Align glucokinase; EC 2.7.1.2 (characterized)
to candidate WP_010632185.1 RH97_RS09765 ROK family glucokinase
Query= CharProtDB::CH_014478 (324 letters) >NCBI__GCF_000246965.1:WP_010632185.1 Length = 323 Score = 355 bits (911), Expect = e-103 Identities = 170/319 (53%), Positives = 231/319 (72%) Query: 3 MDDKWLVGVDLGGTTIKMAFINHYGEIIHKWEINTDVSEQGRKIPTDIAKAIDKKLNDLG 62 M +K +GVDLGGTT KMA I+ G+ I KW I T+ + G I DI+++I KKL Sbjct: 1 MSEKMNIGVDLGGTTTKMALIDDAGKTIDKWAIVTNTIDNGSHIAADISESIKKKLKQYN 60 Query: 63 EVKSRLVGIGIGAPGPVNFANGSIEVAVNLGWEKFPIKDILEVETSLPVVVDNDANIAAI 122 S + GIG+GAPG ++ A+G + AVN+GWE +P+K+ LE T LP +++NDAN+AA+ Sbjct: 61 LGSSEVRGIGMGAPGFIDMASGFVYKAVNIGWEDYPLKEELEKFTGLPAIIENDANMAAL 120 Query: 123 GEMWKGAGDGAKDLLCVTLGTGVGGGVIANGEIVQGVNGAAGEIGHITSIPEGGAPCNCG 182 GEMW GAG GAK+L+CVTLGTGVGGG+I +G+IV GV+G AGEIGHIT +P+GG+PCNCG Sbjct: 121 GEMWLGAGRGAKNLICVTLGTGVGGGIIIDGDIVHGVSGMAGEIGHITVVPKGGSPCNCG 180 Query: 183 KTGCLETIASATGIVRLTMEELTETDKPSELRTVLEQNGQVTSKDVFDAARSKDGLAMHV 242 K GCLET++SATGI R+ ++ L D S LR + E+NG ++++DVF+ A D L++ V Sbjct: 181 KKGCLETVSSATGIRRMGLDALDYNDSDSILRDLFEKNGDISAEDVFNCAAKGDQLSVAV 240 Query: 243 VDKVAFHLGLALANSANALNPEKIVLGGGVSRAGEVLLAPVRDYFKRFAFPRVAQGAELA 302 +K A++LG AL + +NPEKIV+GGGVS AG+ L P+ YFK F+ PRV ++ Sbjct: 241 AEKAAYYLGYALGAISIVVNPEKIVIGGGVSHAGKTLTDPLTKYFKEFSLPRVFDACKID 300 Query: 303 IATLGNDAGIIGGAWLVKS 321 IA L NDAG++GGAWL K+ Sbjct: 301 IAQLSNDAGVVGGAWLAKT 319 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: 349 Number of extensions: 17 Number of successful extensions: 1 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: 323 Length adjustment: 28 Effective length of query: 296 Effective length of database: 295 Effective search space: 87320 Effective search space used: 87320 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: 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