYGPHGMRGM-AG 124 Query: 126 VARAARWGRIDNYMAQANESLCLLVQVESKVALENLDAILEVEGIDGVFIGPADLSASLG 185 + RA R+G++D+Y A + LCL+VQVE++ LENLDAI +G+D VFIGPADLSAS+G Sbjct: 125 MTRATRYGKVDDYFDVAEDELCLIVQVETQTGLENLDAIAGTDGVDAVFIGPADLSASMG 184 Query: 186 YPDNAGHPEVQRIIESCIYRIRAAGKAAGFLAVDPAMAQKCLAWGANFVAVGVDTMLYTE 245 HP+V + + + I R+ G AG +A+DP +A + LA GA FVAV VD ++ + Sbjct: 185 LRGQMTHPDVDKAVSNAINRLGEMGVPAGVMALDPDIADRYLALGATFVAVAVDLVVLAD 244 Query: 246 ALDS 249 A+ + Sbjct: 245 AVSN 248 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: 142 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: 254 Length adjustment: 24 Effective length of query: 243 Effective length of database: 230 Effective search space: 55890 Effective search space used: 55890 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