Align glucokinase (EC 2.7.1.2) (characterized)
to candidate WP_012759075.1 RLEG_RS18545 N-acetylglucosamine kinase
Query= reanno::SB2B:6937235 (310 letters) >NCBI__GCF_000023185.1:WP_012759075.1 Length = 304 Score = 142 bits (358), Expect = 1e-38 Identities = 99/303 (32%), Positives = 150/303 (49%), Gaps = 10/303 (3%) Query: 7 DLGGTKIELVTLNEKGEEVFRKRVPTPKD-YRATLEAVAGLVHDSEKETG-QVSSVGIGI 64 D+GGT I+ + + + + R PTPKD + A +E + ++ ETG Q S + + I Sbjct: 6 DIGGTAIKGGIAHSEIDILPLGRRPTPKDDFAAFVETLRDII----AETGEQPSRIALSI 61 Query: 65 PGVVSAVTGRVKNSNAVWLNGQPMDKDLGAMLGREVRIANDANCFAVSESVDGGGAGKTL 124 GVV T R+ +N ++ + + DL LG V IANDA+CFA++E+ G G G + Sbjct: 62 AGVVDPDTQRLICANIPCIHHRTLGADLEVELGLPVLIANDADCFAMAEAGLGAGRGHRI 121 Query: 125 VFGAILGTGCGAGIAINHKVHGGGNGIGGEWGHNPLPWMTADE----FNSTRCFCGNADC 180 VFGAILGTG G G+ + ++ G GEWGH P+ A + C CG C Sbjct: 122 VFGAILGTGVGGGLVADGRLVNEAGGFAGEWGHGPIIASAAGNPPVAIPAYACGCGQRGC 181 Query: 181 IETFVSGTGFVRDFRAHGGEAASGIEIVALMGKGEPLAEAAFGRFIDRLARALAHVINLL 240 ++T G R + S EI+A G+GE A ++D +A LA IN+ Sbjct: 182 VDTVGGARGLERLHQTLHDLDLSSEEIIAQWGRGEEKATRTIDVYVDLVASPLALTINIT 241 Query: 241 DPDVIVLGGGVSNIDEIYEYLPALLPKYVLGGECATKVVKNHHGASSGVRGAAWLWAPGE 300 ++ +GGG+SN++ + L + +L VV++ G+ GAA L E Sbjct: 242 GATIVPVGGGLSNVEPLLAELDHAVRARILRKFDRPLVVRSECRIEPGLIGAALLGLKAE 301 Query: 301 QAA 303 AA Sbjct: 302 TAA 304 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: 24 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: 304 Length adjustment: 27 Effective length of query: 283 Effective length of database: 277 Effective search space: 78391 Effective search space used: 78391 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 24 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