Align Fructokinase; D-fructose kinase; Manno(fructo)kinase; EC 2.7.1.4 (characterized)
to candidate AZOBR_RS11685 AZOBR_RS11685 hypothetical protein
Query= SwissProt::P23917 (302 letters) >FitnessBrowser__azobra:AZOBR_RS11685 Length = 299 Score = 260 bits (664), Expect = 3e-74 Identities = 137/303 (45%), Positives = 182/303 (60%), Gaps = 5/303 (1%) Query: 1 MRIGIDLGGTKTEVIALGDAGEQLYRHRLPTPRDDYRQTIETIATLVDMAEQATGQR-GT 59 MRIG+DLGGTK L G + RHR TPR Y +T++ +A V E+ G+R T Sbjct: 1 MRIGVDLGGTKIAATLLAPDGTERARHRADTPRG-YAETLQALAGAVAALEERAGRRDAT 59 Query: 60 VGMGIPGSISPYTGVVKNANSTWLNGQPFDKDLSARLQREVRLANDANCLAVSEAVDGAA 119 VG+ +PG + G V+ N WL+G+PF DL+ L R VR+ANDAN +SEA+DGAA Sbjct: 60 VGLCLPGIVDAAAGTVRAVNLPWLDGRPFAADLARALDRPVRIANDANAFVLSEAMDGAA 119 Query: 120 AGAQTVFAVIIGTGCGAGVAFNGRAHIGGNGTAGEWGHNPLPWMDEDELRYREEVPCYCG 179 AGA VF +I+GTG G G+ + R G N AGEWGHNPLPW ++ VPC CG Sbjct: 120 AGAPLVFGIILGTGVGGGIVADRRILPGANALAGEWGHNPLPWRVTED---GPPVPCGCG 176 Query: 180 KQGCIETFISGTGFAMDYRRLSGHALKGSEIIRLVEESDPVAELALRRYELRLAKSLAHV 239 ++GCIET + G G A + +G L EI + D A L R+ LA++LA V Sbjct: 177 REGCIETLLCGAGLARLHLWRTGETLTPPEIAARAQSGDAPARATLDRHADALARALAAV 236 Query: 240 VNILDPDVIVLGGGMSNVDRLYQTVGQLIKQFVFGGECETPVRKAKHGDSSGVRGAAWLW 299 VN+LDPDV+V+GGG+S + LY+ V ++ T +A+HG SG+RGAAWLW Sbjct: 237 VNLLDPDVVVVGGGLSELPGLYEAVPARWGRWALSPAPRTRFLRARHGAESGMRGAAWLW 296 Query: 300 PQE 302 P+E Sbjct: 297 PKE 299 Lambda K H 0.318 0.137 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: 302 Number of extensions: 12 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: 302 Length of database: 299 Length adjustment: 27 Effective length of query: 275 Effective length of database: 272 Effective search space: 74800 Effective search space used: 74800 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 (21.7 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