Align L-rhamnonate dehydratase; RhamD; EC 4.2.1.90 (uncharacterized)
to candidate AZOBR_RS25270 AZOBR_RS25270 mandelate racemase
Query= curated2:A9BQY2 (395 letters) >FitnessBrowser__azobra:AZOBR_RS25270 Length = 397 Score = 126 bits (317), Expect = 1e-33 Identities = 105/353 (29%), Positives = 159/353 (45%), Gaps = 24/353 (6%) Query: 60 LVVEIEDSAGRVGFA---VTTGGEPAAYIVEKHLARFLEGARVTDIERIWDQMYLSTLYY 116 L V IE +G G+ VT G E +A L G + +I ++ Q L Sbjct: 20 LFVRIETESGIYGWGEGYVTAGKEKVVAAYVDAIAPLLIGREIWNIRQL-AQTLLDDFSI 78 Query: 117 GRKGI-VINTISGVDLALWDLLGKVRGEPVHQLLGGAVRDELQFYATG------ARPDLA 169 R + + +S V++A WD++GK G PVH+LLGGAVR++++ YA G + D A Sbjct: 79 RRTSVDFLCALSAVEIASWDIVGKRAGLPVHKLLGGAVREKIRVYANGWWFGASSIDDTA 138 Query: 170 QKMGFI--GGKMPLHHGPAEG-------EEGLRRNLQELATMRERVGPDFWLMLDCWMSL 220 + + G L P G + L ++ + +RE VGP+ L++D L Sbjct: 139 NRAAAVVAQGYDALKWDPIPGPWRNYVDPKDLDHAVENVRAVREAVGPNVELLIDGHRRL 198 Query: 221 DVNYATRLAQGAQAHGLKWIEEALPPDDYWGYAALRKNVPTGMLVTTGEHEATRWGFRQL 280 N+A RL + + G+ W EE PP++ A +R+ T + + +GE T+ + L Sbjct: 199 SPNHAIRLIERLREFGIAWYEEPCPPENLDLTAEVRRT--TNVPIVSGEALYTKEQYLPL 256 Query: 281 LEMGCCDIIQPDVGWCGGITELLKISALADAHQALVIPHGSSVYSYHFVATRHNSPFAEF 340 E DII PD+ GGI +L I+ALA H V PH + AT H S Sbjct: 257 FEKRAADIINPDISAVGGILAMLDIAALAQPHSIAVSPHNFNSPIVGLAATVHLSALVTN 316 Query: 341 LMMAPKADEVVPMFHPQLLGEPVPVNGRMRLSALDRPGFGVELNPECALHRPY 393 +A +V L +G + + D PG GV+L+ E PY Sbjct: 317 FTIAELFVNLVEPTRELALQGLTIADGYVDIP--DTPGLGVDLDVEVLRRHPY 367 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: 359 Number of extensions: 19 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: 397 Length adjustment: 31 Effective length of query: 364 Effective length of database: 366 Effective search space: 133224 Effective search space used: 133224 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