Align NAD-dependent glycerol dehydrogenase; Dha-forming NAD-dependent glycerol dehydrogenase; EC 1.1.1.6 (characterized)
to candidate Pf6N2E2_5889 Short-chain dehydrogenase/reductase SDR
Query= SwissProt::Q92EU6 (254 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5889 Length = 253 Score = 141 bits (356), Expect = 1e-38 Identities = 90/263 (34%), Positives = 149/263 (56%), Gaps = 25/263 (9%) Query: 1 MTFKGFDKDFNITDKVAVVTGAASGIGKAMAELFSEKGAYVVLLDIK--------EDVKD 52 MTF G +VAVVTGAA+GIG+A A F+ +G VV+ D+ + ++D Sbjct: 3 MTFSG---------QVAVVTGAAAGIGRATALAFAAEGLKVVVADLDVAGGEGTVQSIRD 53 Query: 53 VAAQINPSRTLALQVDITKKENIEKVVAEIKKVYPKIDILANSAGVALLE-KAEDLPEEY 111 + + ++ ++T + ++++++ E+ K Y ++D N+AG+ + + K D + Sbjct: 54 AGGE-----AVFVRCNVTLENDVQQLMDEVIKTYGRLDYAFNNAGIEIEKGKLADGTLDE 108 Query: 112 WDKTMELNLKGSFLMAQIIGREMIATGGGKIVNMASQASVIALDKHVAYCASKAAIVSMT 171 +D M +N+KG +L + ++A GGG IVN AS A + A K Y ASK A++ +T Sbjct: 109 FDAIMGVNVKGVWLCMKYQLPLLLAQGGGAIVNTASVAGLGAAPKMSIYAASKHAVIGLT 168 Query: 172 QVLAMEWAPYNINVNAISPTVILTELGKKAWAG--QVGEDMKKLIPAGRFGYPEEVAACA 229 + A+E+A I VNA+ P VI T++ ++A+ + GE + P GR G EE+A+ Sbjct: 169 KSAAIEYAKKKIRVNAVCPAVIDTDMFRRAYEADPKKGEFANAMHPVGRIGKVEEIASAV 228 Query: 230 LFLVSDAASLITGENLIIDGGYT 252 L+L SD A+ TG +L +DGG T Sbjct: 229 LYLCSDGAAFTTGHSLAVDGGVT 251 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: 142 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: 253 Length adjustment: 24 Effective length of query: 230 Effective length of database: 229 Effective search space: 52670 Effective search space used: 52670 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