Align L-rhamnonate dehydratase; RhamD; EC 4.2.1.90 (uncharacterized)
to candidate WP_012405926.1 BPHY_RS33585 mandelate racemase/muconate lactonizing enzyme family protein
Query= curated2:A9BQY2 (395 letters) >NCBI__GCF_000020045.1:WP_012405926.1 Length = 368 Score = 138 bits (348), Expect = 2e-37 Identities = 114/346 (32%), Positives = 166/346 (47%), Gaps = 30/346 (8%) Query: 54 INVLGTLVVEIEDSAGRVGFAVTTGGEP---AAYIVEKHLARFLEGARVTDIERIWDQMY 110 + V+ +LVV++ G VG+ T G +++K LA L G V E+ ++ Sbjct: 31 LQVVDSLVVKVRTDDGTVGWGETFGFTAIPSVKLVIDKILAPELIGRDVALREKSMLELQ 90 Query: 111 LSTLYYGRKGIVINTISGVDLALWDLLGKVRGEPVHQLLGGAVRDELQFYATGAR---PD 167 +GR G I +S +D+ALWD+ GK +PVHQLLGGA L YA+ R P+ Sbjct: 91 KKFHIFGRSGAFIYGLSAIDIALWDIAGKRANQPVHQLLGGAGATSLACYASLIRYADPE 150 Query: 168 LAQKMGFIGGKMPLHHGPAEGEEGLRRN---LQELATMRERVGPDFWLMLDCWMSLDVNY 224 L + + G L+ + ++ + RE GPD + LD V Sbjct: 151 LV--------AINVRRAVDAGYRHLKLHEITVETVRAAREAAGPDIEITLDVNCPWTVRE 202 Query: 225 ATRLAQGAQAHGLKWIEEAL-PPDDYWGYAALRKNVPTGMLVTTGEHEATRWGFRQLLEM 283 A + + + L+WIEE + PP++Y G A +R+ G+ V GE+ +T F+ LLE Sbjct: 203 ALDMTEKLRPFNLRWIEEPVWPPENYAGLATVRQQ--GGVPVAAGENASTLMDFQHLLEA 260 Query: 284 GCCDIIQPDVGWCGGITELLKISALADAHQALVIPHGSSVYSYHFVATRHNSPFAEFLMM 343 G D IQP GGITEL K+ ALA+AH V+ V++++ S A + Sbjct: 261 GSVDFIQPSPAKMGGITELQKVFALANAHNVTVM-----VHTFYDGPGLLASVHASAALG 315 Query: 344 APKADEVVPMF--HPQLLGEP-VPVNGRMRLSALDRPGFGVELNPE 386 PKA F QL G+ VP NG R+ PG G+E NPE Sbjct: 316 GPKALVEWRYFDLEAQLYGDAIVPRNG--RIDVPQSPGLGIEPNPE 359 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: 416 Number of extensions: 17 Number of successful extensions: 5 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: 368 Length adjustment: 30 Effective length of query: 365 Effective length of database: 338 Effective search space: 123370 Effective search space used: 123370 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