Align NAD-dependent glycerol dehydrogenase; Dha-forming NAD-dependent glycerol dehydrogenase; EC 1.1.1.6 (characterized)
to candidate 350961 BT1433 putative oxidoreductase (NCBI ptt file)
Query= SwissProt::Q92EU6 (254 letters) >FitnessBrowser__Btheta:350961 Length = 270 Score = 131 bits (330), Expect = 1e-35 Identities = 91/263 (34%), Positives = 141/263 (53%), Gaps = 23/263 (8%) Query: 10 FNITDKVAVVTGAASGIGKAMAELFSEKGAYVVLLDIKED-----VKDVAAQINPSRTLA 64 FN+ DKV V+TG A +GK +A +++GA VV+LD E+ V+ + A+ N + + Sbjct: 5 FNVKDKVVVITGGAGILGKGIAAYLAKEGAKVVVLDRSEEAGKALVESIKAEGNEA--MF 62 Query: 65 LQVDITKKENIEKVVAEIKKVYPKIDILANSAG-------VALLEKAEDLPEEYWDKTME 117 L D+ KE +E EI K Y +ID+L N+AG +A + DL + + K ++ Sbjct: 63 LYTDVMDKEVLEGNKVEIMKAYGRIDVLLNAAGGNMAGATIAPDKTFFDLQIDAFKKVVD 122 Query: 118 LNLKGSFLMAQIIGREMIATGGGKIVNMASQASVIALDKHVAYCASKAAIVSMTQVLAME 177 LNL G+ L + M+ G IVN S++++ L + V Y A+KAAI + T+ +A E Sbjct: 123 LNLFGTVLPTMVFAEIMVEQKKGSIVNFCSESALRPLTRVVGYGAAKAAIANFTKYMAGE 182 Query: 178 WA---PYNINVNAISPTVILTELGKKAWAGQVGE--DMKKLI----PAGRFGYPEEVAAC 228 A + VNAI+P LT+ + G D K I P RFG PE++ Sbjct: 183 LALKFGNGLRVNAIAPGFFLTDQNRALLTNPDGSLTDRSKTILAHTPFNRFGEPEDLYGT 242 Query: 229 ALFLVSDAASLITGENLIIDGGY 251 +L+SDA++ +TG +IDGG+ Sbjct: 243 IHYLISDASNFVTGTVAVIDGGF 265 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: 182 Number of extensions: 13 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: 270 Length adjustment: 25 Effective length of query: 229 Effective length of database: 245 Effective search space: 56105 Effective search space used: 56105 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