Align Glucokinase; EC 2.7.1.2; Glucose kinase (uncharacterized)
to candidate WP_078429099.1 BK574_RS14475 ROK family protein
Query= curated2:Q9KCZ4 (330 letters) >NCBI__GCF_002019605.1:WP_078429099.1 Length = 302 Score = 160 bits (404), Expect = 5e-44 Identities = 96/305 (31%), Positives = 154/305 (50%), Gaps = 24/305 (7%) Query: 10 DVGGTTIKMAFLTTAGEIVDKWEIPTNKQDGGALITTNIADALDKRLSGHHKSKSDLIGI 69 D+GGT+IK G+++ +PT+ GGA + + LS K D+ G+ Sbjct: 7 DIGGTSIKYGVANKEGQLLFSSSVPTDAYLGGAAVIQKVV-----LLSKELMKKWDIHGV 61 Query: 70 GLGAPGFIEMDTGFIYHAV-NI-GWRDFPLKDKLEEETKLPVIVDNDANIAALGEMWKGA 127 + G I+ D G + +A NI + +++++ ++ KLPV V+ND N A+GE W+GA Sbjct: 62 SISTAGQIDSDNGIVVYATDNIPNYTGLNIEERIYDQLKLPVKVENDVNCTAIGEHWQGA 121 Query: 128 GDGAKNMLLITLGTGVGGGIVANGNILHGVNGMAGEIGHITVIPEGGAPCNCGKTGCLET 187 + L ITLGTGVGG + NG + G AGEIGH+T+ P G C CG GC E Sbjct: 122 AQNTDDFLCITLGTGVGGALFLNGRLYTGQGFSAGEIGHMTLYPH-GEKCTCGSNGCYEQ 180 Query: 188 VASATGIARIATEGVTEHKESQLALDYDKHG-VLTAKDVFSAADASDAFALSVVDHIAYY 246 AS++ + + ++ K+G ++ D F + + ++ + + Sbjct: 181 YASSSALEDLVSK---------------KYGHAISLIDFFVHVKSGETKSIQIYNQWIDD 225 Query: 247 LGFAIANLANALNPEKIVIGGGVSKAGDTLLKPIKQHFEAYALPRVADGAEFRIATLGND 306 L + L + +NP+ IVIGGG+S+ G+ LL IK +P A E ++A GN Sbjct: 226 LTTGLKTLIHIINPKLIVIGGGISEQGEFLLNSIKNSVYQKVMPNHARNLEIQLAEYGNK 285 Query: 307 AGVIG 311 A ++G Sbjct: 286 ANLLG 290 Lambda K H 0.316 0.137 0.405 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: 261 Number of extensions: 13 Number of successful extensions: 4 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: 330 Length of database: 302 Length adjustment: 27 Effective length of query: 303 Effective length of database: 275 Effective search space: 83325 Effective search space used: 83325 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 Apr 09 2024. 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