Align Putative L-rhamnonate dehydratase; RhamD; EC 4.2.1.90 (uncharacterized)
to candidate H281DRAFT_06497 H281DRAFT_06497 L-alanine-DL-glutamate epimerase
Query= curated2:A8MA91 (398 letters) >FitnessBrowser__Burk376:H281DRAFT_06497 Length = 374 Score = 132 bits (332), Expect = 2e-35 Identities = 105/345 (30%), Positives = 161/345 (46%), Gaps = 30/345 (8%) Query: 67 VVEVESSDGEVGFGISTGGYPAAWI----IENHLSRFVVGKYVGEVEKTWDQMFKATIYY 122 +V+V SSDG G G G A I +E L+ + G+ EVE W +M++ ++ Sbjct: 34 LVKVRSSDGAEGIGFCYVGNAAGEIFRVAVEQLLAPVLNGRDSLEVEGLWKEMYQESLLQ 93 Query: 123 GRRGIVMNAISAVDLALWDLMGKVRGLPVYDLLGGPVRDELTFYATGPRPDVAKSLGFIG 182 GR G VM A+SA+D+ALWDL + GLP++ LG D + YA+G K+ +G Sbjct: 94 GRMGTVMRALSALDIALWDLNARTAGLPLHKYLGAVELDHVDAYASGGYYVDGKTAEEVG 153 Query: 183 GKLPLIHGPADGIEGLR----------ENVRIFKEAREKVGDDFLLMYDC---WMSLDLP 229 ++ A G + ++ E R+ K ARE +G D LM DC W +D Sbjct: 154 EEMASY--VALGFKAVKMKTGRWSPAGEESRV-KAAREAIGPDVELMLDCNNGW--VDTV 208 Query: 230 YAQRLLSELKPYGLFWIEEPFIPDDYWSFGALANIAP-PTLVASGEHESTVHGFRLLLEL 288 A + L + Y ++IEEPF PDD S LA + P A + H + LL++ Sbjct: 209 QAMQYLRRFEQYDPYFIEEPFSPDDIESHARLAKLTRIPVATAEIGYGRWYH--KQLLDM 266 Query: 289 GKVNVIQPDVTWVGGVTPMIKIAALAEAYGAWVIPHGSSVYGYHFIITRVNSPFAEYLVV 348 G +++Q D GG+T +IAA+A YG + PH + N+ + E+ Sbjct: 267 GGASILQTDAAVCGGITEWRRIAAMASGYGIQMCPHWFHDVHAPLVAATQNARYVEFFWD 326 Query: 349 SPDATKIVPQFHPLLRDEPIPQNGKVRLSRKPGFGVELNRDLLVR 393 V F L+ + + G+V L + PG G + + R Sbjct: 327 DQ-----VLNFRRLVDRQLTHKEGRVLLHQTPGLGFNFDEAEVAR 366 Lambda K H 0.321 0.141 0.440 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: 375 Number of extensions: 20 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: 398 Length of database: 374 Length adjustment: 30 Effective length of query: 368 Effective length of database: 344 Effective search space: 126592 Effective search space used: 126592 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: 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