Align Glucose kinase (characterized, see rationale)
to candidate PfGW456L13_1890 Glucokinase (EC 2.7.1.2)
Query= uniprot:Q8P6S9 (338 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1890 Length = 319 Score = 153 bits (387), Expect = 5e-42 Identities = 116/317 (36%), Positives = 157/317 (49%), Gaps = 18/317 (5%) Query: 19 VAADVGGTHVRLALACESNDPRKPVTVLDYRKYRCADYPGLAEIMAAFFAELSCAPVRRG 78 + D+GGT+ R AL N + V VL AD+P E ++ + L AP G Sbjct: 5 LVGDIGGTNARFALW--KNQQLESVQVL-----ATADFPSPEEAISLYLNGLGLAPGSIG 57 Query: 79 VI--ASAGYALEDGRVITANLPWVLAPEQIRQQLGMQALHLVNDFEAVAYAANYMTGNQV 136 + + AG D T N W L+ + Q L + L LVNDF A+A MT Q Sbjct: 58 SVCLSVAGPVSGDEFKFTNN-HWRLSRKGFCQTLQVDQLLLVNDFSAMALG---MTRLQP 113 Query: 137 MQLSGPAQGAPGP---ALVLGPGTGLGAALWIPNG-GNSVVLPTEAGHAALAAASDLEVA 192 + +G P P A+V+GPGTGLG + G G LP E GH L +S E Sbjct: 114 GEFRVVCEGTPEPLRPAVVIGPGTGLGVGTLLDLGAGRFAALPGEGGHVDLPLSSPRETQ 173 Query: 193 LLQELRRTRTHVATEHFLSGPGLLTLYTALATLRDAPAVHATPAAVTAAALAGDDVLAHE 252 L Q + HV+ E LSG GL +Y A+ + V TP A+TAA LAGD + A E Sbjct: 174 LWQHIFNEIGHVSAETALSGGGLPRVYRAICAVDGHTPVLDTPEAITAAGLAGDPI-AVE 232 Query: 253 ALQTFCGFMGSVVGDMMLLYGVRSGVYLAGGFLPQIADFIARSDFAARLLDKGPLRPALE 312 L+ FC ++G V G+ +L G R GVY+ GG +P+ ADF S FA DKG + + Sbjct: 233 VLEQFCCWLGRVAGNNVLTTGGRGGVYIVGGVIPRFADFFLESGFARCFADKGCMSDYFK 292 Query: 313 QVPVRIVEHGQLGVIGA 329 +PV +V G++GA Sbjct: 293 GIPVWLVTAPYSGLMGA 309 Lambda K H 0.321 0.136 0.407 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: 247 Number of extensions: 18 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: 338 Length of database: 319 Length adjustment: 28 Effective length of query: 310 Effective length of database: 291 Effective search space: 90210 Effective search space used: 90210 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