Align L-rhamnose-1-dehydrogenase; EC 1.1.1.173 (characterized)
to candidate WP_040663927.1 ON16_RS13885 SDR family oxidoreductase
Query= SwissProt::A3LZU7 (258 letters) >NCBI__GCF_000307265.1:WP_040663927.1 Length = 251 Score = 124 bits (312), Expect = 1e-33 Identities = 83/249 (33%), Positives = 131/249 (52%), Gaps = 11/249 (4%) Query: 8 KVVAITGGVTGIGRAIAIEMARNGAKVVVNHLPSEEQAQLAKELKEEISDG--ENNVLTI 65 +V ITG GIG+A A+ MA GAKVV+ E + +E+K + + +T Sbjct: 6 QVAIITGSTKGIGKATALLMAAEGAKVVIVGTTEEAGNAVVEEIKAAGGEAFFQKTNVTS 65 Query: 66 PGDISLPETGRRIVELAVEKFGEINVFVSNAGVCG-FREFLEITPETLFQTVNINLNGAF 124 D+ +V A++++G+I++ V+NAGV G +IT E + + NL F Sbjct: 66 AADLDA------LVSAALDQYGKIDILVNNAGVGGSLANMDQITDEEWDKVLATNLTAPF 119 Query: 125 FAIQAAAQQMVKQGKGGSIIGISSISALVGGAHQTHYTPTKAGILSLMQSTACALGKYGI 184 ++ M K G GG I+ ++S+++ G YT K G+L L + + G GI Sbjct: 120 QVMKRVIPVMEKAG-GGKIVNVASMASTAAGRGGIAYTTAKHGVLGLTRQVSLDHGHAGI 178 Query: 185 RCNAILPGTISTALNEEDLKDPEKRKYMEGRI-PLGRVGDPKDIAGPAIFLASDMSNYVN 243 R NA+LPG I T + L P+ M+ ++ P GR G P+++A +FLAS+ S+++ Sbjct: 179 RVNAVLPGPIDTQMIARVLAMPQHPLNMKIKMSPAGRPGQPEEVAKAILFLASEDSSFIQ 238 Query: 244 GAQLLVDGG 252 GA L VDGG Sbjct: 239 GAALAVDGG 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: 122 Number of extensions: 8 Number of successful extensions: 4 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 24 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