Align Probable glucarate dehydratase; GDH; GlucD; EC 4.2.1.40 (uncharacterized)
to candidate HSERO_RS05730 HSERO_RS05730 glucarate dehydratase
Query= curated2:Q9RDE9 (431 letters) >FitnessBrowser__HerbieS:HSERO_RS05730 Length = 424 Score = 383 bits (983), Expect = e-111 Identities = 203/427 (47%), Positives = 273/427 (63%), Gaps = 14/427 (3%) Query: 5 LTITAVHLTPILVADPPLLNTQGVHQPYTPRLIVEVETADGVTGVGETYGDAKYLELARP 64 + IT V +TPI D PLLN G+H+PY R I+E+ET +G G+GE+YGDA L++ Sbjct: 1 MKITRVTVTPIAFKDGPLLNASGIHEPYALRSIIEIETDNGYIGLGESYGDAPALKILDL 60 Query: 65 FAAKLVGRQVSDLNGLFTLADEVAV---DSSRVFGQVDVGGLRGVQTADKLRLSVVSGFE 121 +LVG +LNGL + V +S ++ G A K + S FE Sbjct: 61 VKERLVGLDPFNLNGLRAIVRGVVAAMAPASNAGAELAPGS-----HASKAVSNAYSAFE 115 Query: 122 VACLDALGKALGLPVHALLGGKVRDAVEYSAYLFYKWADHPEGVASEKDDWGAAVDPAGV 181 VACLDA + L +P+ LLGG VR + +SAYLF+K+A H + + D WG A+ + Sbjct: 116 VACLDAQARYLNVPLVDLLGGAVRKEIPFSAYLFFKYAQHIDSPYAP-DAWGEALSEEQI 174 Query: 182 VAQARAFTERYGFTSFKLKGGVFPPEEEIAAVKALAEAFPGHPLRLDPNGAWSVETSLKV 241 VAQAR E GF S KLK G PE E+A +KAL +AFP PLR+DPNG WS++T++++ Sbjct: 175 VAQARKMIEENGFQSIKLKAGALAPEHEVACIKALRKAFPDAPLRIDPNGNWSLQTAIRM 234 Query: 242 AAELGDVLEYLEDPALGTPAMAEVAAKTGVPLATNMCVTTFAEIQEAFTKGAVQVVLSDH 301 A LGD L+Y EDP G MAE+ +TG+PLATNM VT F E++ + +VQ+VL+DH Sbjct: 235 AELLGDDLQYYEDPTPGLEGMAELHRRTGLPLATNMVVTDFDELRRSVALDSVQIVLADH 294 Query: 302 HYWGGLRNTQQLAAVCRTFGVGVSMHSNTHLGISLAAMTHVAATVPDLHHACDSHYPWQS 361 HYWGGLR+TQQLA +C FG+GVSMHSN+HLGISL AM+HVAA V +L +ACD+HYPWQ Sbjct: 295 HYWGGLRDTQQLAKMCDVFGLGVSMHSNSHLGISLMAMSHVAAAVENLSYACDTHYPWQE 354 Query: 362 ED---VLTERLAFDGGKVAVSDAPGLGVALDRERLAFLHRRWLDDDGTLRDRDDAAAMRV 418 D + +L G V ++DAPGLGV +D+++L LH+ +L+ +R RDD MR Sbjct: 355 PDEEVIQGGKLPIRNGCVQITDAPGLGVEVDQDQLRKLHQLYLECG--IRQRDDVGQMRK 412 Query: 419 ADPEWVT 425 P+W T Sbjct: 413 YQPDWKT 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: 512 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