Align L-rhamnose-1-dehydrogenase; EC 1.1.1.173 (characterized)
to candidate WP_086508208.1 BZY95_RS01345 NAD(P)-dependent oxidoreductase
Query= SwissProt::A3LZU7 (258 letters) >NCBI__GCF_002151265.1:WP_086508208.1 Length = 341 Score = 117 bits (294), Expect = 2e-31 Identities = 86/252 (34%), Positives = 124/252 (49%), Gaps = 6/252 (2%) Query: 2 TGLLNGKVVAITGGVTGIGRAIAIEMARNGAKVVVNHLPSEEQAQLAKELKEEISDGENN 61 +G L G+ ITGG +GIGRA AI AR GA V +N+L EE A+E+ E I Sbjct: 94 SGRLVGRKALITGGDSGIGRAAAIAYAREGADVAINYLEVEEPD--AREVIELIEAEGRT 151 Query: 62 VLTIPGDISLPETGRRIVELAVEKFGEINVFVSNAGVCGFRE-FLEITPETLFQTVNINL 120 + IPGDI +VE AVE+ G +++ V+NA + E ++++ E T+ NL Sbjct: 152 AVAIPGDIRDEAFCHELVETAVERLGGLDILVNNAARQQWAESIMDVSTEIFDDTMKTNL 211 Query: 121 NGAFFAIQAAAQQMVKQGKGGSIIGISSISALVGGAHQTHYTPTKAGILSLMQSTACALG 180 F+ +AA M +G SII ++S+ A A Y TKA I++ ++ + + Sbjct: 212 YAMFWITKAALPHM---EEGASIINVASMVAEDPPAILLEYNMTKAAIVNFTKTLSKQVA 268 Query: 181 KYGIRCNAILPGTISTALNEEDLKDPEKRKYMEGRIPLGRVGDPKDIAGPAIFLASDMSN 240 GIR N I PG T L + E +GR G P +IAG + LAS S+ Sbjct: 269 DQGIRVNTISPGPFWTPLQPSGGQPQEVVATFGEDSLMGRPGQPVEIAGVFVLLASQESS 328 Query: 241 YVNGAQLLVDGG 252 + G GG Sbjct: 329 FATGQNYSATGG 340 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: 177 Number of extensions: 13 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: 341 Length adjustment: 26 Effective length of query: 232 Effective length of database: 315 Effective search space: 73080 Effective search space used: 73080 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: 48 (23.1 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