Align L-rhamnonate dehydratase; RhamD; EC 4.2.1.90 (characterized)
to candidate BWI76_RS19990 BWI76_RS19990 L-rhamnonate dehydratase
Query= SwissProt::Q8ZNF9 (405 letters) >FitnessBrowser__Koxy:BWI76_RS19990 Length = 401 Score = 822 bits (2122), Expect = 0.0 Identities = 389/401 (97%), Positives = 396/401 (98%) Query: 5 MTLPKIKHVRAWFIGGATAEKGAGGGDYHDQGGNHWIDDHIATPMSKYRDYEQSRQSFGI 64 MTLPKIKHVRAWFIGGATAEKGAGGGDYHDQG NHWIDDHIATPMSKY+ YEQSRQSFGI Sbjct: 1 MTLPKIKHVRAWFIGGATAEKGAGGGDYHDQGANHWIDDHIATPMSKYKQYEQSRQSFGI 60 Query: 65 NVLGTLIVEVEAENRQTGFAVSTAGEMGCFIVEKHLNRFIEGKCVSDIKLIHDQMLGATM 124 NVLGTLIVEVEAEN QTGFAVSTAGEMGCFIVEKHLNRFIEGKCVSDIKLIHDQML ATM Sbjct: 61 NVLGTLIVEVEAENGQTGFAVSTAGEMGCFIVEKHLNRFIEGKCVSDIKLIHDQMLNATM 120 Query: 125 YYSGSGGLVMNTISCVDLALWDLFGKVVGLPVYKLLGGAVRDEIQFYATGARPDLAKEMG 184 YYSGSGGLVMNTISC+DLALWDLFGKVVGLPVYKLLGGAVRDEIQFYATGARPDLAKEMG Sbjct: 121 YYSGSGGLVMNTISCIDLALWDLFGKVVGLPVYKLLGGAVRDEIQFYATGARPDLAKEMG 180 Query: 185 FIGGKMPTHWGPHDGDAGIRKDAAMVADMREKCGPDFWLMLDCWMSQDVNYATKLAHACA 244 FIGGKMPTHWGPHDGDAGIRKDAAMVADMREKCGPDFWLMLDCWMSQDVNYATKLAHACA Sbjct: 181 FIGGKMPTHWGPHDGDAGIRKDAAMVADMREKCGPDFWLMLDCWMSQDVNYATKLAHACA 240 Query: 245 PFNLKWIEECLPPQQYEGYRELKRNAPAGMMVTSGEHHGTLQSFRTLAETGIDIMQPDVG 304 P NLKWIEECLPPQQYEGYRELKRNAPAGMMVTSGEHHGTLQSFRTL+ETGIDIMQPDVG Sbjct: 241 PSNLKWIEECLPPQQYEGYRELKRNAPAGMMVTSGEHHGTLQSFRTLSETGIDIMQPDVG 300 Query: 305 WCGGLTTLVEIAALAKSRGQLVVPHGSSVYSHHAVITFTNTPFSEFLMTSPDCSTLRPQF 364 WCGGLTTLVEIAA+AKSRGQLVVPHGSSVYSHHAVITFTNTPFSEFLMTSPDCST+RPQF Sbjct: 301 WCGGLTTLVEIAAIAKSRGQLVVPHGSSVYSHHAVITFTNTPFSEFLMTSPDCSTMRPQF 360 Query: 365 DPILLDEPVPVNGRIHKSVLDKPGFGVELNRDCHLKRPYSH 405 DPIL+DEPVPVNGRIHKSVLDKPGFGVELNRDC+LKRPYSH Sbjct: 361 DPILVDEPVPVNGRIHKSVLDKPGFGVELNRDCNLKRPYSH 401 Lambda K H 0.321 0.138 0.441 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: 694 Number of extensions: 17 Number of successful extensions: 1 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: 405 Length of database: 401 Length adjustment: 31 Effective length of query: 374 Effective length of database: 370 Effective search space: 138380 Effective search space used: 138380 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 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