Align NAD-dependent glycerol dehydrogenase; Dha-forming NAD-dependent glycerol dehydrogenase; EC 1.1.1.6 (characterized)
to candidate WP_211248857.1 Q394_RS0118475 glucose 1-dehydrogenase
Query= SwissProt::Q92EU6 (254 letters) >NCBI__GCF_000621325.1:WP_211248857.1 Length = 255 Score = 129 bits (325), Expect = 4e-35 Identities = 90/248 (36%), Positives = 136/248 (54%), Gaps = 8/248 (3%) Query: 11 NITDKVAVVTGAASGIGKAMAELFSEKGAYVVLLDIK-EDVKDVAAQINPSRTLALQV-- 67 N+ KV V+TGA+SGIG+A A F +G +VL + E+ + VAA I + A+ V Sbjct: 8 NLAGKVVVITGASSGIGEAAAHAFGREGCKLVLGARRAEEGEAVAAAIRATGGEAVFVCT 67 Query: 68 DITKKENIEKVVAEIKKVYPKIDILANSAGVALLEKA--EDLPEEYWDKTMELNLKGSFL 125 D+ ++ +I ++V + +D+L N+AG + A E EY D TM N++ Sbjct: 68 DVLQEADIARLVQTALDTFGGLDVLFNNAGTEGVSSAFTEQSTAEY-DFTMNTNVRSVLW 126 Query: 126 MAQIIGREMIATGGGKIVNMASQASVIALDKHVAYCASKAAIVSMTQVLAMEWAPYNINV 185 Q R M + GG I+N AS + + Y ASKAA+V MT+V A+E+ I + Sbjct: 127 GMQHAIRAM-QSAGGAIINNASIVAHVGFANTALYSASKAAVVGMTRVAAVEYFKQGIRI 185 Query: 186 NAISPTVILTELGKKAWAGQVGED-MKKLIPAGRFGYPEEVAACALFLVSDAASLITGEN 244 NA+ P + T + ++ G+ ++ PAGR G PEE+AA +FL S AS I+G+ Sbjct: 186 NAVCPGITYTPMSQRLLGGEDEQNAFMATTPAGRTGQPEEIAAAVVFLASGNASYISGQC 245 Query: 245 LIIDGGYT 252 L +DGGYT Sbjct: 246 LNVDGGYT 253 Lambda K H 0.316 0.133 0.369 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: 145 Number of extensions: 9 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: 254 Length of database: 255 Length adjustment: 24 Effective length of query: 230 Effective length of database: 231 Effective search space: 53130 Effective search space used: 53130 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 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