Align glucokinase; EC 2.7.1.2 (characterized)
to candidate WP_011782033.1 MVAN_RS24565 ROK family protein
Query= CharProtDB::CH_014478 (324 letters) >NCBI__GCF_000015305.1:WP_011782033.1 Length = 392 Score = 151 bits (381), Expect = 3e-41 Identities = 99/319 (31%), Positives = 154/319 (48%), Gaps = 17/319 (5%) Query: 2 NMDDKWLVGVDLGGTTIKMAFINHYGEIIHKWEINTDVSEQGRKIPTDIAKAIDKKLNDL 61 N D ++ +GG+ ++A N G+++ +I+ + + + + K ++ L + Sbjct: 74 NADAGVVLTAAVGGSRTRLAVCNLAGDVLTAADIDQEPGLGPQDLMPQVVKGLEVLLAES 133 Query: 62 GEVKSRLVGIGIGAPGPVNFANGS-IEVAVNLGWEKFPIKDILEVETSLPVVVDNDANIA 120 G + G+G+ PG V+ GS I+ V GW+ P+ T PVV+ NDAN+ Sbjct: 134 GH-SDAVYGVGLSLPGTVDQERGSSIDTPVLSGWDGAPLIPYFRQLTEAPVVLGNDANVI 192 Query: 121 AIGEMWKGAGDGAKDLLCVTLGTGVGGGVIANGEIVQGVNGAAGEIGHITSIPEGGAPCN 180 A+ E GAG G DLL V TG+G G+IA G +G AAGE GH + G PC Sbjct: 193 ALAEWRAGAGRGFDDLLVVKASTGLGAGIIAGGAPQRGAIRAAGEFGHNKTPAAEGRPCR 252 Query: 181 CGKTGCLETIASATGIVRLTMEELTETDKPSELRTVLEQNGQVTSKDVFDAARSKDGLAM 240 CG TGCLET+A +VR L + +P +D+ + A S D LA Sbjct: 253 CGDTGCLETVAGGWALVR----TLAQEGRPVR-----------NLRDLVELAHSGDALAR 297 Query: 241 HVVDKVAFHLGLALANSANALNPEKIVLGGGVSRAGEVLLAPVRDYFKRFAFPRVAQGAE 300 + ++G LA + N LNP +V+ G + A ++ +A +R+ A + E Sbjct: 298 RQIRDSGRYIGEVLAGAVNLLNPAALVVAGDAAGAYDIFVAGLRETLYGNATALATRVLE 357 Query: 301 LAIATLGNDAGIIGGAWLV 319 + A LG+ G IG A +V Sbjct: 358 IRPAQLGDRGGSIGSAMMV 376 Lambda K H 0.316 0.137 0.404 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: 307 Number of extensions: 21 Number of successful extensions: 2 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: 324 Length of database: 392 Length adjustment: 29 Effective length of query: 295 Effective length of database: 363 Effective search space: 107085 Effective search space used: 107085 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 (21.6 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