Align NAD-dependent glycerol dehydrogenase; Dha-forming NAD-dependent glycerol dehydrogenase; EC 1.1.1.6 (characterized)
to candidate CCNA_01345 CCNA_01345 short chain dehydrogenase
Query= SwissProt::Q92EU6 (254 letters) >FitnessBrowser__Caulo:CCNA_01345 Length = 260 Score = 156 bits (394), Expect = 5e-43 Identities = 97/257 (37%), Positives = 147/257 (57%), Gaps = 15/257 (5%) Query: 8 KDFNITDKVAVVTGAASGIGKAMAELFSEKGAYVVLLDIKEDVKD--VAAQINPSRT-LA 64 K F++T +VA+VTG + G+G +A +E GA V L+ K+ D VAA RT + Sbjct: 7 KLFDLTGRVAIVTGGSRGLGLQIARALAEYGAAVALVARKQGELDAAVAALTAEGRTAVG 66 Query: 65 LQVDITKKENIEKVVAEIKKVYPKIDILANSAGVALLEKAEDLPEEYWDKTMELNLKGSF 124 L D+ + + + + A + + + +IDIL N+AG A AED P E W+K M+LN+ G F Sbjct: 67 LVADLGQAGSAQDLTARVLERFGRIDILVNNAGAAWGAPAEDYPLEGWNKVMDLNVTGLF 126 Query: 125 LMAQIIGRE-MIATGGGKIVNMASQASVIALDKH-------VAYCASKAAIVSMTQVLAM 176 L+ Q + RE + G G +VN+ AS+ L H +AY +K A+++MT+ LA Sbjct: 127 LLTQAVAREAFLKQGKGAVVNV---ASIEGLQGHHHSQLGTIAYNTAKGAVINMTRALAA 183 Query: 177 EWAPYNINVNAISPTVILTELGKKAWAGQVGEDMKKLIPAGRFGYPEEVAACALFLVSDA 236 EW P NI VNA++P +++ GQ G+DM + P G+ G ++ AL L SDA Sbjct: 184 EWGPRNIRVNAVAPGYFPSKM-TMTTLGQHGDDMLRQTPLGKLGGDTDLMGPALLLASDA 242 Query: 237 ASLITGENLIIDGGYTI 253 ITG+ +++DGG TI Sbjct: 243 GGHITGQIIVVDGGMTI 259 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: 168 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: 260 Length adjustment: 24 Effective length of query: 230 Effective length of database: 236 Effective search space: 54280 Effective search space used: 54280 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 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