Align Putative L-rhamnonate dehydratase; RhamD; EC 4.2.1.90 (uncharacterized)
to candidate WP_053939463.1 WG78_RS19245 galactonate dehydratase
Query= curated2:A8MA91 (398 letters) >NCBI__GCF_001294205.1:WP_053939463.1 Length = 382 Score = 128 bits (322), Expect = 2e-34 Identities = 101/352 (28%), Positives = 173/352 (49%), Gaps = 28/352 (7%) Query: 68 VEVESSDGEVGFG--ISTGGYPAAWIIENHLSRFVVGKYVGEVEKTWDQMFKATIYYGRR 125 +++E+ +G VG+G + G + +S +++G+ + W +++A Y G Sbjct: 18 LKIETDEGIVGWGEPVLEGRAKTVEAAVHEMSEYLIGQDPARINDLWQVLYRAGFYRGG- 76 Query: 126 GIVMNAISAVDLALWDLMGKVRGLPVYDLLGGPVRDELTFYA--TGPRP-DVAKSL---- 178 GI+M+AI+ +D ALWD+ GK G+PVY LLGG VRD + Y+ G RP D+ + + Sbjct: 77 GILMSAIAGIDQALWDIKGKALGVPVYQLLGGLVRDRVKTYSWVGGDRPADIIRDIQARV 136 Query: 179 --GFIGGKLPLIHGPA--DGIEGLRENVRIFKEAREKVGDDFLLMYDCWMSLDLPYAQRL 234 GF K+ A D + VR E RE G+ D + P A+ L Sbjct: 137 DVGFDTFKMNGCEELAVIDNSRAIDAAVRKVAEIREAFGNKIEFGLDFHGRVTAPMARVL 196 Query: 235 LSELKPYGLFWIEEPFIPD--DYWSFGALANIAPPTLVASGEHESTVHGFRLLLELGKVN 292 + EL+PY +IEEP + + +Y+ A P +A+GE + F+ +L G ++ Sbjct: 197 IKELEPYRPLFIEEPVLAEQAEYYPKLAAQTHIP---LAAGERMYSRFEFKNVLAAGGLS 253 Query: 293 VIQPDVTWVGGVTPMIKIAALAEAYGAWVIPHGSSVYGYHFIITRVNSPFAEYLVVSPDA 352 ++QPD++ GG+T +KIA++AEAY + PH G + + F + + Sbjct: 254 ILQPDLSHAGGITECMKIASMAEAYDVALAPH--CPLGPIALAACLQVDFVSWNAFIQEQ 311 Query: 353 TKIVPQ-------FHPLLRDEPIPQNGKVRLSRKPGFGVELNRDLLVRPFKS 397 + + + L + + +NG ++ KPG GVEL+ L++ K+ Sbjct: 312 SMGIHYNKGGEVLDYVLNKADFALENGHIKPFTKPGLGVELDEALIIERSKN 363 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: 412 Number of extensions: 25 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 398 Length of database: 382 Length adjustment: 30 Effective length of query: 368 Effective length of database: 352 Effective search space: 129536 Effective search space used: 129536 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 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