Align NAD(P)+-dependent L-rhamnose 1-dehydrogenase (EC 1.1.1.378; EC 1.1.1.173) (characterized)
to candidate WP_211248857.1 Q394_RS0118475 glucose 1-dehydrogenase
Query= metacyc::MONOMER-16230 (256 letters) >NCBI__GCF_000621325.1:WP_211248857.1 Length = 255 Score = 147 bits (372), Expect = 2e-40 Identities = 95/249 (38%), Positives = 136/249 (54%), Gaps = 7/249 (2%) Query: 3 LIDKTVIVTGASRGIGRAAARECARQGARVVIGHSGSDEGRAGALSLAEEIAAFGGTAIA 62 L K V++TGAS GIG AAA R+G ++V+G ++EG A +A I A GG A+ Sbjct: 9 LAGKVVVITGASSGIGEAAAHAFGREGCKLVLGARRAEEGEA----VAAAIRATGGEAVF 64 Query: 63 VGADAADLDSGEKLVAAAVEAFGSVDVLVNNAGICPFHS-FLDMPRELYLKTVGTNLNGA 121 V D +LV A++ FG +DVL NNAG S F + Y T+ TN+ Sbjct: 65 VCTDVLQEADIARLVQTALDTFGGLDVLFNNAGTEGVSSAFTEQSTAEYDFTMNTNVRSV 124 Query: 122 YFTVQAAARRMKEQGRGGAIIAVSSISALVGGAMQTHYTPTKAGLLSLMQSCAIALGPYG 181 + +Q A R M Q GGAII +SI A VG A Y+ +KA ++ + + A+ G Sbjct: 125 LWGMQHAIRAM--QSAGGAIINNASIVAHVGFANTALYSASKAAVVGMTRVAAVEYFKQG 182 Query: 182 IRCNAVLPGTIATDINKEDLSDLEKRERMTSRVPLGRLGEPDDLAGPIVFLASDMARYVT 241 IR NAV PG T +++ L +++ + P GR G+P+++A +VFLAS A Y++ Sbjct: 183 IRINAVCPGITYTPMSQRLLGGEDEQNAFMATTPAGRTGQPEEIAAAVVFLASGNASYIS 242 Query: 242 GASLLVDGG 250 G L VDGG Sbjct: 243 GQCLNVDGG 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: 170 Number of extensions: 6 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: 255 Length adjustment: 24 Effective length of query: 232 Effective length of database: 231 Effective search space: 53592 Effective search space used: 53592 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 Apr 09 2024. 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