Align L-rhamnose-1-dehydrogenase; EC 1.1.1.173 (characterized)
to candidate WP_008511219.1 BIBO1_RS19100 SDR family oxidoreductase
Query= SwissProt::A3LZU7 (258 letters) >NCBI__GCF_000182725.1:WP_008511219.1 Length = 249 Score = 148 bits (374), Expect = 9e-41 Identities = 88/248 (35%), Positives = 133/248 (53%), Gaps = 10/248 (4%) Query: 5 LNGKVVAITGGVTGIGRAIAIEMARNGAKVVVNHLPSEEQAQLAKELKEEISDGENNVLT 64 + GKV+A+TGG +G+G + +A +GA+V+ + E + VL Sbjct: 9 VRGKVIAVTGGSSGLGLRMVHMLAGHGARVI---------SISRTHAGESLCPSGGEVLE 59 Query: 65 IPGDISLPETGRRIVELAVEKFGEINVFVSNAGVCGFREFLEITPETLFQTVNINLNGAF 124 I D++ PE R + +FG I+ +NAGV L+ T + L +N+ GAF Sbjct: 60 IMADVTRPEEIARAFDEGESRFGPISTLFNNAGVAHMARALDTTRDMLEHIFEVNVAGAF 119 Query: 125 FAIQAAAQQMVKQGKGGSIIGISSISALVGGAHQTHYTPTKAGILSLMQSTACALGKYGI 184 FA Q A++M+ QG+GGSII ++SI Y+ +KA + + ++ A + I Sbjct: 120 FAAQEVARRMIAQGQGGSIINVTSILGERPQKGAAAYSMSKACVSQMTRALALEWAAHDI 179 Query: 185 RCNAILPGTISTALNEEDLKDPEKRKYMEGRIPLGRVGDPKDIAGPAIFLASDMSNYVNG 244 R NAI PG T +NEE L+ P Y++GR P+ R+GDP D+ G + LASD S Y+ G Sbjct: 180 RVNAISPGWFPTRINEEQLQGP-AAGYLKGRNPMRRLGDPNDLDGVVLLLASDASRYMTG 238 Query: 245 AQLLVDGG 252 + L VDGG Sbjct: 239 SILTVDGG 246 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: 119 Number of extensions: 5 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: 249 Length adjustment: 24 Effective length of query: 234 Effective length of database: 225 Effective search space: 52650 Effective search space used: 52650 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