Align glucokinase (EC 2.7.1.2) (characterized)
to candidate BWI76_RS11225 BWI76_RS11225 N-acetylglucosamine kinase
Query= reanno::SB2B:6937235 (310 letters) >FitnessBrowser__Koxy:BWI76_RS11225 Length = 303 Score = 204 bits (518), Expect = 3e-57 Identities = 118/296 (39%), Positives = 172/296 (58%), Gaps = 5/296 (1%) Query: 5 GIDLGGTKIELVTLNEKGEEVFRKRVPTPKD-YRATLEAVAGLVHDSEKETGQVSSVGIG 63 G D+GG+KI L ++ + KRV TPK+ Y A L+AV LV ++++ G SVGIG Sbjct: 4 GFDIGGSKIALGIFDKARRLQWEKRVATPKESYEAFLQAVEALVQEADQRFGCQGSVGIG 63 Query: 64 IPGVVSAVTGRVKNSNAVWLNGQPMDKDLGAMLGREVRIANDANCFAVSESVDGGGAGKT 123 IPG+ G + +N +G+ + DL LGR+VR+ NDANCFA+SE+ D Sbjct: 64 IPGMPETEDGTLYAANVPAASGRRLRADLSERLGRDVRLDNDANCFALSEAWDDEFTQYP 123 Query: 124 LVFGAILGTGCGAGIAINHKVHGGGNGIGGEWGHNPLP----WMTADEFNSTRCFCGNAD 179 LV G ILGTG G G+ +N K G I GE+GH LP + +F TRC CG Sbjct: 124 LVMGLILGTGVGGGLVLNGKSITGHRYITGEFGHIRLPVDALEVVGRDFPLTRCGCGQLG 183 Query: 180 CIETFVSGTGFVRDFRAHGGEAASGIEIVALMGKGEPLAEAAFGRFIDRLARALAHVINL 239 CIE ++SG GF ++ ++ + EIVAL +G+ A R++D LA L +++ + Sbjct: 184 CIENYLSGRGFAWLYQHFYQQSLTSPEIVALWQQGDAKAREHVERYLDLLAVCLGNILTI 243 Query: 240 LDPDVIVLGGGVSNIDEIYEYLPALLPKYVLGGECATKVVKNHHGASSGVRGAAWL 295 +DPD++VLGGG+SN I E L LP+++L ++ + HG + G+RGAA+L Sbjct: 244 VDPDLLVLGGGLSNFTAITEGLAQRLPRHLLPVASVPRIERARHGDAGGMRGAAFL 299 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: 259 Number of extensions: 14 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: 303 Length adjustment: 27 Effective length of query: 283 Effective length of database: 276 Effective search space: 78108 Effective search space used: 78108 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