Align tagatose-6-phosphate kinase (EC 2.7.1.144) (characterized)
to candidate PP_0794 PP_0794 1-phosphofructokinase monomer
Query= BRENDA::P0A0B9 (310 letters) >FitnessBrowser__Putida:PP_0794 Length = 315 Score = 172 bits (435), Expect = 1e-47 Identities = 101/280 (36%), Positives = 157/280 (56%), Gaps = 4/280 (1%) Query: 2 ILTLTLNPSVDISYPLTALKLDDVNRVQEVSKTAGGKGLNVTRVLAQVGEPVLASGFIGG 61 ILTLTLNP++DI+ L L+ VNR Q A GKGLNV +VLA +G V GF+GG Sbjct: 4 ILTLTLNPALDITIGLDTLRPGQVNRSQAQHSHAAGKGLNVAQVLADLGHSVTVGGFLGG 63 Query: 62 ELGQFIAKKLDHADIKHAFYNIKGETRNCIAILH-EGQQTEILEQGPEIDNQEAAGFIKH 120 + Q +D F + GETR+ I ++ +G+ T+I QGPE+D + + Sbjct: 64 DNLQPFEALIDGRGFTDCFVRVPGETRSNIKLVEADGRVTDINGQGPEVDEAARSALLHR 123 Query: 121 FEQLLEKVEAVAISGSLPKGLNQDYYAQIIERCQNKGVPVILDCSGATLQTVLENPYKPT 180 EQ+ +AV ++GSLP+G++ D++ Q++ER + +G+ V+LD SG L+ L++ P Sbjct: 124 LEQIAPGHDAVVVAGSLPRGISADWFRQLLERLKAQGLKVVLDSSGEALRVGLQS--APW 181 Query: 181 VIKPNISELYQLLNQPLDESLESLKQAVSQPLFEGIEWIIVSLGAQGAFAKHNHTFYRVN 240 ++KPN EL ++L +D +L + A + L G+E ++VS G QG + Sbjct: 182 LVKPNTEELGEVLGLAVD-NLTQQRAAAKRLLDSGVEHVVVSAGEQGVSWFSRDLALQAR 240 Query: 241 IPTISVLNPVGSGDSTVAGITSAILNHENDHDLLKKANTL 280 P + V + VG+GDS VAG+ +L E L +A + Sbjct: 241 PPKVRVASTVGAGDSLVAGMVHGLLLAEAPAQTLTRATAI 280 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: 216 Number of extensions: 12 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: 310 Length of database: 315 Length adjustment: 27 Effective length of query: 283 Effective length of database: 288 Effective search space: 81504 Effective search space used: 81504 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