Align L-rhamnose-1-dehydrogenase ( EC 1.1.1.173) (characterized)
to candidate CCNA_01559 CCNA_01559 2-deoxy-D-gluconate 3-dehydrogenase
Query= reanno::BFirm:BPHYT_RS28235 (260 letters) >FitnessBrowser__Caulo:CCNA_01559 Length = 255 Score = 152 bits (384), Expect = 7e-42 Identities = 95/255 (37%), Positives = 138/255 (54%), Gaps = 13/255 (5%) Query: 3 LKDKVVIVTGGSRGIGRAIAVACAAEGADVAINYWGDNDVSYGRRSAVAEVVAEIEALGR 62 L+ KV ++TG + GIG+ IA+A AA GAD+A RSA E A +EALGR Sbjct: 7 LEGKVALITGANTGIGQGIAIALAAAGADIAA----------AGRSAPTETQAAVEALGR 56 Query: 63 RVIAIEGNVAARETGQQLVRHTVEAFGKVDVLASNAGICPFHAFLDMPPEVLESTVAVNL 122 + ++I+ + ++ E Q++V TV AFGKVD+L +NAGI ++ ++ + NL Sbjct: 57 KFLSIKADFSSIEPVQRVVDETVAAFGKVDILVNNAGIIRRADSIEFSEADWDAVMDTNL 116 Query: 123 NGAFYVTQAAAQQMKLQGTGGA---IVATSSISALVGGGMQTHYTPTKAGVHSLMQSCAV 179 F++TQA A+Q QG G ++ +S+ + GG YT +K+G+ L + A Sbjct: 117 KVVFFLTQAFAKQALKQGFEGGQAKVINIASLLSFQGGIRVPSYTASKSGLAGLTKILAN 176 Query: 180 ALGPYGIRCNSVMPGTIATDLNAQDLADEAKKAYFEKRIPLGRLGRPEDVADCVTFLASD 239 GI N++ PG T+ AD+ + A RIP GR GRPED+ FLAS Sbjct: 177 EWATKGINVNAIAPGYFDTNNTEALRADQDRNAAILARIPAGRWGRPEDIGGAAVFLASS 236 Query: 240 RARYVTGAALLVDGG 254 + YV G L VDGG Sbjct: 237 ASDYVQGITLPVDGG 251 Lambda K H 0.319 0.134 0.386 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: 145 Number of extensions: 5 Number of successful extensions: 2 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: 260 Length of database: 255 Length adjustment: 24 Effective length of query: 236 Effective length of database: 231 Effective search space: 54516 Effective search space used: 54516 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