Align Gluconokinase; Gluconate kinase; EC 2.7.1.12 (characterized)
to candidate Pf1N1B4_557 Gluconokinase (EC 2.7.1.12)
Query= SwissProt::Q5FQ97 (178 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_557 Length = 177 Score = 126 bits (317), Expect = 2e-34 Identities = 70/148 (47%), Positives = 86/148 (58%) Query: 15 LVVMGVSGTGKTTVATGLATRLGWHFQEGDALHPPANVEKMSTGQPLTDADRAPWLALCH 74 LV+MGV+G GKT V+ L G EGD HP AN+EKMS G PL D DRA WL Sbjct: 8 LVIMGVAGCGKTCVSQSLCQLSGATAIEGDTFHPAANIEKMSAGIPLNDEDRAGWLDSLC 67 Query: 75 DWLREQVKAGHGAVLTCSALKRSYREQLRGDDLPIEFVHIDTSTGELADRLQRREGHFMP 134 D LR G VLTCSALK SYRE+LR + FV ++ + ADR+ R GHFMP Sbjct: 68 DELRRVDAKGERPVLTCSALKHSYRERLRSALPGLGFVFLELTPEVAADRVSHRPGHFMP 127 Query: 135 ASLLPSQLATLEVPGDDEPVIRVSGEKH 162 ++L+ SQ ATLE P + + + H Sbjct: 128 STLIDSQFATLESPVGEPLTLALDASSH 155 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: 127 Number of extensions: 6 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: 177 Length adjustment: 19 Effective length of query: 159 Effective length of database: 158 Effective search space: 25122 Effective search space used: 25122 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: 44 (21.6 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