Align Probable glucarate dehydratase; GDH; GlucD; EC 4.2.1.40 (uncharacterized)
to candidate SMa0056 SMa0056 dehydratase/enolase
Query= curated2:Q9RDE9 (431 letters) >FitnessBrowser__Smeli:SMa0056 Length = 377 Score = 155 bits (392), Expect = 2e-42 Identities = 107/306 (34%), Positives = 152/306 (49%), Gaps = 34/306 (11%) Query: 7 ITAVHLTPILVA-DPPLLNTQGVHQPYTPRLIVEVETADGVTGVGETYGDAKYLELA-RP 64 IT + T + V + PL ++ G H R IVEVET G+ G+GE G + E A R Sbjct: 6 ITDIRATTVTVPLEAPLRHSNGAHWGRFVRTIVEVETDVGIVGLGEMGGGGESAEAAFRA 65 Query: 65 FAAKLVGRQVSDLNGL-FTLADEVAVDSSRVFGQVDVGGLRGVQTADKLRLSVVSGFEVA 123 L+G +L L F + + A + R + + E A Sbjct: 66 LKPYLLGHDTFELENLRFMICNPTA-------------------SLYNNRTQMHAAIEFA 106 Query: 124 CLDALGKALGLPVHALLGGKVRDAVEYSAYLFYKWA--DHPEGVASEKDDWGAAVDPAGV 181 CLD +GK LG+PV LLGGK+RDAV +++Y+F++ D EG D + Sbjct: 107 CLDIMGKFLGVPVCDLLGGKMRDAVPFASYMFFRLPNKDTGEGETRTADQ---------L 157 Query: 182 VAQARAFTERYGFTSFKLKGGVFPPEEEIAAVKALAEAFPGHPLRLDPNGAWSVETSLKV 241 + Q A ++ GFTS KLK GVFPP+ E+ +A A+A +R DPN A+SVE +++ Sbjct: 158 IEQTLALKKKCGFTSHKLKSGVFPPDYELEVFRAWAKALGPDSVRYDPNAAFSVEEAIRF 217 Query: 242 AAELGDV-LEYLEDPALGTPAMAEVAAKTGVPLATNMCVTTFAEIQEAFTKGAVQVVLSD 300 A + D+ +Y EDP G M V T +PLATN V F ++ AV V+L D Sbjct: 218 AKGIEDLNNDYYEDPTWGLNGMRRVRENTTMPLATNTVVVNFEQLATNILNPAVDVILLD 277 Query: 301 HHYWGG 306 +WGG Sbjct: 278 TTFWGG 283 Lambda K H 0.319 0.135 0.410 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: 362 Number of extensions: 16 Number of successful extensions: 4 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: 431 Length of database: 377 Length adjustment: 31 Effective length of query: 400 Effective length of database: 346 Effective search space: 138400 Effective search space used: 138400 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 (21.7 bits) S2: 50 (23.9 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