Align 2-keto-3-deoxy-L-rhamnonate aldolase; KDR aldolase; EC 4.1.2.53; 2-dehydro-3-deoxyrhamnonate aldolase (uncharacterized)
to candidate Pf6N2E2_1103 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase (EC 4.1.2.n4)
Query= curated2:B5R262 (267 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1103 Length = 266 Score = 277 bits (709), Expect = 1e-79 Identities = 136/261 (52%), Positives = 174/261 (66%) Query: 7 NPFKEGLRKGDTQIGLWLSSTTSYMAEIAATSGYDWLLIDGEHAPNTVQDLYHQLQAIAP 66 N FK L Q G+W T Y AEI A +GYDW+LIDGEHAPNTV + QLQA+AP Sbjct: 6 NAFKAALTSTQPQYGIWAGFATGYAAEIIAGTGYDWMLIDGEHAPNTVPSILGQLQAVAP 65 Query: 67 YASQPVIRPIEGSKALIKQVLDIGAQTLLIPMVDTAEQARQVVSATRYPPLGQRGVGASV 126 YA+ PV+R + G LIKQ+LD+GAQTL+IPMV+TAEQA+ +V A RYPP G RGVG + Sbjct: 66 YATAPVVRAVTGDANLIKQLLDVGAQTLMIPMVETAEQAQALVRAMRYPPHGIRGVGGGL 125 Query: 127 ARAARWGRIDNYMAQANESLCLLVQVESKVALENLDAILEVEGIDGVFIGPADLSASLGY 186 RA RW + NY+ A+E LCL+VQVES+ +EN++AI VEG+D VFIGPADLS LG+ Sbjct: 126 TRATRWDGVANYLTTAHEELCLIVQVESRTGVENVEAIAAVEGVDAVFIGPADLSIGLGH 185 Query: 187 PDNAGHPEVQRIIESCIYRIRAAGKAAGFLAVDPAMAQKCLAWGANFVAVGVDTMLYTEA 246 N GHPEVQ I + A GKA G LA + A A++ AWG F+AV +D L ++ Sbjct: 186 AGNPGHPEVQERIRHAVDATLATGKACGILAPNEADARRYQAWGCQFIAVAIDISLLRQS 245 Query: 247 LDSRLAMFKSVQSVSTAKRSY 267 + LA ++ +V R+Y Sbjct: 246 AQATLARYREPATVQAPSRTY 266 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: 202 Number of extensions: 9 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: 266 Length adjustment: 25 Effective length of query: 242 Effective length of database: 241 Effective search space: 58322 Effective search space used: 58322 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