Align uronate dehydrogenase (EC 1.1.1.203) (characterized)
to candidate BPHYT_RS24165 BPHYT_RS24165 NAD-dependent dehydratase
Query= BRENDA::Q88NN6 (268 letters) >FitnessBrowser__BFirm:BPHYT_RS24165 Length = 280 Score = 296 bits (757), Expect = 4e-85 Identities = 144/263 (54%), Positives = 190/263 (72%), Gaps = 2/263 (0%) Query: 5 PFNRLLLTGAAGGLGKVLRERLKGYAEVLRLSDISPMAPAAGPHEEVITCDLADKAAVHT 64 PF RLLLTGAAG LGK LR L +A+++R++DI+P+ A HEE D+AD+AAVH Sbjct: 14 PFRRLLLTGAAGNLGKQLRGALAAWADIVRITDIAPLGEVAA-HEEASIVDIADEAAVHA 72 Query: 65 LVEGVDAIIHFGGVSTEHAFEEILGPNICGVFHVYEAARKHGVKRIIFASSNHTIGFYRQ 124 L+EGVDA++H GG+S E FE++L NI G++++Y AA+K GVKRI++ASSNH +GF+ Sbjct: 73 LLEGVDAVVHLGGISVEAPFEDLLQANIRGLYNLYSAAQKQGVKRIVYASSNHAVGFHPV 132 Query: 125 DERIDAHAPRRPDSYYGLSKCYGEDVASFYFDRYGIETVSIRIGSSFPQPQNLRMLCTWL 184 E +D AP RPDS YG++KC+GE ++ +YFDR+G+ETV +RIGSSF QP+N RML T+L Sbjct: 133 TEVVDIDAPLRPDSLYGVTKCFGESLSRYYFDRFGLETVCLRIGSSFEQPKNPRMLVTYL 192 Query: 185 SYDDLVQLIERGLFTPGVGHTIVYGASDNRTVWWDNRHAAHLGYVPKDSSETFRAAVE-A 243 S+ DL++L+ LFT VGH IVYG SDNRT W DN AA LG+ P+DSS F Sbjct: 193 SFRDLIELVRCSLFTNRVGHAIVYGVSDNRTKWVDNTKAAFLGFRPQDSSVEFEHLFPVT 252 Query: 244 QPAPAADDPSMVYQGGAFAVAGP 266 P DDP+ +QGG F +AGP Sbjct: 253 APTADLDDPTQRFQGGPFVLAGP 275 Lambda K H 0.321 0.138 0.427 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: 257 Number of extensions: 10 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: 268 Length of database: 280 Length adjustment: 25 Effective length of query: 243 Effective length of database: 255 Effective search space: 61965 Effective search space used: 61965 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: 47 (22.7 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