Align tagatose-6-phosphate kinase (EC 2.7.1.144) (characterized)
to candidate PfGW456L13_5074 1-phosphofructokinase (EC 2.7.1.56)
Query= BRENDA::P0A0B9 (310 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5074 Length = 312 Score = 142 bits (357), Expect = 1e-38 Identities = 90/283 (31%), Positives = 147/283 (51%), Gaps = 5/283 (1%) Query: 2 ILTLTLNPSVDISYPLTALKLDDVNRVQEVSKTAGGKGLNVTRVLAQVGEPVLASGFIGG 61 ILTLTLNP++D++ L L VNR + A GKG+NV +VLA +G + SGF+G Sbjct: 4 ILTLTLNPALDLTVQLPRLDAGQVNRSDVMHTHAAGKGVNVAQVLADLGHQLTVSGFLGE 63 Query: 62 ELGQFIAKKLDHADIKHAFYNIKGETRNCIAILH-EGQQTEILEQGPEIDNQEAAGFIKH 120 + Q AF + GETR+ I + +G+ T+I GP++ + Sbjct: 64 DNLQAFETLFAKRGFVDAFIRVPGETRSNIKLAESDGRITDINGPGPQVSEAAQQALMDR 123 Query: 121 FEQLLEKVEAVAISGSLPKGLNQDYYAQIIERCQNKGVPVILDCSGATLQTVLENPYKPT 180 EQ+ +AV ++GSLP G++ + +I R +N G+ V LD SG L+ L+ P Sbjct: 124 LEQIAPGHDAVVVAGSLPLGVSAQWLQALILRLKNLGLNVALDTSGEALRAALK--AGPW 181 Query: 181 VIKPNISELYQLLNQPLDESLESLKQAVSQPLFEGIEWIIVSLGAQGAFAKHNHTFYRVN 240 +IKPN EL ++L + + S ++L A + +GIE +++S G G + Sbjct: 182 LIKPNTEELAEVLGEVVSVSAQAL--AAERLHAQGIEHVVISHGVDGVNWFSVGSALHAT 239 Query: 241 IPTISVLNPVGSGDSTVAGITSAILNHENDHDLLKKANTLGML 283 P ++V + VG+GDS +AG+ +L+ + L+ A + + Sbjct: 240 PPRVNVASTVGAGDSLLAGMLHGLLSADTPEQTLRTATAIAAM 282 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: 204 Number of extensions: 16 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: 312 Length adjustment: 27 Effective length of query: 283 Effective length of database: 285 Effective search space: 80655 Effective search space used: 80655 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