Align tagatose-6-phosphate kinase (EC 2.7.1.144) (characterized)
to candidate GFF781 PS417_03970 1-phosphofructokinase
Query= BRENDA::P0A0B9 (310 letters) >FitnessBrowser__WCS417:GFF781 Length = 306 Score = 148 bits (374), Expect = 1e-40 Identities = 91/284 (32%), Positives = 153/284 (53%), Gaps = 13/284 (4%) Query: 2 ILTLTLNPSVDISYPLTALKLDDVNRVQEVSKTAGGKGLNVTRVLAQVGEPVLASGFIGG 61 ILTLTLNP++D++ L L+ +VNR + + A GKG+NV +VLA +G + SGF+G Sbjct: 4 ILTLTLNPALDLTVRLARLEPGEVNRSETLLTHAAGKGVNVAQVLADLGHELTVSGFLGE 63 Query: 62 ELGQFIAKKLDHADIKHAFYNIKGETRNCIAIL-HEGQQTEILEQGPEIDNQEAAGFIKH 120 Q + AF + GETR+ I I +G+ T+I GP++ Q + Sbjct: 64 GNPQAFEALIAQRGFTDAFIRVPGETRSNIKIAEQDGRVTDINAPGPQVTEQAQNALLDK 123 Query: 121 FEQLLEKVEAVAISGSLPKGLNQDYYAQIIERCQNKGVPVILDCSGATLQT-VLENPYKP 179 Q+ +AV ++GSLP+G++ ++ ++E+ + G+ V LD SG L+ +L P+ Sbjct: 124 LAQIAPGFDAVVVAGSLPRGVSPQWFKGLLEQLKRYGLKVALDTSGEALRAGLLAGPW-- 181 Query: 180 TVIKPNISELYQLLNQPLDESLESLKQAVSQPLFEGIEWIIVSLGAQGAFAKHNHTFYRV 239 ++KPN E L E+L++ AVSQ +G+E ++VS GA G + + Sbjct: 182 -LVKPNTEE--------LAEALDNATDAVSQLHRQGVEHVVVSDGAAGVSWYSPNAALQA 232 Query: 240 NIPTISVLNPVGSGDSTVAGITSAILNHENDHDLLKKANTLGML 283 P ++V + VG+GDS +AG+ +L + L++A + + Sbjct: 233 TPPKVTVASTVGAGDSLLAGMLHGLLTGDTPEQTLRRATAIAAM 276 Lambda K H 0.315 0.135 0.380 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: 208 Number of extensions: 9 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: 310 Length of database: 306 Length adjustment: 27 Effective length of query: 283 Effective length of database: 279 Effective search space: 78957 Effective search space used: 78957 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: 42 (22.0 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