Align Glucosamine kinase GspK; GlcN kinase; EC 2.7.1.8 (characterized)
to candidate 202608 SO3507 conserved hypothetical protein (NCBI ptt file)
Query= SwissProt::Q9KUA9 (294 letters) >FitnessBrowser__MR1:202608 Length = 300 Score = 154 bits (389), Expect = 2e-42 Identities = 91/280 (32%), Positives = 139/280 (49%), Gaps = 1/280 (0%) Query: 4 YVGIDGGGTSCRARIRNQQGEWVGEAKSGSANIMLGVEVALRSVVDAITQAAEQGGLSPD 63 ++G+DGGG+ CRA I G +G +G AN + G+ S+ + QA G+ Sbjct: 12 FIGVDGGGSKCRATIYTADGTVLGTGVAGRANPLHGLAQTFESIEASAHQALLDAGMKAT 71 Query: 64 DFPSMHVGLALAGAEQKEAWHAFMQQAHPFASITLNTDAYGACLGAHLGEEGAIMIAGTG 123 D + GL LAG + + HPFA++ + TD + AC+GAH G +GA++I GTG Sbjct: 72 DSHLLVAGLGLAGVNVPRLYQDVVNWQHPFAAMYVTTDLHTACIGAHRGADGAVIITGTG 131 Query: 124 SCGILLKGGKQYVVGGREFPISDQGSGAVMGLRLIQQVLLAQDGIRPHTPLCDVVMNHFN 183 SCG G +GG F + D+GSGA +GL+ + VLLA DG T L +++++H Sbjct: 132 SCGYAHVGDASLSIGGHGFALGDKGSGAWLGLKAAEHVLLALDGFATPTALTEMLLSHLG 191 Query: 184 -HDIDSIVAWSKTALPRDYGQFSPQIFSHAYCGDPLAIELLKQTAADIEMFLIALHHKGA 242 D IV Y Q + + A GD +AI ++++ A I L Sbjct: 192 VKDALGIVEHLAGKSSSCYAQLARNVLDCANAGDQVAIAIVQEGADYISEMARKLFMLNP 251 Query: 243 ERICLMGSIAERIQDWLSPPVQQWIVKPQSDAIEGALMFA 282 R ++G +AE +Q WL V I + + GA+ +A Sbjct: 252 VRFSMIGGLAEPLQAWLGSDVVAKISETLAPPELGAMYYA 291 Lambda K H 0.320 0.137 0.421 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: 290 Number of extensions: 16 Number of successful extensions: 2 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: 294 Length of database: 300 Length adjustment: 26 Effective length of query: 268 Effective length of database: 274 Effective search space: 73432 Effective search space used: 73432 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