Align Fructokinase (EC 2.7.1.4) (characterized)
to candidate WP_007152220.1 MDG893_RS02890 carbohydrate kinase
Query= reanno::Dyella79:N515DRAFT_1919 (326 letters) >NCBI__GCF_000170835.1:WP_007152220.1 Length = 328 Score = 270 bits (689), Expect = 5e-77 Identities = 147/320 (45%), Positives = 197/320 (61%), Gaps = 6/320 (1%) Query: 5 ILCFGEALIDFHA------EGRDAQGFPRSFIPFAGGAPANVSVAVARLGGPAAFAGMLG 58 ++ FGEAL+D + + ++ F F GGAPANV+ A+ +LGG + FAG +G Sbjct: 4 VISFGEALVDMLSSRVSEDQSENSDSVNERFTKFPGGAPANVAAAIGKLGGDSYFAGKVG 63 Query: 59 QDMFGDFLLDSLRRAGVDTAGVARTGEANTALAFVALDSHGERSFSFYRPPSADLLFRPE 118 DMFGDFL+ SL V T + +T EA TALAFV+LD GERSF FYR PSADL+F P Sbjct: 64 ADMFGDFLVKSLESMHVRTDYLLQTSEAKTALAFVSLDKTGERSFEFYRGPSADLIFAPH 123 Query: 119 HFRAESFRGAAVFHVCSNSMTEPALAEATREGMRRAHTAGAWVSFDLNLRPALWPNQSAS 178 F+ E F +FH CSN++TEP + EAT+ G+ +A +AG VSFD+NLR LWP + Sbjct: 124 EFQPEWFDDQGIFHFCSNTLTEPGILEATQAGLEKARSAGWLVSFDMNLRNNLWPKGTDP 183 Query: 179 HDELWPALHLADVVKLSAEEFHWLAGDEGEEATLDRLWAGRARLLVVTDGSRTLRWFHPD 238 +W + AD+VKLSAEE +L + E L ++ A L++VTDG + LR+ P Sbjct: 184 FAPVWACVEQADLVKLSAEELAFLCRHQNETEVLKQILNAGASLVLVTDGEKPLRYLTPS 243 Query: 239 ASGEMPVYAVPTVDSTAAGDAFVGGLLHRLATVEKGADQLDHLVAELPRLHAMLRFAAAC 298 G + V VDSTAAGDAFVGGLL+RL+ + A L L + +L ML FA+AC Sbjct: 244 HYGSIEPRNVQMVDSTAAGDAFVGGLLYRLSDLNITAASLKALGEDPEQLEDMLTFASAC 303 Query: 299 GALTVTRLGSFAAMPDEAEV 318 GA VT G+F ++P +V Sbjct: 304 GAHAVTHPGAFTSLPGLQDV 323 Lambda K H 0.322 0.135 0.418 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: 328 Number of extensions: 12 Number of successful extensions: 1 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: 326 Length of database: 328 Length adjustment: 28 Effective length of query: 298 Effective length of database: 300 Effective search space: 89400 Effective search space used: 89400 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 (22.0 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