Align Fructokinase (EC 2.7.1.4) (characterized)
to candidate WP_057508915.1 ABB28_RS12320 carbohydrate kinase
Query= reanno::Dyella79:N515DRAFT_1919 (326 letters) >NCBI__GCF_001431535.1:WP_057508915.1 Length = 331 Score = 342 bits (878), Expect = 6e-99 Identities = 190/319 (59%), Positives = 222/319 (69%), Gaps = 7/319 (2%) Query: 5 ILCFGEALIDFHAEGRDAQGFPRSFIPFAGGAPANVSVAVARLGGPAAFAGMLGQDMFGD 64 I+CFGE LID A+ + PR+F+ +AGGAPANV+VA ARLG F GMLG+DMFGD Sbjct: 4 IVCFGEILIDLLAQPPASPSEPRAFLQYAGGAPANVAVAAARLGVDTQFVGMLGRDMFGD 63 Query: 65 FLLDSLRRAGVDTAGVARTGEANTALAFVALDSHGERSFSFYRPPSADLLFRPEHFRAES 124 FL DSL++ GV +ART A TALAFVALD HGERSFSFYRPP+ADLLFR EHF A Sbjct: 64 FLADSLQQHGVGIDYIARTEAAKTALAFVALDPHGERSFSFYRPPAADLLFRAEHFHAAC 123 Query: 125 FRGAAVFHVCSNSMTEPALAEATREGMRRAHTAGAWVSFDLNLRPALWPNQSASHDELWP 184 F A FHVCSNS+TE A+A+AT EGM+RA AGA VS DLNLRPALWP + LW Sbjct: 124 FAQARCFHVCSNSLTEAAIAQATFEGMQRARDAGALVSLDLNLRPALWPADADPLPTLWQ 183 Query: 185 ALHLADVVKLSAEEFHWLA---GDEGEEATLDRLWAGRARLLVVTDGSRTLRWFHPDASG 241 AL LADVVKLS EE +LA G+ G + L RL+A +AR +VVTDG+ LRW+ A G Sbjct: 184 ALALADVVKLSREELDFLAAPLGEGGADQVLQRLFAAQARWVVVTDGAAALRWYTRSAQG 243 Query: 242 EMPVYAVPTVDSTAAGDAFVGGLLHRLATVEKGAD--QLDHLVAELPRLHAMLRFAAACG 299 + + V TVDSTAAGDAFVGGLL A VE+G D L + +H +LRF AA G Sbjct: 244 QATSFRVTTVDSTAAGDAFVGGLL--TALVERGVDAASLPAFCNDEAAMHEVLRFGAAVG 301 Query: 300 ALTVTRLGSFAAMPDEAEV 318 AL VTR G+FAAMP EV Sbjct: 302 ALAVTRKGAFAAMPTRDEV 320 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: 396 Number of extensions: 19 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: 326 Length of database: 331 Length adjustment: 28 Effective length of query: 298 Effective length of database: 303 Effective search space: 90294 Effective search space used: 90294 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: 49 (23.5 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