Align glucokinase; EC 2.7.1.2 (characterized)
to candidate WP_075388699.1 BK574_RS12335 ROK family glucokinase
Query= CharProtDB::CH_014478 (324 letters) >NCBI__GCF_002019605.1:WP_075388699.1 Length = 316 Score = 393 bits (1009), Expect = e-114 Identities = 196/319 (61%), Positives = 241/319 (75%), Gaps = 6/319 (1%) Query: 3 MDDKWLVGVDLGGTTIKMAFINHYGEIIHKWEINTDVSEQGRKIPTDIAKAIDKKLNDLG 62 M KW VGVDLGGTTIK+AF++ YG+II K E+ T+ + G I TDIAK ID+ L LG Sbjct: 1 MVTKWFVGVDLGGTTIKLAFVDPYGDIIFKGEVPTNTTNGGTNITTDIAKWIDQALEHLG 60 Query: 63 EVKSRLVGIGIGAPGPVNFANGSIEVAVNLGWEKFPIKDILEVETSLPVVVDNDANIAAI 122 K RL IG+GAPG +N G I AVN+GW+ F +KD LE++TSLPV +DNDANIAA+ Sbjct: 61 VSKDRLHSIGMGAPGFINMETGYIYQAVNIGWKDFHLKDRLEMDTSLPVTIDNDANIAAL 120 Query: 123 GEMWKGAGDGAKDLLCVTLGTGVGGGVIANGEIVQGVNGAAGEIGHITSIPEGGAPCNCG 182 GEMW+GAG+GAK+LLCVTLGTGVGGGVI NG IV GVNG AGEIGHIT+IP+GG PCNCG Sbjct: 121 GEMWRGAGNGAKNLLCVTLGTGVGGGVIVNGSIVHGVNGMAGEIGHITAIPKGGFPCNCG 180 Query: 183 KTGCLETIASATGIVRLTMEELTETDKPSELRTVLEQNGQVTSKDVFDAARSKDGLAMHV 242 K GCLETI+SATGI R+ E + +D P+ L NG + +K VF+AA D A+ V Sbjct: 181 KAGCLETISSATGISRIAKEFV--SDFPNSLLA----NGNINAKMVFEAAEKNDECALKV 234 Query: 243 VDKVAFHLGLALANSANALNPEKIVLGGGVSRAGEVLLAPVRDYFKRFAFPRVAQGAELA 302 +D + ++LG ALAN AN+LNPEKIV+GGGVS+AGE LL P+ ++F+ F PRVAQ + Sbjct: 235 IDHITYYLGFALANLANSLNPEKIVIGGGVSKAGETLLKPLENHFQLFVLPRVAQSVSIV 294 Query: 303 IATLGNDAGIIGGAWLVKS 321 ATLGNDAG+IGGAWL K+ Sbjct: 295 PATLGNDAGVIGGAWLAKT 313 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: 373 Number of extensions: 11 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: 316 Length adjustment: 28 Effective length of query: 296 Effective length of database: 288 Effective search space: 85248 Effective search space used: 85248 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