Align Glucokinase; EC 2.7.1.2 (characterized, see rationale)
to candidate WP_085638909.1 MGEO_RS13935 glucokinase
Query= uniprot:A8LLL9 (323 letters) >NCBI__GCF_002115805.1:WP_085638909.1 Length = 322 Score = 308 bits (788), Expect = 2e-88 Identities = 162/321 (50%), Positives = 216/321 (67%), Gaps = 4/321 (1%) Query: 1 MTSLRDAPALVADIGGTNTRVALADGPVLRAGSVEKYRNADYSSLDSVLRSYL-EKMEVA 59 MT ALVAD+GGTNTRVAL DG +R +++++RNA++ L SVLR+YL ++ V Sbjct: 1 MTETTPVTALVADLGGTNTRVALTDGGAVRTDTIKRFRNAEHPDLLSVLRAYLADQTVVP 60 Query: 60 GCSGACVALAGPVRNGIGHLTNLDWRMDEDLLSEATGAPVVALLNDLQAQGFALGHLEAA 119 C ACVA+AGPVR+G+G LTNL W +D D +++ATGA VA+LNDLQAQG AL L+ Sbjct: 61 DC--ACVAMAGPVRDGVGELTNLSWTVDRDSVADATGAKTVAVLNDLQAQGHALDLLKPE 118 Query: 120 CLRPVISRPPPAAQETRLMIGLGTGFNAASVLYTPAGRIVTPSEAGHANLPVRTEQELRL 179 L+ ++ + RL+IG+GTG NAA+V +V PSEAGH +LP + ELRL Sbjct: 119 VLQTILPGQKTGPKAARLVIGIGTGMNAAAVYRLGDRTLVPPSEAGHVSLPAQNADELRL 178 Query: 180 CRFVETAHGFPAVEDVLSGRGLERVYNFLSPTPDQPQRLSAAEVMAAA-AREERQALDAL 238 ++ HG P +ED+LSGRG ERVY +L L A+ +M A + A +A Sbjct: 179 LDWIAKKHGTPGLEDILSGRGFERVYEWLCSEAGVDAPLDASGIMQAVNDGSSKIAEEAA 238 Query: 239 ELFIGLLGTVAGNLSLIHLPFGGVYLCGGVARHIGPYLGSMGFAEAFANKGRFADFMRDF 298 +F+ ++G AGNL+L+HLPFGG+YL GGVARH P+L +GF EAF +KGRF++FM F Sbjct: 239 RMFVRMMGRAAGNLALVHLPFGGIYLIGGVARHFAPHLERLGFREAFHDKGRFSEFMEQF 298 Query: 299 PVWLVEDDFAALTGCASFLDE 319 PV LVEDD+AALTG A+ L E Sbjct: 299 PVHLVEDDYAALTGSAAHLME 319 Lambda K H 0.321 0.137 0.412 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: 339 Number of extensions: 16 Number of successful extensions: 3 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: 323 Length of database: 322 Length adjustment: 28 Effective length of query: 295 Effective length of database: 294 Effective search space: 86730 Effective search space used: 86730 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: 48 (23.1 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