Align uronate dehydrogenase (EC 1.1.1.203) (characterized)
to candidate AO353_03260 AO353_03260 epimerase
Query= BRENDA::Q88NN6 (268 letters) >FitnessBrowser__pseudo3_N2E3:AO353_03260 Length = 247 Score = 139 bits (350), Expect = 6e-38 Identities = 88/233 (37%), Positives = 124/233 (53%), Gaps = 7/233 (3%) Query: 8 RLLLTGAAGGLGKVLRERLKGYAEVLRLSDISPMAPAAGPHEEVITCDLADKAAVHTLVE 67 ++LLTGA G +GK E K + P PH DL+D AAV +E Sbjct: 5 KVLLTGACGRIGKTFFEASKDRYTFTLTDRVEPGFTVNAPHR-FFCLDLSDAAAVSAALE 63 Query: 68 GVDAIIHFGGVSTEHA-FEEILGPNICGVFHVYEAARKHGVKRIIFASSNHTIGFYRQDE 126 G+D I+H G+ A F+E+L NI +++EA+ G KR++FASS TI Y D Sbjct: 64 GIDVIVHLAGIPHATASFDELLPNNILATTYLFEASVAAGCKRLVFASSAQTIEGYPVDR 123 Query: 127 RIDAHAPRRPDSYYGLSKCYGEDVASFYFDRYGIETVSIRIGS-SFP---QPQNLRMLCT 182 +I P P + YG+SKCYGE + +FY + G+ T+++RIG+ FP + N R L Sbjct: 124 QITPGMPVMPANLYGVSKCYGEALCAFYSAKRGLSTIALRIGAFEFPDRHELTNARDLSA 183 Query: 183 WLSYDDLVQLIERGLFTPGVGHTIVYGASDNRTVWWDNRHAAH-LGYVPKDSS 234 WLS D VQL++R + GV + I +G S+NR D LGY P D + Sbjct: 184 WLSPRDAVQLLQRSVEVEGVQYLIGHGISNNRFKRLDLSETTRVLGYEPVDDA 236 Lambda K H 0.321 0.138 0.427 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: 177 Number of extensions: 12 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: 268 Length of database: 247 Length adjustment: 24 Effective length of query: 244 Effective length of database: 223 Effective search space: 54412 Effective search space used: 54412 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: 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