Align Fructokinase (EC 2.7.1.4) (characterized)
to candidate WP_086509383.1 BZY95_RS07810 carbohydrate kinase
Query= reanno::Dyella79:N515DRAFT_1919 (326 letters) >NCBI__GCF_002151265.1:WP_086509383.1 Length = 326 Score = 244 bits (623), Expect = 2e-69 Identities = 146/317 (46%), Positives = 183/317 (57%), Gaps = 2/317 (0%) Query: 4 NILCFGEALIDFHAE--GRDAQGFPRSFIPFAGGAPANVSVAVARLGGPAAFAGMLGQDM 61 +++ FGEAL+D + G A P++F P+AGGAPANV+VA ARLG P+ F GMLG+D Sbjct: 3 SVIAFGEALVDMLSSRLGDLAGDAPKTFTPYAGGAPANVAVACARLGVPSRFLGMLGEDH 62 Query: 62 FGDFLLDSLRRAGVDTAGVARTGEANTALAFVALDSHGERSFSFYRPPSADLLFRPEHFR 121 FGDFL L GVDT+GV RT EA TALAFV+ D+ GER+F FYRPP+ADLL+R EH Sbjct: 63 FGDFLAGELAAHGVDTSGVVRTREARTALAFVSRDASGERTFDFYRPPAADLLYRLEHLP 122 Query: 122 AESFRGAAVFHVCSNSMTEPALAEATREGMRRAHTAGAWVSFDLNLRPALWPNQSASHDE 181 F A+ H CSNS+TEP +A+ T A AG VS D NLR LW SA Sbjct: 123 PGVFAEPAIVHFCSNSLTEPEIADTTLAMADMASRAGCLVSVDANLRHNLWAGGSADITL 182 Query: 182 LWPALHLADVVKLSAEEFHWLAGDEGEEATLDRLWAGRARLLVVTDGSRTLRWFHPDASG 241 + + A +VKLS +E +L D EA L A RLLV+TDG +R Sbjct: 183 VTQLIDRAGLVKLSTDELDYLRADHPAEAWLAERLAAGVRLLVITDGPGEVRAIGVGREL 242 Query: 242 EMPVYAVPTVDSTAAGDAFVGGLLHRLATVEKGADQLDHLVAELPRLHAMLRFAAACGAL 301 V VD+TA GDAF+GGLL LA + L LR AA CGA Sbjct: 243 RHAPPRVEAVDTTAGGDAFIGGLLAELADYLGATAGDGDWHKDDDFLRRALRTAANCGAH 302 Query: 302 TVTRLGSFAAMPDEAEV 318 VTR G++AA+P+ ++ Sbjct: 303 AVTRPGAYAALPNRGDL 319 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: 391 Number of extensions: 20 Number of successful extensions: 4 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: 326 Length adjustment: 28 Effective length of query: 298 Effective length of database: 298 Effective search space: 88804 Effective search space used: 88804 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