Align glycerone kinase (EC 2.7.1.29) (characterized)
to candidate SM_b20313 SM_b20313 glycerone kinase
Query= BRENDA::P76014 (210 letters) >FitnessBrowser__Smeli:SM_b20313 Length = 227 Score = 124 bits (311), Expect = 1e-33 Identities = 73/203 (35%), Positives = 109/203 (53%), Gaps = 8/203 (3%) Query: 14 RCGDIFSTESE-------YLTGLDREIGDADHGLNMNRGFSKVVEKLPAIADKDIGFILK 66 R GDI T ++ YL+ +D +IGD DHG+NM +GF E+L D + L Sbjct: 22 RAGDIVLTLADRIIENRAYLSEIDGKIGDGDHGVNMAKGFGLAAERLKG-KDASLAEALD 80 Query: 67 NTGMTLLSSVGGASGPLFGTFFIRAAQATQARQSLTLEELYQMFRDGADGVISRGKAEPG 126 G L++ +GG+ GPL+G F A+ + ++ +M G +G+ S G A+ G Sbjct: 81 TLGTVLMTEIGGSMGPLYGVMFTEFAEKIEGADAIDAAAYSRMLHAGLEGIRSIGSAKVG 140 Query: 127 DKTMCDVWVPVVESLRQSSEQNLSVPVALEAASSIAESAAQSTITMQARKGRASYLGERS 186 DKT+ D VP V++ ++ AL+A S AE+ ST + AR GRAS LGERS Sbjct: 141 DKTLLDTLVPAVDAFDAATADGRPFAEALDALVSAAEAGRDSTRDLIARIGRASRLGERS 200 Query: 187 IGHQDPGATSVMFMMQMLALAAK 209 +G D GATS +++ L+ A+ Sbjct: 201 LGVLDAGATSCAIILRELSHGAR 223 Lambda K H 0.316 0.130 0.364 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: 110 Number of extensions: 5 Number of successful extensions: 2 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: 210 Length of database: 227 Length adjustment: 22 Effective length of query: 188 Effective length of database: 205 Effective search space: 38540 Effective search space used: 38540 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 (21.7 bits) S2: 45 (21.9 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