Align L-rhamnonate dehydratase; RhamD; EC 4.2.1.90 (uncharacterized)
to candidate WP_086509088.1 BZY95_RS06130 galactonate dehydratase
Query= curated2:A9BQY2 (395 letters) >NCBI__GCF_002151265.1:WP_086509088.1 Length = 384 Score = 124 bits (310), Expect = 6e-33 Identities = 96/282 (34%), Positives = 140/282 (49%), Gaps = 32/282 (11%) Query: 60 LVVEIEDSAGRVGFA--VTTGGEPAAYIVEKHLARFLEGARVTDIERIWDQMYLSTLYYG 117 L ++IE G G+ V G LA +L G IE +W+ +Y + Y G Sbjct: 16 LFLKIETDEGCYGWGEPVIEGRAATVEAAVHELADYLIGQDPHRIEHLWNTLYRAGFYRG 75 Query: 118 RKGIVINTISGVDLALWDLLGKVRGEPVHQLLGGAVRDELQF--YA-----------TGA 164 I+++ I+G+D ALWDL G+ G PVHQLLGGAVR+ ++ YA GA Sbjct: 76 GP-ILMSAIAGIDQALWDLKGRDLGVPVHQLLGGAVRERMRMRMYAWTGGDRPSEVGAGA 134 Query: 165 RPDLAQKMGFIGGKMPLHHGPAE-----GEEGLRRNLQELATMRERVGPDFWLMLDCWMS 219 R +A+ GF KM +G AE + + +A RE VGP+ + +D Sbjct: 135 RELVAR--GFTAFKM---NGTAEMQIVDSHRKIDEAVARVAEAREAVGPEVGISIDFHGR 189 Query: 220 LDVNYATRLAQGAQAHGLKWIEEALPPDDYWGYAALRKNVPTGML--VTTGEHEATRWGF 277 + A L + + + ++EE L P+ + K++ G+ + TGE TR+ F Sbjct: 190 VHRPMAKALLRELEPYHPMFVEEPLAPE----HLPALKHIADGLAYPLATGERLHTRFEF 245 Query: 278 RQLLEMGCCDIIQPDVGWCGGITELLKISALADAHQALVIPH 319 R LL G DI+QPD+ C GI+E LKI+ALA AH + PH Sbjct: 246 RDLLAEGMIDIVQPDLSHCDGISEGLKIAALASAHDVALAPH 287 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: 470 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: 384 Length adjustment: 30 Effective length of query: 365 Effective length of database: 354 Effective search space: 129210 Effective search space used: 129210 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 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