Align Glucokinase; EC 2.7.1.2; Glucose kinase (uncharacterized)
to candidate WP_057506803.1 ABB28_RS00795 glucokinase
Query= curated2:B4SRZ6 (335 letters) >NCBI__GCF_001431535.1:WP_057506803.1 Length = 341 Score = 178 bits (451), Expect = 2e-49 Identities = 118/319 (36%), Positives = 165/319 (51%), Gaps = 8/319 (2%) Query: 9 LVADIGGTNARFALADTSLDAPLQQDSIREYAVAEFPSLGDAARHHLEQIGATASRGVFA 68 +VAD+GGT AR A + AP + D R Y A++PSL + V A Sbjct: 29 IVADVGGTFARLAWSHGGAHAP-RIDGFRRYRCAQYPSLAAILADFAATATPQPAAAVVA 87 Query: 69 VAGRVDGDEARITNHPWVISRSRTAAMLGFDELHLINDFAAQAMAISLLQSDDVVQVGGA 128 +AG + GD N PW +S T G L LINDF A A+AI ++SD +V + G+ Sbjct: 88 IAGLLQGDTLVNANLPWPVSVDATRQQAGLRSLQLINDFEAVALAIPHVRSDALVALHGS 147 Query: 129 AWVPGKPGQPRNYAVIGPGTGLGVGGLILRHGRCYPLETEGGHVSFPPGTPEEIRILEIL 188 A P V+GPGTGLG L G L +E GH + GT E+ +L +L Sbjct: 148 A----DPATAWPALVLGPGTGLG-AALRFADGARPVLASEVGHSALSAGTALELDVLRLL 202 Query: 189 SEQFGRVSNERLICGPGLVNIHRAVCEMAGIDPGQLQPVDVTARALHG-DPQAMRTVDVF 247 +++ V NER++ G GL+N+++ +C++ G + A A G DP A TVDVF Sbjct: 203 LQRWDHVDNERVLSGTGLLNLYQCLCQLRGASAHCDDTEALLAAAHRGDDPLARETVDVF 262 Query: 248 CAVFGAIAGDLVLTQGAWDGVFLTGGLTPKMLDSLQHSGFRQRFEHKGRFSSIMARVPSL 307 C G+ GDL +T GA V+L GG++ + L S F RF +KG S++ +VP Sbjct: 263 CGWLGSFVGDLAITFGA-RAVYLAGGVSAHIAPFLPDSPFVARFLNKGVLGSVLQQVPVW 321 Query: 308 AVMHPHAGLLGAAAYAADA 326 V H G+LGAAA+ A A Sbjct: 322 RVEHGELGVLGAAAWNASA 340 Lambda K H 0.321 0.137 0.414 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: 300 Number of extensions: 21 Number of successful extensions: 5 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: 335 Length of database: 341 Length adjustment: 28 Effective length of query: 307 Effective length of database: 313 Effective search space: 96091 Effective search space used: 96091 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 (21.8 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