Align L-rhamnose-1-dehydrogenase; EC 1.1.1.173 (characterized)
to candidate Ga0059261_2966 Ga0059261_2966 2-deoxy-D-gluconate 3-dehydrogenase
Query= SwissProt::A3LZU7 (258 letters) >FitnessBrowser__Korea:Ga0059261_2966 Length = 251 Score = 149 bits (377), Expect = 4e-41 Identities = 92/248 (37%), Positives = 131/248 (52%), Gaps = 7/248 (2%) Query: 5 LNGKVVAITGGVTGIGRAIAIEMARNGAKVVVNHLPSEEQAQLAKELKEEISDGENNVLT 64 L G+V +TG TGIG+ IA+ +A+ GA + A E E++ Sbjct: 7 LTGRVAVVTGANTGIGQGIALALAQAGADIAA------VGRSAATETVEKVRALGRKAEI 60 Query: 65 IPGDISLPETGRRIVELAVEKFGEINVFVSNAGVCGFREFLEITPETLFQTVNINLNGAF 124 + D+S E +R+V+ VEK G +++ V+NAG+ + +E T E ++ NL F Sbjct: 61 VSADLSTIEPVQRVVDETVEKLGGLDILVNNAGIIRRADSVEFTEEDWDAVMDTNLKSVF 120 Query: 125 FAIQAAAQQMVKQGKGGSIIGISSISALVGGAHQTHYTPTKAGILSLMQSTACALGKYGI 184 F QAAA+ M+ G GG II I+S+ GG YT +K+G+ L + A GI Sbjct: 121 FLCQAAARHMIANG-GGKIINIASMLTFQGGIRVPSYTASKSGVGGLTKLLANEWASKGI 179 Query: 185 RCNAILPGTISTALNEEDLKDPEKRKYMEGRIPLGRVGDPKDIAGPAIFLASDMSNYVNG 244 NAI PG I+T + KD + + + RIP GR GDP D+ G A+FLAS S+YV G Sbjct: 180 TVNAIAPGYIATNNTDALQKDETRNRQIMERIPAGRWGDPADLGGAAVFLASRASDYVQG 239 Query: 245 AQLLVDGG 252 L VDGG Sbjct: 240 HILAVDGG 247 Lambda K H 0.317 0.136 0.382 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: 125 Number of extensions: 8 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: 258 Length of database: 251 Length adjustment: 24 Effective length of query: 234 Effective length of database: 227 Effective search space: 53118 Effective search space used: 53118 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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