Align Gluconokinase; Gluconate kinase; EC 2.7.1.12 (characterized)
to candidate N515DRAFT_1927 N515DRAFT_1927 gluconokinase
Query= SwissProt::Q5FQ97 (178 letters) >FitnessBrowser__Dyella79:N515DRAFT_1927 Length = 164 Score = 133 bits (334), Expect = 2e-36 Identities = 72/155 (46%), Positives = 93/155 (60%), Gaps = 1/155 (0%) Query: 13 RFLVVMGVSGTGKTTVATGLATRLGWHFQEGDALHPPANVEKMSTGQPLTDADRAPWLAL 72 R +VVMGV+G GK+TV + R G EGDA HP +N+ KMS G PL DADRA WLA Sbjct: 2 RAVVVMGVAGCGKSTVGAAICNRTGARMIEGDAFHPQSNIRKMSAGIPLDDADRAGWLAR 61 Query: 73 CHDWLREQVKAGHGAVLTCSALKRSYREQLRGDDLPIEFVHIDTSTGELADRLQRREGHF 132 + L V G AVL CSALKR YR+ LR + FV++ + E A+R+ R GHF Sbjct: 62 LGEELASTVATGDTAVLACSALKRRYRDTLRAAAPDVGFVYLALTPTEAAERVSHRPGHF 121 Query: 133 MPASLLPSQLATLEVPGDDEPVIRVSG-EKHPDVV 166 MPA+L+ SQ LE P + V+ V+ + P +V Sbjct: 122 MPATLIESQFRDLETPTGEPRVLTVNATDPWPSIV 156 Lambda K H 0.318 0.135 0.411 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: 116 Number of extensions: 2 Number of successful extensions: 1 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: 178 Length of database: 164 Length adjustment: 18 Effective length of query: 160 Effective length of database: 146 Effective search space: 23360 Effective search space used: 23360 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: 43 (21.2 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