Align Fructokinase; EC 2.7.1.4 (characterized)
to candidate WP_075620294.1 GY23_RS16555 fructokinase
Query= SwissProt::P26420 (307 letters) >NCBI__GCF_001939075.1:WP_075620294.1 Length = 312 Score = 192 bits (487), Expect = 1e-53 Identities = 118/299 (39%), Positives = 163/299 (54%), Gaps = 5/299 (1%) Query: 9 GDAVVDLLPDGEGR--LLQCPGGAPANVAVGVARLGGDSGFIGRVGDDPFGRFMRHTLAQ 66 GDA VD + + GGA NVAVGVARLG S FI GDDP F+R L Sbjct: 13 GDAFVDYIAEDRTNTSFSMFLGGATVNVAVGVARLGVPSAFITITGDDPTSEFVRGELKF 72 Query: 67 EQVDVNYMRLDAAQRTSTVVVDLDSHGERTFTFMVRPSADLFLQPEDL--PPFAAGQWLH 124 E+V + Y +L+ +R S V V L +R F + + D+ ++ +DL F L+ Sbjct: 73 EEVIMEYAKLEPEKRVSGVYVHLTEDNDRVFHKYIDDAPDIQVEADDLIEEAFEKASILN 132 Query: 125 VCSIALSAEPSRSTTFAALEAIKRAGGYVSFDPNIRSDLWQDPQDLRDCLDRALALADAI 184 +CS L + T+ A+E K+ G SFD NIR W + R+ + AD + Sbjct: 133 LCSGTLFHPKALETSRIAVEFAKKHGALFSFDANIRPLRWSSEKQCRETISSFFKDADLL 192 Query: 185 KLSEEELAFISGSDDIVSGIARLNARFQPTLLLVTQGKAGVQAALRGQVSHFPARPVVAV 244 K + EELAF++ + + G+A+L A + ++LVT G+ G AAL GQV H P PVV V Sbjct: 193 KFTREELAFLTETQTLEDGLAKL-APLEIPIILVTAGEEGTYAALNGQVQHVPVEPVVPV 251 Query: 245 DTTGAGDAFVAGLLAGLAAHGIPDNLAALAPDLALAQTCGALATTAKGAMTALPYKDDL 303 DTTGAGDAF+AG+L + +G+P + +L A GALATT GA+TA+P DL Sbjct: 252 DTTGAGDAFMAGILRYVHLNGLPKTIKSLIECCTFANRLGALATTKAGALTAMPRLSDL 310 Lambda K H 0.321 0.137 0.406 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: 184 Number of extensions: 8 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: 307 Length of database: 312 Length adjustment: 27 Effective length of query: 280 Effective length of database: 285 Effective search space: 79800 Effective search space used: 79800 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 (21.8 bits) S2: 48 (23.1 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