Align L-rhamnonate dehydratase; RhamD; EC 4.2.1.90 (uncharacterized)
to candidate SM_b21107 SM_b21107 mandelate racemase or evolutionary related enzyme of the mandelate racemase muconate lactonizing enzyme family protein
Query= curated2:A9BQY2 (395 letters) >FitnessBrowser__Smeli:SM_b21107 Length = 370 Score = 123 bits (309), Expect = 8e-33 Identities = 98/311 (31%), Positives = 140/311 (45%), Gaps = 28/311 (9%) Query: 59 TLVVEIEDSAGRVG----FAVTTGGEPAAYIVEKHLARFLEGARVTDIERIWDQMYLSTL 114 T +V I D+ G G + + TGG ++ HL L G IE +W +M +T Sbjct: 32 TPIVTITDADGATGTGYSYTIGTGGSSVMRLLSDHLVPILLGEDADCIEALWQKMEFATH 91 Query: 115 YYGRKGIVINTISGVDLALWDLLGKVRGEPVHQLLGGAVRDELQFYATG---------AR 165 I ++ VD ALWDL K + P+ +L GGA ++ Y T A Sbjct: 92 ATTIGAITALALAAVDTALWDLRAKKQKLPLWKLAGGA-KESCPLYTTEGGWLHIEKQAL 150 Query: 166 PD---LAQKMGFIGGKMPLHHGPAEGEEGLRRNLQELATMRERVGPDFWLMLDCWMSLDV 222 D A+ GF G K+ + G G E R L+ MR +G F +M DC V Sbjct: 151 VDDALQAKANGFSGSKVKI--GKPSGAEDYDR----LSAMRAALGDGFEIMTDCNQGFTV 204 Query: 223 NYATRLAQGAQAHGLKWIEEALPPDDYWGYAALRKNVPTGMLVTTGEHEATRWGFRQLLE 282 + A R A + L WIEE LP DD G+ L ++ PT + V GE + FR+ ++ Sbjct: 205 DEAIRRAARLRELDLAWIEEPLPADDLDGHIRLTRSTPTPIAV--GESIYSIRHFREYMQ 262 Query: 283 MGCCDIIQPDVGWCGGITELLKISALADAHQALVIPHGSSVYSYHFVATRHNSPFAEFLM 342 G C I+Q DV GGIT LK++ A+A V PH V N + E++ Sbjct: 263 KGACSIVQVDVARIGGITPWLKVAHAAEAFDIPVCPHFLMELHVSLVCAVPNGKYVEYI- 321 Query: 343 MAPKADEVVPM 353 P+ D++ M Sbjct: 322 --PQLDDLTQM 330 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: 383 Number of extensions: 21 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: 395 Length of database: 370 Length adjustment: 30 Effective length of query: 365 Effective length of database: 340 Effective search space: 124100 Effective search space used: 124100 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