Align L-rhamnonate dehydratase; RhamD; EC 4.2.1.90 (uncharacterized)
to candidate CA265_RS12250 CA265_RS12250 enolase
Query= curated2:A9BQY2 (395 letters) >FitnessBrowser__Pedo557:CA265_RS12250 Length = 388 Score = 141 bits (355), Expect = 4e-38 Identities = 111/369 (30%), Positives = 176/369 (47%), Gaps = 34/369 (9%) Query: 43 PEYRQSRRSFGI--NVLGTLVVEIEDSA----GRVGFAVTTGGEPAAYI--VEKHLARFL 94 PE +Q +G+ + TLVV DS G AV + G A+ + +E L L Sbjct: 16 PEAKQHVSDYGLLTSFDMTLVVITTDSGLQGFGEAKAAVGSCGICASIVNCIENELKPML 75 Query: 95 EGARVTDIERIWDQMYLSTLYY------------GRKGIVINTISGVDLALWDLLGKVRG 142 G V +I R+W++MY T + GR+G+ I+ +SG+D ALWDL GK+ Sbjct: 76 LGKSVKNITRLWEEMYNGTRDHYALSRGRKFPILGRRGLTISAMSGIDTALWDLKGKMLN 135 Query: 143 EPVHQLLGGAVRDELQFYATGARPDL----AQKMGFIG-GKMPLHHGPAEGEEGLRRNLQ 197 PV LLGGA R ++ YA+G D Q MG++ G + ++ +++++ Sbjct: 136 VPVADLLGGACRTKMPAYASGGWADEQNIGEQLMGYVNKGFKGVKMRVGVMDDTVQKSIN 195 Query: 198 ELATMRERVGPDFWLMLDCWMSLDVNYATRLAQGAQAHGLKWIEEALPPDDYWGYAALRK 257 + R +GPD LM+D + V A + +G + + W EE + PD+ G A +R Sbjct: 196 RVKAARAALGPDIKLMVDAHGTFSVPEAKQFCRGVEDCNVYWFEEPISPDNRKGTAEVR- 254 Query: 258 NVPTGMLVTTGEHEATRWGFRQLLEMGCCDIIQPDVGWCGGITELLKISALADAHQALVI 317 T + + GE E T + LL++ D++QPD GGI+E +++S LA HQ + Sbjct: 255 -AATDIPIAAGESEFTSFDIHDLLQIRAIDVVQPDAAIIGGISEAMRVSHLASVHQVELA 313 Query: 318 PH--GSSVYSYHFVATRHNSPFAEFLMMAPKADEVVPMFHPQLLGEPVPVNGRMRLSALD 375 PH GS+ + S A + + + PM + + + VNG +SA Sbjct: 314 PHCWGSAFSFMAGLTVAFASASATIIEFSLGGN---PMMYDLVNEQIAVVNG--EISAPT 368 Query: 376 RPGFGVELN 384 PG G+ N Sbjct: 369 APGLGLTPN 377 Lambda K H 0.322 0.139 0.442 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: 401 Number of extensions: 25 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: 395 Length of database: 388 Length adjustment: 31 Effective length of query: 364 Effective length of database: 357 Effective search space: 129948 Effective search space used: 129948 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 (21.9 bits) S2: 50 (23.9 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