Align Probable glucarate dehydratase; GDH; GlucD; EC 4.2.1.40 (uncharacterized)
to candidate Pf1N1B4_5057 mandelate racemase family protein Pfl_3283
Query= curated2:Q9RDE9 (431 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5057 Length = 424 Score = 389 bits (998), Expect = e-112 Identities = 203/424 (47%), Positives = 277/424 (65%), Gaps = 8/424 (1%) Query: 5 LTITAVHLTPILVADPPLLNTQGVHQPYTPRLIVEVETADGVTGVGETYGDAKYLELARP 64 L I V +TPI DPPLLN G+H+P+ R I+E+E+ +G G+GE+YGDA L + + Sbjct: 1 LKIKRVTVTPIAFRDPPLLNASGIHEPFALRSIIEIESDNGYIGLGESYGDAPALAIQQQ 60 Query: 65 FAAKLVGRQVSDLNGLFTLADEVAVDSSRVFGQVDVGGLRGVQTADKLRLSVVSGFEVAC 124 ++L+G +LN L + + V +++ G + L A K + S FEVA Sbjct: 61 LQSQLIGLDPFNLNQLRAIV-QATVAANKTQG-IAGAELAPGSHASKAVSNAYSAFEVAF 118 Query: 125 LDALGKALGLPVHALLGGKVRDAVEYSAYLFYKWADHPEGVASEKDDWGAAVDPAGVVAQ 184 LD +L +P+ LLGG +RD V +SAYLF+K+A H + + D WG A++ +VAQ Sbjct: 119 LDLQAHSLNVPLVDLLGGAIRDEVPFSAYLFFKYAQHIDS-PYKPDSWGEALNEEQIVAQ 177 Query: 185 ARAFTERYGFTSFKLKGGVFPPEEEIAAVKALAEAFPGHPLRLDPNGAWSVETSLKVAAE 244 AR E YGF S KLK G PPE E++ +KAL +AFPG+PLR+DPNG WS+ETS+++A Sbjct: 178 ARRMIEAYGFKSIKLKAGALPPEHEVSCIKALKKAFPGYPLRIDPNGNWSLETSIRMAEL 237 Query: 245 LGDVLEYLEDPALGTPAMAEVAAKTGVPLATNMCVTTFAEIQEAFTKGAVQVVLSDHHYW 304 LGD L+Y EDP G MAE+ +TG+PLATNM VT F E + + +VQ+VL+DHHYW Sbjct: 238 LGDDLQYYEDPTPGLDGMAELHKRTGLPLATNMVVTDFDEFRRSVALNSVQIVLADHHYW 297 Query: 305 GGLRNTQQLAAVCRTFGVGVSMHSNTHLGISLAAMTHVAATVPDLHHACDSHYPWQSED- 363 GGLR+TQ LA +C TFG+GVSMHSN+HLGISL AM HVAA+VP+L +ACD+HYPWQ D Sbjct: 298 GGLRDTQALAKMCDTFGLGVSMHSNSHLGISLMAMAHVAASVPNLDYACDTHYPWQEPDE 357 Query: 364 --VLTERLAFDGGKVAVSDAPGLGVALDRERLAFLHRRWLDDDGTLRDRDDAAAMRVADP 421 + +L+ G V ++ APGLG+ LD ++L LH ++L +R RDD M+ P Sbjct: 358 EVIKGGKLSIVDGCVKITRAPGLGLELDHDQLGKLHDQYLSCG--IRQRDDVKQMQRYKP 415 Query: 422 EWVT 425 EW T Sbjct: 416 EWKT 419 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: 519 Number of extensions: 15 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: 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