Align glucokinase (EC 2.7.1.2) (characterized)
to candidate 5208927 Shew_1428 fructokinase (RefSeq)
Query= reanno::SB2B:6938110 (299 letters) >FitnessBrowser__PV4:5208927 Length = 296 Score = 485 bits (1248), Expect = e-142 Identities = 228/296 (77%), Positives = 260/296 (87%) Query: 1 MMRMGVDLGGTKIELVALGEDGSELFRKRIATPREYQGTLNAVVTLVNEAEATLGTQGSL 60 MMRMGVDLGGTKIELVAL E G ELFRKRI TPREY+ TL+A+ LVNEAE+TLG +G++ Sbjct: 1 MMRMGVDLGGTKIELVALSEAGKELFRKRIPTPREYKATLDAIEALVNEAESTLGQKGTV 60 Query: 61 GIGIPGVISPYTGLVKNANSTWINGHPLDRDLGALLNREVRVANDANCFAVSEAVDGAAA 120 G+GIPGVISP++GLVKNANSTWINGHPLD DLGA L REVRVANDANCFAVSEAVDGAAA Sbjct: 61 GVGIPGVISPFSGLVKNANSTWINGHPLDLDLGARLEREVRVANDANCFAVSEAVDGAAA 120 Query: 121 GKRVVFGAILGTGCGAGLAFDGRVHEGGNGIGGEWGHNPLPWMRPDEFNTTECFCGNKDC 180 GK +VFG I+GTGCG G+A +G+VH GGNGIGGEWGHNPLPWM PDEFN+TECFCGNKDC Sbjct: 121 GKGLVFGVIIGTGCGGGIAINGKVHGGGNGIGGEWGHNPLPWMTPDEFNSTECFCGNKDC 180 Query: 181 IETFVSGTGFVRDFRNSGGTAQNGAEIMSLVDAGDELANLVFDRYLDRLARSLAHVINML 240 IETF+SGTGFVRD++ +GG A +G EI ++ G+ LA F+RY+DRLARSLAH+INML Sbjct: 181 IETFISGTGFVRDYKAAGGDAPSGIEIARRMEQGEALATAAFERYIDRLARSLAHMINML 240 Query: 241 DPDAIVLGGGMSNVQAIYARLPAILPKYVVGRECRTPVVQNLYGCSSGVRGAAWLW 296 DPD IVLGGG+SN++AIY RLP L KYV+G ECRTPVVQN+YG SSGVRGAAWLW Sbjct: 241 DPDIIVLGGGVSNIEAIYPRLPEALSKYVLGGECRTPVVQNMYGGSSGVRGAAWLW 296 Lambda K H 0.320 0.139 0.429 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: 412 Number of extensions: 13 Number of successful extensions: 1 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: 299 Length of database: 296 Length adjustment: 26 Effective length of query: 273 Effective length of database: 270 Effective search space: 73710 Effective search space used: 73710 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 (21.8 bits) S2: 48 (23.1 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