Align Glucarate dehydratase; GDH; GlucD; EC 4.2.1.40 (characterized)
to candidate WP_011778290.1 MVAN_RS05135 glucarate dehydratase
Query= SwissProt::P42206 (451 letters) >NCBI__GCF_000015305.1:WP_011778290.1 Length = 445 Score = 638 bits (1645), Expect = 0.0 Identities = 305/441 (69%), Positives = 362/441 (82%), Gaps = 3/441 (0%) Query: 14 PVITDLKVVPVAGHDSMLLNLSGAHGPLFTRNILILTDSSGHVGVGEVPGGEGIRKTLED 73 PVITD+ VVP+AGHDSMLLNLSGAHGP FTRN++I+ DS G+ GVGEVPGGE IR+TL+D Sbjct: 4 PVITDVTVVPIAGHDSMLLNLSGAHGPFFTRNLVIVEDSEGNTGVGEVPGGEPIRRTLQD 63 Query: 74 ARHLLINQSIGNYQSLLNKVRNAFADRDVGGRGLQTFDLRIAVHAVTAVESALLDLLGQH 133 AR ++ +SIG+Y ++LN++R FADRD GGRG QTFDLR+ VHAVTA+ESAL+DLLGQH Sbjct: 64 ARGIVTGRSIGDYHAVLNEMRRTFADRDAGGRGAQTFDLRVTVHAVTAIESALMDLLGQH 123 Query: 134 LQVPVAALLGEGQQRDAVEMLGYLFYVGDRNKTDLGYRS---EHEADNEWFRLRNKEALT 190 L+VPVAALLG+GQQR V+ LGYLF+VGDR +TDL YRS E ++WF +R++EA+T Sbjct: 124 LEVPVAALLGDGQQRSRVQALGYLFFVGDRTRTDLAYRSPSDEEPGADDWFTVRHEEAMT 183 Query: 191 PESVVALAEAAYDRYGFKDFKLKGGVLRGEDEIAAVTALSERFPDARITLDPNGAWSLKE 250 P++VV LAEAA RYGF DFKLKGGVL DE AV AL+ERFPD+RITLDPNG W L + Sbjct: 184 PDAVVRLAEAARARYGFADFKLKGGVLPAADEAKAVIALAERFPDSRITLDPNGGWLLAD 243 Query: 251 AVALCRDQHHVLAYAEDPCGAENGYSGREVMAEFRRSTGLRTATNMIATDWRQMGHAIQL 310 A+ CR+ VLAYAEDP G E+G+SGREVMAEF+R+TGL TATNMIATDWR+MGHAI+ Sbjct: 244 AIRTCRELKDVLAYAEDPVGPEDGFSGREVMAEFKRATGLPTATNMIATDWREMGHAIRS 303 Query: 311 QSVDIPLADPHFWTMQGSVRVAQMCNEWGLTWGSHSNNHFDISLAMFTHVAAAAPGNITA 370 +VDIPLADPHFWTM GSVRVAQ+C+ WGLTWGSHSNNHFD+SLAMFTHVAAAAPG+ITA Sbjct: 304 GAVDIPLADPHFWTMTGSVRVAQLCDAWGLTWGSHSNNHFDVSLAMFTHVAAAAPGDITA 363 Query: 371 IDTHWIWQDGQRLTKEPLQIKGGLVEVPKKPGLGVELDWDALMKAHEVYKSMGLGARDDA 430 IDTHWIWQDGQ +T P I G + VP PGLGV LD A+ AH +Y+ GLG RDDA Sbjct: 364 IDTHWIWQDGQAITTNPYPIVDGYLSVPDAPGLGVTLDEPAVQAAHALYQREGLGGRDDA 423 Query: 431 TAMRYLVSGWEFNNKRPCMVR 451 AM+YL+ GW F+ KRP + R Sbjct: 424 VAMQYLIPGWTFDGKRPALDR 444 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: 661 Number of extensions: 18 Number of successful extensions: 2 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: 451 Length of database: 445 Length adjustment: 33 Effective length of query: 418 Effective length of database: 412 Effective search space: 172216 Effective search space used: 172216 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 (21.8 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Sep 24 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