Align 4-carboxy-4-hydroxy-2-oxoadipic acid aldolase; CHA aldolase; Gallate degradation protein C; EC 4.1.3.17 (characterized)
to candidate Pf1N1B4_178 Demethylmenaquinone methyltransferase
Query= SwissProt::Q88JX9 (238 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_178 Length = 203 Score = 84.7 bits (208), Expect = 1e-21 Identities = 54/172 (31%), Positives = 85/172 (49%), Gaps = 2/172 (1%) Query: 41 KGLLNTAVRPIQQGVAVAGSAVTVLVAPGDNWMFHVAVEQCRPGDVLVVAPSSPCSDGYF 100 +G ++ +R + V + G A+T+ + D + A+ +PGDVLV+ Sbjct: 24 EGFADSQLRAMVPNVRLVGRALTLKLVGADAIAVNQALALIQPGDVLVIDTDGDWQHAPV 83 Query: 101 GDLLATSLQARGVLGLVIDAGVRDSQTLRDMGFAVWSRAINAQGTVKEVLGS--VNLPLL 158 G + + G +G+V+D V D LR+ G V++R + T G +N P+ Sbjct: 84 GAVTRCAASCAGAVGIVVDGAVTDLLELREAGLPVFARGTSLLTTKLHGRGDSQINQPIH 143 Query: 159 CAGQLVNAGDIVVADDDGVVVVRHGEAQAVLEAATQRADLEERKRLRLAAGE 210 CAG V+ GD+V+ADD+GV+ + AQ V+E A E R RL AGE Sbjct: 144 CAGVTVHPGDLVLADDNGVLFLNPATAQNVIERALASDRAEPRLLERLRAGE 195 Lambda K H 0.320 0.138 0.400 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: 123 Number of extensions: 9 Number of successful extensions: 2 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: 238 Length of database: 203 Length adjustment: 22 Effective length of query: 216 Effective length of database: 181 Effective search space: 39096 Effective search space used: 39096 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 45 (21.9 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