Align glucokinase (EC 2.7.1.2) (characterized)
to candidate 7025547 Shewana3_2698 N-acetylglucosamine kinase (RefSeq)
Query= reanno::SB2B:6937235 (310 letters) >FitnessBrowser__ANA3:7025547 Length = 308 Score = 185 bits (469), Expect = 1e-51 Identities = 111/294 (37%), Positives = 165/294 (56%), Gaps = 4/294 (1%) Query: 5 GIDLGGTKIELVTLNEKGEEVFRKRVPTP-KDYRATLEAVAGLVHDSEKETGQVSSVGIG 63 G+D+GGTKIEL + + + R+ TP +DY A + +A + ++++ G+ +VGI Sbjct: 4 GLDIGGTKIELAIFDTQLALQDKWRLSTPGQDYSAFMATLAEQIEKADQQCGERGTVGIA 63 Query: 64 IPGVVSAVTGRVKNSNAVWLNGQPMDKDLGAMLGREVRIANDANCFAVSESVDGGGAGKT 123 +PGVV A G V +SN LN + + DL +L R V I ND CFA+SE+V G G G + Sbjct: 64 LPGVVKA-DGTVISSNVPCLNQRRVAHDLAQLLNRTVAIGNDCRCFALSEAVLGVGRGYS 122 Query: 124 LVFGAILGTGCGAGIAINHKVHGGGNGIGGEWGHNPLPWMTA--DEFNSTRCFCGNADCI 181 V G ILGTG G G+ I+ K++ G N + GE+GH + A + C CG C Sbjct: 123 RVLGMILGTGTGGGLCIDGKLYLGANRLAGEFGHQGVSANVACRHQLPLYVCGCGLEGCA 182 Query: 182 ETFVSGTGFVRDFRAHGGEAASGIEIVALMGKGEPLAEAAFGRFIDRLARALAHVINLLD 241 ET+VSGTG R ++ G+ A + + +PLA F ++D L +A ++ +D Sbjct: 183 ETYVSGTGLGRLYQDIAGQTADTFAWLNALRCNDPLAIKTFDTYMDILGSLMASLVLAMD 242 Query: 242 PDVIVLGGGVSNIDEIYEYLPALLPKYVLGGECATKVVKNHHGASSGVRGAAWL 295 PD+IVLGGG+S ++EI LP ++ G + G++SGVRGAA L Sbjct: 243 PDIIVLGGGLSEVEEILAALPQATKAHLFDGVTLPQFKLADFGSASGVRGAALL 296 Lambda K H 0.318 0.138 0.424 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: 310 Number of extensions: 17 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: 310 Length of database: 308 Length adjustment: 27 Effective length of query: 283 Effective length of database: 281 Effective search space: 79523 Effective search space used: 79523 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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