Align glucokinase (EC 2.7.1.2) (characterized)
to candidate CCNA_02549 CCNA_02549 glucokinase
Query= reanno::SB2B:6938110 (299 letters) >FitnessBrowser__Caulo:CCNA_02549 Length = 296 Score = 312 bits (799), Expect = 7e-90 Identities = 159/297 (53%), Positives = 197/297 (66%), Gaps = 6/297 (2%) Query: 1 MMRMGVDLGGTKIELVALGEDGSELFRKRIATPREYQGTLNAVVTLVNEAEATLGTQ-GS 59 M+R GVD GGTKIE+ AL G + R R P Y L V LV +AE+ G Sbjct: 1 MIRFGVDFGGTKIEVAALNAAGDFVARVRKPNPGNYDEALEVVAALVADAESMAGGSCAR 60 Query: 60 LGIGIPGVISPYTGLVKNANSTWINGHPLDRDLGALLNREVRVANDANCFAVSEAVDGAA 119 LG+GIPG ISP TGL++NANST++NG P +L L R VR+ANDANC A+SEA DGA Sbjct: 61 LGLGIPGSISPRTGLIRNANSTYLNGRPFGENLETRLARPVRIANDANCLALSEAADGAG 120 Query: 120 AGKRVVFGAILGTGCGAGLAFDGRVHEGGNGIGGEWGHNPLPWMRPDEFNTTECFCGNKD 179 AG VVF AI+GTGCG G+ DG++ G NGIGGEWGH PLPW +P+E+ +C+CG K Sbjct: 121 AGASVVFAAIVGTGCGGGVVVDGKIINGHNGIGGEWGHAPLPWPKPEEYPGPDCWCGRKG 180 Query: 180 CIETFVSGTGFVRDFRNSGGTAQNGAEIMSLVDAGDELANLVFDRYLDRLARSLAHVINM 239 C+ET+++G F RD G A NG M + GD A+ DRY+DRLARSLA V ++ Sbjct: 181 CLETWIAGPAFARD----AGFA-NGQAAMQAIGEGDVKASAALDRYVDRLARSLAVVCDL 235 Query: 240 LDPDAIVLGGGMSNVQAIYARLPAILPKYVVGRECRTPVVQNLYGCSSGVRGAAWLW 296 +DPD IVLGGGMSNV A+Y RLPA + +V TPV + ++G SSGVRGA WLW Sbjct: 236 IDPDIIVLGGGMSNVDALYERLPAAIAPHVFSDIFETPVRKAVHGDSSGVRGAVWLW 292 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: 323 Number of extensions: 18 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: 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