Align L-rhamnonate dehydratase; RhamD; EC 4.2.1.90 (uncharacterized)
to candidate CA265_RS13665 CA265_RS13665 galactonate dehydratase
Query= curated2:A9BQY2 (395 letters) >FitnessBrowser__Pedo557:CA265_RS13665 Length = 388 Score = 147 bits (370), Expect = 7e-40 Identities = 109/347 (31%), Positives = 165/347 (47%), Gaps = 38/347 (10%) Query: 71 VGFAVTTGGEPAAYIVEKHLARFLEGARVTDIERIWDQMYLSTLYYGRKGIVINTISGVD 130 VG A G P + KH+ + + G + IW ++Y + G G + ISG+D Sbjct: 32 VGEATNWPGSPIVFEATKHVGQRIIGLDPMKTDFIWTKLYRDLNWMGPFGASMCAISGID 91 Query: 131 LALWDLLGKVRGEPVHQLLGGAVRDELQFYAT-------------GARPDLAQKMGFIGG 177 +AL DL KV G P ++LLGGA R ++ YA A+ ++ GF G Sbjct: 92 MALLDLKAKVLGVPCYELLGGAFRKDILLYANYWFTGGGHNTADYAAQAKKVKEAGFTGL 151 Query: 178 KM-PLHHGPAEGEEGLRRNLQELA-----------TMRERVGPDFWLMLDCWMSLDVNYA 225 K P H E L NLQ A +R+ VGP+F +M++ L+ A Sbjct: 152 KFDPFAHTNYLYGEDLSSNLQLTAPQQDLAFNVSKAVRDAVGPEFDIMIETHAMLNYRVA 211 Query: 226 TRLAQGAQAHGLKWIEEALPPDDYWGYAALRKNVPTGMLVTTGEHEATRWGFRQLLEMGC 285 +AQ + W EE P++ A+R +P+ + + GE TR G R +LE Sbjct: 212 VTMAQRLSELNITWYEEPAGPENANTLKAMRDRIPSNVSICVGERHYTRHGIRDVLEKHI 271 Query: 286 CDIIQPDVGWCGGITELLKISALADAHQALVIPHG-----SSVYSYHFVATRHNSPFAEF 340 CDI+ PD+ CGG +E+ +++ + +A+ L+ PH S++ S A+ N EF Sbjct: 272 CDIMMPDITRCGGPSEMKRMATMMEAYNVLLAPHNPNGPLSTLASAQVCASVPNFFRQEF 331 Query: 341 LMM-APKADEVVPMFHPQLLGEPVPVNGRMRLSALDRPGFGVELNPE 386 + P DEV+ HP + + V NG ++LS DRPG GV+L E Sbjct: 332 MFNDVPWRDEVIS--HP--IADMVQ-NGHLKLS--DRPGLGVDLIEE 371 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: 418 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: 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