Align hexokinase (EC 2.7.1.1) (characterized)
to candidate 202608 SO3507 conserved hypothetical protein (NCBI ptt file)
Query= BRENDA::Q96Y14 (299 letters) >FitnessBrowser__MR1:202608 Length = 300 Score = 104 bits (260), Expect = 2e-27 Identities = 77/245 (31%), Positives = 120/245 (48%), Gaps = 28/245 (11%) Query: 3 IIVGVDAGGTKTKAVAYDCEGNFIGEGSSGPGNYHNVGLTRAIENIK--------EAVKI 54 + +GVD GG+K +A Y +G +G G +G N + GL + E+I+ +A Sbjct: 11 LFIGVDGGGSKCRATIYTADGTVLGTGVAGRANPLH-GLAQTFESIEASAHQALLDAGMK 69 Query: 55 AAKGEADVVGMGVAGLD------SKFDWENFTPLASLIAPKVIIQHDGVIALFAETLGEP 108 A V G+G+AG++ +W++ P A++ + D A G Sbjct: 70 ATDSHLLVAGLGLAGVNVPRLYQDVVNWQH--PFAAMY-----VTTDLHTACIGAHRGAD 122 Query: 109 GVVVIAGTGSVVEGYNGKEFLRVGGRGWLLSDDGSAYWVGRKALRKVLKMMDGLENKTIL 168 G V+I GTGS + G L +GG G+ L D GS W+G KA VL +DG T L Sbjct: 123 GAVIITGTGSCGYAHVGDASLSIGGHGFALGDKGSGAWLGLKAAEHVLLALDGFATPTAL 182 Query: 169 YNKVLKTINVKDLDELV--MWSYTSSCQIDLVASIAKAVDEAANEGDTVAMDILKQGAEL 226 +L + VKD +V + +SSC A +A+ V + AN GD VA+ I+++GA+ Sbjct: 183 TEMLLSHLGVKDALGIVEHLAGKSSSC----YAQLARNVLDCANAGDQVAIAIVQEGADY 238 Query: 227 LASQA 231 ++ A Sbjct: 239 ISEMA 243 Lambda K H 0.317 0.137 0.395 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: 225 Number of extensions: 15 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: 300 Length adjustment: 27 Effective length of query: 272 Effective length of database: 273 Effective search space: 74256 Effective search space used: 74256 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