Align Probable glucarate dehydratase; GDH; GlucD; EC 4.2.1.40 (uncharacterized)
to candidate GFF4626 PS417_23670 muconate cycloisomerase
Query= curated2:Q9RDE9 (431 letters) >FitnessBrowser__WCS417:GFF4626 Length = 375 Score = 112 bits (281), Expect = 1e-29 Identities = 115/413 (27%), Positives = 173/413 (41%), Gaps = 60/413 (14%) Query: 5 LTITAVHLTPILVADPPLLNTQ--GVHQPYTPRL-IVEVETADGVTGVGE-------TYG 54 + I A+ ++ D P L +H L I+ + ADG+ G+GE +YG Sbjct: 1 MPICAIESIDTIIVDLPTLRPHKLAMHTMQNQTLVIIRLRCADGIEGIGEATTIGGLSYG 60 Query: 55 ----DAKYLELARPFAAKLVGRQVSDLNGLFTLADEVAVDSSRVFGQVDVGGLRGVQTAD 110 D+ + + R FA L+G+ S++N + +RG A Sbjct: 61 NESPDSIKVNIDRHFAPLLIGQDASNINAAMLRLER---------------SIRGNTFAK 105 Query: 111 KLRLSVVSGFEVACLDALGKALGLPVHALLGGKVRDAVEYSAYLFYKWADHPEGVASEKD 170 SG E A LDALGK L LPV LLGG+VRDA+ + L +EKD Sbjct: 106 -------SGIESALLDALGKRLNLPVSELLGGRVRDALPVAWTL--------ASGNTEKD 150 Query: 171 DWGAAVDPAGVVAQARAFTERYGFTSFKLKGGVFPPEEEIAAVKALAEAFPGH-PLRLDP 229 +A+A + FKLK G ++A V A+ +A +R+D Sbjct: 151 -----------IAEAEKMLDLRRHRLFKLKIGAGEVSHDLAHVIAIKKALGDRASVRVDV 199 Query: 230 NGAWSVETSLKVAAELGD-VLEYLEDPAL--GTPAMAEVAAKTGVPLATNMCVTTFAEIQ 286 N AW +L+ LGD ++ +E P MA + + P+ + + + Sbjct: 200 NQAWDEAVALRACKVLGDNGIDLIEQPISRNNRGGMARLNLSSPAPIMADESIECVEDAF 259 Query: 287 EAFTKGAVQVVLSDHHYWGGLRNTQQLAAVCRTFGVGVSMHSNTHLGISLAAMTHVAATV 346 +GA V GG R + AA+ G+G+ + GI A H T+ Sbjct: 260 NLAREGAASVFALKIAKNGGPRAVLRTAAIAEAAGIGLYGGTMLEGGIGTLASAHAFLTL 319 Query: 347 PDLHHACDSHYP-WQSEDVLTERLAFDGGKVAVSDAPGLGVALDRERLAFLHR 398 L + P +ED+LTE + ++ VS APGLG+A+D ERLAF R Sbjct: 320 NKLAWDTELFGPLLLTEDILTEPPVYRDFQLHVSTAPGLGLAIDEERLAFFRR 372 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: 340 Number of extensions: 17 Number of successful extensions: 5 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: 375 Length adjustment: 31 Effective length of query: 400 Effective length of database: 344 Effective search space: 137600 Effective search space used: 137600 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