Align Glucokinase; EC 2.7.1.2; Glucose kinase (uncharacterized)
to candidate WP_020175085.1 A3OQ_RS0109155 hypothetical protein
Query= curated2:B9JYQ5 (340 letters) >NCBI__GCF_000385335.1:WP_020175085.1 Length = 332 Score = 195 bits (496), Expect = 1e-54 Identities = 123/328 (37%), Positives = 172/328 (52%), Gaps = 2/328 (0%) Query: 11 PFPVLVGDIGGTNARFWILMDAHAAPKEFANIHTADFPTIDQAIQDCILDKSGFQPRSAI 70 PFPVL+ DIGGTN RF + A + ++ T+D P+++ AI+ S P S I Sbjct: 6 PFPVLLSDIGGTNVRFALAKAPGLALEHGPHMKTSDHPSLEAAIEASRAFFSA-TPHSMI 64 Query: 71 LAVAGPIKDDEIPLTNCPWVIRPKAMIADLGFDDVLVVNDFEAQALAAASLGRNDREPIG 130 AGPI ++ +TN W I + A D L++NDFEAQAL+ A+L + IG Sbjct: 65 ACAAGPIDGRKVKMTNAAWSIDGATVAAAAKLDQGLLLNDFEAQALSLAALPAAATQWIG 124 Query: 131 PLTETSLNSRVILGPGTGLGVGGLLYTHHTWFPVPGEGGHVDIGPRSDRDWQIFPHIERI 190 E + +++LGPGTGLGV LL + +P E GHV+ G + + I+ I Sbjct: 125 DPREGT-GPQLVLGPGTGLGVSLLLKIDQKFVALPSEAGHVEFGATNLEEASIWSKITGP 183 Query: 191 EGRISGEQILCGRGILHLYNAICAADGIEPVWTDPADVTQHALKGNDPVCVETMTLFVTY 250 R + E +L G G++ L+ A AA G EP D V A T+ LF Sbjct: 184 PFRTTAEALLSGPGLVRLHFARLAALGKEPPSLDEVSVVAQAHAHPQGEEAATLRLFWNL 243 Query: 251 LGRIAGDMALVFMARGGVFLSGGISQKIIPLLKSPVFRAAFEDKAPHTEMMKTIPTFVAI 310 + R AGDMAL F+A+GGV +GG+ KI L FR FE+KAP+ +M+ I T + I Sbjct: 244 IARFAGDMALAFLAKGGVTFAGGVLPKITAFLDETEFRKHFENKAPYVALMQKIGTRLII 303 Query: 311 HPQAALSGLAAYARTPSSYGVKHEGRRW 338 P + L G+AA A +P Y + E R W Sbjct: 304 APDSVLDGMAAIAASPERYALDEERRAW 331 Lambda K H 0.322 0.140 0.445 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: 292 Number of extensions: 22 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: 340 Length of database: 332 Length adjustment: 28 Effective length of query: 312 Effective length of database: 304 Effective search space: 94848 Effective search space used: 94848 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Sep 24 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