Align Glucarate dehydratase; GDH; GlucD; EC 4.2.1.40 (characterized)
to candidate BWI76_RS22830 BWI76_RS22830 glucarate dehydratase
Query= SwissProt::P42206 (451 letters) >FitnessBrowser__Koxy:BWI76_RS22830 Length = 446 Score = 588 bits (1515), Expect = e-172 Identities = 289/442 (65%), Positives = 344/442 (77%), Gaps = 5/442 (1%) Query: 13 APVITDLKVVPVAGHDSMLLNLSGAHGPLFTRNILILTDSSGHVGVGEVPGGEGIRKTLE 72 +PVITD+KV+PVAG DSMLLN+ GAH FTRNI++LTDS+G+ GVGE PGGE I +TL Sbjct: 6 SPVITDMKVIPVAGQDSMLLNIGGAHNAYFTRNIVVLTDSAGNTGVGEAPGGEVIYQTLV 65 Query: 73 DARHLLINQSIGNYQSLLNKVR--NAFADRDVGGRGLQTFDLRIAVHAVTAVESALLDLL 130 DA +++ Q I ++ +V N AD D G+G TF+LR V+AV A+E+ALLDLL Sbjct: 66 DAIPMVLGQEIARLNKVVQQVHKGNQAADFDTFGKGAWTFELR--VNAVAALEAALLDLL 123 Query: 131 GQHLQVPVAALLGEGQQRDAVEMLGYLFYVGDRNKTDLGYRSEHEADNEWFRLRNKEALT 190 G+ L VPV LLG G+QRDAV +LGYLFYVGDR KTDL Y + W+RLR+++AL Sbjct: 124 GKALNVPVCELLGPGKQRDAVTVLGYLFYVGDRTKTDLPYLESTPGSHAWYRLRHQQALN 183 Query: 191 PESVVALAEAAYDRYGFKDFKLKGGVLRGEDEIAAVTALSERFPDARITLDPNGAWSLKE 250 E+VV LAEAA DRYGFKDFKLKGGVL GE EI AL +RFPDARIT+DPNGAW L E Sbjct: 184 SEAVVRLAEAAQDRYGFKDFKLKGGVLPGEQEIETARALKKRFPDARITVDPNGAWLLDE 243 Query: 251 AVALCRDQHHVLAYAEDPCGAENGYSGREVMAEFRRSTGLRTATNMIATDWRQMGHAIQL 310 A+ALC+ + VL YAEDPCGAE G+SGREVMAEFRR+TGL ATNMIAT+WR+MGHA+ L Sbjct: 244 AIALCKGLNDVLTYAEDPCGAEQGFSGREVMAEFRRATGLPVATNMIATNWREMGHAVML 303 Query: 311 QSVDIPLADPHFWTMQGSVRVAQMCNEWGLTWGSHSNNHFDISLAMFTHVAAAAPGNITA 370 +VDIPLADPHFWT+ G+VRVAQ+C++WGLTWG HSNNHFDISLAMFTHV AAAPGN TA Sbjct: 304 NAVDIPLADPHFWTLSGAVRVAQLCDDWGLTWGCHSNNHFDISLAMFTHVGAAAPGNPTA 363 Query: 371 IDTHWIWQDGQ-RLTKEPLQIKGGLVEVPKKPGLGVELDWDALMKAHEVYKSMGLGARDD 429 IDTHWIWQ+G RLTK PL+IK G + VP PGLGVELDW+ + KAHE Y + GAR+D Sbjct: 364 IDTHWIWQEGDCRLTKNPLEIKHGKIAVPDAPGLGVELDWEQVQKAHEAYTRLPGGARND 423 Query: 430 ATAMRYLVSGWEFNNKRPCMVR 451 A M+YL+ GW F+ KRP R Sbjct: 424 AGPMQYLIPGWTFDRKRPVFGR 445 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: 621 Number of extensions: 15 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: 451 Length of database: 446 Length adjustment: 33 Effective length of query: 418 Effective length of database: 413 Effective search space: 172634 Effective search space used: 172634 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 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