Align NAD(P)+-dependent L-rhamnose 1-dehydrogenase (EC 1.1.1.378; EC 1.1.1.173) (characterized)
to candidate AZOBR_RS09410 AZOBR_RS09410 2-dehydro-3-deoxy-D-gluconate 5-dehydrogenase
Query= metacyc::MONOMER-16230 (256 letters) >FitnessBrowser__azobra:AZOBR_RS09410 Length = 253 Score = 171 bits (434), Expect = 1e-47 Identities = 105/252 (41%), Positives = 143/252 (56%), Gaps = 5/252 (1%) Query: 3 LIDKTVIVTGASRGIGRAAARECARQGARVVIGHSGSDEGRAGALSLAEEIAAFGGTAIA 62 L ++T +VTGAS G+GR A A GARV + + R + EI A GG AIA Sbjct: 5 LTNRTALVTGASAGLGRHFAGVLAAAGARVAL----AARRRESLDAAVAEIEAAGGQAIA 60 Query: 63 VGADAADLDSGEKLVAAAVEAFGSVDVLVNNAGICPFHSFLDMPRELYLKTVGTNLNGAY 122 V D D S V A A G +D+LVNNAG LD E + + + TNL GA+ Sbjct: 61 VPLDVTDAASVRNGVREAAGALGGLDILVNNAGATVAKPALDYAEEEWDRVIDTNLKGAF 120 Query: 123 FTVQAAARRMKEQGRGGAIIAVSSISALVGGAMQTHYTPTKAGLLSLMQSCAIALGPYGI 182 T Q AR M+EQGRGG+I+ ++SI L YT +KAGL+ + Q+ A+ YGI Sbjct: 121 LTAQETARVMREQGRGGSIVNIASILGLRVAGHVVAYTASKAGLVQMTQAVALEWARYGI 180 Query: 183 RCNAVLPGTIATDINKEDLSDLEKRERMTSRVPLGRLGEPDDLAGPIVFLASDMARYVTG 242 R NA+ PG + TD+N++ L+ + + + RVP RLG DL GP++ L SD + Y+TG Sbjct: 181 RVNALAPGYMETDLNRDFLA-TDAGQALIRRVPQRRLGRLADLDGPLLLLCSDASAYMTG 239 Query: 243 ASLLVDGGLFVN 254 A + VDGG V+ Sbjct: 240 AVVPVDGGHLVS 251 Lambda K H 0.319 0.136 0.383 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: 182 Number of extensions: 7 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: 256 Length of database: 253 Length adjustment: 24 Effective length of query: 232 Effective length of database: 229 Effective search space: 53128 Effective search space used: 53128 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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