Align fructokinase; EC 2.7.1.4 (characterized)
to candidate AO356_23520 AO356_23520 fructoselysine kinase
Query= CharProtDB::CH_006622 (307 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_23520 Length = 284 Score = 78.6 bits (192), Expect = 2e-19 Identities = 77/264 (29%), Positives = 117/264 (44%), Gaps = 31/264 (11%) Query: 3 AKVWVLGDAVVDLLPESEGRLLQCPGGAPANVAVGVARLGGNSGFIGAVGGDPFGRYMRH 62 A + +GD +D+ + + ++ PGG NVAV ARLG S ++G VG D G+Y+ Sbjct: 2 ASLIAVGDNTLDVYLD---QTIEYPGGNALNVAVFAARLGARSAYLGCVGDDRHGQYLLD 58 Query: 63 TLQQEQVDVSHMYLDDQHRTSTVVVDLDDQGERTFTFMVRPSADLFLVEEDLPQFAAGQW 122 LQQE VD S V ++ +GER F +D + + + A Sbjct: 59 CLQQEAVDASRCRTLSGANGWACVDNV--EGERVFL-----GSDPGVCRQ--LRLDADDL 109 Query: 123 LHVCSIALSAEPSRSTTFAAMESIRSAGGRVSFDPNIRPDLWQD---QALLLACLDRALH 179 ++ + L+ S + +R A G +SFD + D W + QAL + Sbjct: 110 AYIGTFPLAHSSLYSGLEDQLAQVRQASGCLSFDFS---DNWVEFDWQAL--------IQ 158 Query: 180 MANVVKLSEEELVFISSSNDLAYGIASVTERYQPELLLVTRGKAGVLAAFQQKFTHFNAR 239 +V S +L S A +A+ P ++++TRG G LA Q AR Sbjct: 159 HVDVAFFSAADL-----STAQAIELANAMRAKGPAVVVITRGAQGALAVDSQGVHERAAR 213 Query: 240 PVASVDTTGAGDAFVAGLLASLAA 263 P A VD+ GAGD F+A L + A Sbjct: 214 PCAFVDSMGAGDGFIAAFLLAWQA 237 Lambda K H 0.320 0.133 0.392 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: 201 Number of extensions: 12 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 307 Length of database: 284 Length adjustment: 26 Effective length of query: 281 Effective length of database: 258 Effective search space: 72498 Effective search space used: 72498 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 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