Align Probable glucarate dehydratase; GDH; GlucD; EC 4.2.1.40 (uncharacterized)
to candidate PfGW456L13_3824 Muconate cycloisomerase (EC 5.5.1.1)
Query= curated2:Q9RDE9 (431 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3824 Length = 424 Score = 106 bits (264), Expect = 2e-27 Identities = 108/414 (26%), Positives = 172/414 (41%), Gaps = 60/414 (14%) Query: 4 DLTITAVHLTPILVADPPLLNTQ--GVHQPYTPRL-IVEVETADGVTGVGET-------Y 53 ++ TA+ ++ D P + +H L I+ V ADG+ G+GE+ Y Sbjct: 42 EMLATAIESIETIIVDLPTIRPHKLAMHTMQNQTLVIIRVRCADGIEGIGESTTIGGLAY 101 Query: 54 G----DAKYLELARPFAAKLVGRQVSDLNGLFTLADEVAVDSSRVFGQVDVGGLRGVQTA 109 G D+ + FA L+G+ +++N + +RG A Sbjct: 102 GNESPDSIKTNIDTHFAPLLIGQDSNNVNAAMLRLER---------------SIRGNTFA 146 Query: 110 DKLRLSVVSGFEVACLDALGKALGLPVHALLGGKVRDAVEYSAYLFYKWADHPEGVASEK 169 SG E A LDALGK LGLPV LLGG+VRDA+ + L Sbjct: 147 K-------SGIETALLDALGKRLGLPVSELLGGRVRDALPVAWTL--------------- 184 Query: 170 DDWGAAVDPAGVVAQARAFTERYGFTSFKLKGGVFPPEEEIAAVKALAEAFPGH-PLRLD 228 A+ D +A+A + FKLK G ++A V A+ +A +R+D Sbjct: 185 ----ASGDTEKDIAEAEKMLDLRRHRIFKLKIGAGEVNRDLAHVIAIKKALGDRASVRVD 240 Query: 229 PNGAWSVETSLKVAAELG-DVLEYLEDPAL--GTPAMAEVAAKTGVPLATNMCVTTFAEI 285 N AW +L+ LG + ++ +E P MA + A + P+ + + + Sbjct: 241 VNQAWDEAVALRACRILGTNGIDLIEQPISRNNRAGMARLNAMSPAPIMADESIECVEDA 300 Query: 286 QEAFTKGAVQVVLSDHHYWGGLRNTQQLAAVCRTFGVGVSMHSNTHLGISLAAMTHVAAT 345 +GA V GG R + A++ G+ + + G+ A H T Sbjct: 301 FNLAREGAASVFALKIAKNGGPRAVLRTASIAEAAGIALYGGTMLEGGLGTMASAHAFVT 360 Query: 346 VPDLHHACDSHYP-WQSEDVLTERLAFDGGKVAVSDAPGLGVALDRERLAFLHR 398 + L + P +ED+L+E L + ++ V + PGLG++LD ERLAF R Sbjct: 361 LNKLAWDTELFGPLLLTEDILSEPLVYRDFELHVPNTPGLGLSLDEERLAFFRR 414 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: 370 Number of extensions: 9 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: 431 Length of database: 424 Length adjustment: 32 Effective length of query: 399 Effective length of database: 392 Effective search space: 156408 Effective search space used: 156408 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: 51 (24.3 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