Align Glucokinase; ATP-dependent glucokinase; ATP-GLK; Glucose kinase; EC 2.7.1.2 (characterized)
to candidate WP_011778519.1 MVAN_RS06320 ROK family protein
Query= SwissProt::Q9X1I0 (317 letters) >NCBI__GCF_000015305.1:WP_011778519.1 Length = 306 Score = 192 bits (488), Expect = 9e-54 Identities = 117/313 (37%), Positives = 169/313 (53%), Gaps = 17/313 (5%) Query: 6 LIGVDLGGTTFSVGLVSEDGKILKKVTRDTLVENGKEDVIRRIAETILEVSDGEEAPY-- 63 ++ +D+GGT + GLV DG ++ + + T + E V A + E D P Sbjct: 5 VLALDIGGTKIAAGLVDADGTLVHRAQQPT-PDGDAETVWDTAAALLAETRDAAPGPVSA 63 Query: 64 VGIGSPGSIDRENGIVRFSP-NFPDWHNVPLTDELAKRTGKKVFLENDANAFVLGEKWFG 122 VGIGS G ID G V SP N +W + P+ +A TG V L D LGE W G Sbjct: 64 VGIGSAGPIDVPGGTV--SPINIAEWSHFPIVRRVADLTGLPVRLGGDGLCMALGEWWRG 121 Query: 123 AGRGHDHIVALTLGTGIGGGVVTHGYLLTGRDGIGAELGHVVVEPNGPMCNCGTRGCLEA 182 AGRG ++ + + TGIGGG+V G GR G +GHVVVEP G C CG RGC+E Sbjct: 122 AGRGAGFLLGMVVSTGIGGGLVLDGAPYHGRSGNAGHVGHVVVEPGGAPCTCGGRGCVET 181 Query: 183 VASATAIRRFLREGYKKYHSSLVYKLAGSPEKADAKHLFDAARQGDRFALMIRDRVVDAL 242 VAS + R+ + A +P+ ADAK L +AA +GD AL R DA+ Sbjct: 182 VASGPHLARWAHDN----------GWAAAPD-ADAKDLAEAAGRGDPVALRAFARGADAV 230 Query: 243 ARAVAGYIHIFNPEIVIIGGGISRAGEILFGPLREKVVDYIMPSFVGTYEVVASPLVEDA 302 AR +A + + ++V++GGG+++AG +LF PLR+ + Y F+ VV + L DA Sbjct: 231 ARTIASVAAVCDLDLVVVGGGVAKAGALLFDPLRQALTMYAGLEFLRGLRVVPAELGGDA 290 Query: 303 GILGAASIIKERI 315 G++GAA+++ + + Sbjct: 291 GLVGAAALVHDSV 303 Lambda K H 0.320 0.142 0.418 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: 292 Number of extensions: 15 Number of successful extensions: 3 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: 317 Length of database: 306 Length adjustment: 27 Effective length of query: 290 Effective length of database: 279 Effective search space: 80910 Effective search space used: 80910 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 (21.7 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