Align Glucose kinase (characterized, see rationale)
to candidate Ga0059261_0355 Ga0059261_0355 glucokinase, proteobacterial type
Query= uniprot:Q8P6M4 (344 letters) >FitnessBrowser__Korea:Ga0059261_0355 Length = 323 Score = 168 bits (425), Expect = 2e-46 Identities = 109/325 (33%), Positives = 163/325 (50%), Gaps = 10/325 (3%) Query: 23 LAADVGGTHVRVGRVSHGADAPIELSQYRTYRCADHASLD----AILADFLRDSRAVDAV 78 +A D+GGTH R + + + T + A+H S A R+ A+ Sbjct: 4 VAVDIGGTHARFAIAEVEGGRVVSIGEPVTQKTAEHGSFQLAWQASARALGREMPRAAAI 63 Query: 79 VIASAGVALDDGRFISNNLPWTIAPRQLRDTLGVRAVHLVNDFEAVAYAAPQMEQRAVVQ 138 IAS ++D N PW I P +++ L V + L+NDF AV +A Q+ + Sbjct: 64 AIASP---INDELIKLTNNPWIIRPPLIKERLEVDSYSLINDFGAVGHAVAQLPSEHFLH 120 Query: 139 LSGPTPRHAQPGGPILVVGPGTGLGAA-VWINGPRQPTVLATEAGQVALASNDPDTAQVL 197 + GP A+ G I V GPGTGLG A V+ GP V++TE G + A D ++ Sbjct: 121 ICGPDAPFAEKGA-ITVCGPGTGLGVAQVFRTGPLSYHVISTEGGHMDFAPLDGIEDSIV 179 Query: 198 RILARDASYLPIEHVLSGPGLRNLYLALCELHAATPIHPLPADITHAALHSDDALARRCL 257 + L + + E +++GPG+ +Y L E+ +I A D+LA L Sbjct: 180 KRLRSTYTRVSAERIVAGPGIVPIYETLAEIEGKRTHRLNDKEIWTLAFEGKDSLAMAAL 239 Query: 258 QLFCALLGSAVGDMALAYGASGGVYLAGGILPSIGQFLAASDFRERFLAKGRMRPVLERI 317 FC LG+ GD+ALA+G + GV +AGG+ + L S F +RF+AKGR + ++ I Sbjct: 240 DRFCLSLGAVAGDLALAHGPT-GVVIAGGLGLKLKDHLVNSGFGQRFIAKGRFQALMSSI 298 Query: 318 PVKLVEHGQLGVLGAASWYLQHHTE 342 PVKL+ H Q G+ GAA+ Y Q HT+ Sbjct: 299 PVKLITHPQPGLYGAAAAYAQEHTQ 323 Lambda K H 0.321 0.136 0.410 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: 372 Number of extensions: 19 Number of successful extensions: 5 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: 344 Length of database: 323 Length adjustment: 28 Effective length of query: 316 Effective length of database: 295 Effective search space: 93220 Effective search space used: 93220 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 (21.9 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Sep 17 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