Align Glucokinase; EC 2.7.1.2; Glucose kinase (uncharacterized)
to candidate WP_083492046.1 ABB28_RS14545 glucokinase
Query= curated2:Q21LZ9 (321 letters) >NCBI__GCF_001431535.1:WP_083492046.1 Length = 374 Score = 190 bits (482), Expect = 5e-53 Identities = 107/315 (33%), Positives = 165/315 (52%), Gaps = 5/315 (1%) Query: 6 YIVADIGGTNARFALV--TGKKGNAFNLEQIQILNGSEFPRLQDAMQHYIDTLGGEKPKA 63 ++ AD+GGT+ R A V +G + + + ++ P L + ++ G +P Sbjct: 55 FLAADVGGTHVRVARVEASGDAAHPVRVLDYRKYRNADHPGLGAILSDFLGD--GMRPAH 112 Query: 64 ACVAIAGPIDGDNARMT-NLNWEFSQAAVKAEFGFDKYDTLNDFGALAVATSSLQADNLI 122 VA AG D +T N+ W S ++ E G +NDF A+A A + + A ++ Sbjct: 113 CVVATAGYAREDGTVITANVPWPLSARQLETEVGVQHVHIVNDFEAVAHAAAQVDASGVL 172 Query: 123 EIKAGTMDPKGNKAILGPGTGLGVAGLACAGDSWLPIPSEGGHVNVAPATQLECEVIRAA 182 ++ P G ++GPGTGLG A + + +E G ++A + LE ++R Sbjct: 173 QLCGPHSAPIGPTLVVGPGTGLGAALWIPTAHGPVVLATEAGQASLAASDALEMAILRHM 232 Query: 183 MAEHGHVSAETFISGPGLVRLYRALATVRGETPKNYEPKDITAGALDGTDDLCKETLDLF 242 + HVS E +SGPGL+ LY AL + P +TA A+ GTD L + LD+F Sbjct: 233 LRGRSHVSVEHALSGPGLINLYTALCALEDRPALLGSPDAVTAAAIAGTDALARRALDVF 292 Query: 243 CSFIGSLSGNLALTYGAKGGVYLAGGVLPRFIDYFKSSDFVKRFSEKGVMSHYVENIPVN 302 C +GS G++AL YGA GGVYLAGG+LP+ DY + S FV R+ KG MS ++ IPV Sbjct: 293 CGLLGSTVGDMALMYGAHGGVYLAGGILPKIRDYLRDSTFVARYLNKGPMSEALQRIPVK 352 Query: 303 LISYEYTAFVGAAAW 317 ++ + +GAA+W Sbjct: 353 VVEHGQLGVIGAASW 367 Lambda K H 0.319 0.137 0.410 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: 312 Number of extensions: 15 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: 321 Length of database: 374 Length adjustment: 29 Effective length of query: 292 Effective length of database: 345 Effective search space: 100740 Effective search space used: 100740 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 (21.7 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