Align L-rhamnose-1-dehydrogenase; EC 1.1.1.173 (characterized)
to candidate GFF1748 HP15_1707 short-chain dehydrogenase/reductase SDR
Query= SwissProt::A3LZU7 (258 letters) >FitnessBrowser__Marino:GFF1748 Length = 256 Score = 137 bits (344), Expect = 3e-37 Identities = 93/255 (36%), Positives = 133/255 (52%), Gaps = 13/255 (5%) Query: 5 LNGKVVAITGGVTGIGRAIAIEMARNGAKVVVNHLPSEEQAQLAKELKEE-ISDGENNVL 63 L GKV ITGG GIG A A+ MA GA V + E LAK+L+ + G + Sbjct: 4 LKGKVAVITGGSVGIGAATALRMAEEGAAVAILDCQDSEGEALAKQLEGRGLKAGYWHC- 62 Query: 64 TIPGDISLPETGRRIVELAVEKFGEINVFVSNAGVCGFREFL-EITPETLFQTVNINLNG 122 D+S + +++++ FG V V+NAG+ G + E+T E ++N+ G Sbjct: 63 ----DVSKEQEVKQVLDAVANTFGTPTVLVNNAGIAGANKPTHELTEEEWDHVQDVNVKG 118 Query: 123 AFFAIQAAAQQMVKQGKGGSIIGISSISALVGGAHQTHYTPTKAGILSLMQSTACALGKY 182 FF + A M K G G SII +SSI LV Y +K + + ++ A Sbjct: 119 VFFCTKHAIPHMKKAGVG-SIINLSSIYGLVSAPDIPPYHASKGAVRLMSKTDALLYATE 177 Query: 183 GIRCNAILPGTISTALNEEDLK----DPEKRKYMEGRI-PLGRVGDPKDIAGPAIFLASD 237 IRCN+I PG I T L E LK DPE+ K + P+G +G+P DIA A++LASD Sbjct: 178 NIRCNSIHPGFIWTPLVEAHLKTTGQDPEEAKKATAAMHPVGHMGEPDDIAWGAVYLASD 237 Query: 238 MSNYVNGAQLLVDGG 252 S +V G++L++DGG Sbjct: 238 ESKFVTGSELVIDGG 252 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: 115 Number of extensions: 5 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: 258 Length of database: 256 Length adjustment: 24 Effective length of query: 234 Effective length of database: 232 Effective search space: 54288 Effective search space used: 54288 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