Align Fructokinase (EC 2.7.1.4) (characterized)
to candidate Ac3H11_2936 Fructokinase (EC 2.7.1.4)
Query= reanno::acidovorax_3H11:Ac3H11_3034 (350 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2936 Length = 337 Score = 330 bits (846), Expect = 3e-95 Identities = 188/329 (57%), Positives = 216/329 (65%), Gaps = 6/329 (1%) Query: 18 PLRVATAGEALFDLIEEPDGRLQPCAGGAVYNLTRALGLQGVGTLYLNPLSGDLLGRQLA 77 P+ A AGEAL DLI PDG PC GGA+YNL RAL QGVGT YL PLS D GR+LA Sbjct: 13 PIHAAIAGEALIDLIRRPDGSYLPCLGGALYNLCRALARQGVGTQYLTPLSRDRFGRELA 72 Query: 78 RGLHDAGVALAAPTPVRAPSALALAALDAEGKASYSFYRDGVADRQVTAAALTAACSALP 137 L GV LA P PV+ ++LA+ LDA G Y+FYR+GVADR V+AA L +C+ALP Sbjct: 73 AQLVADGVVLAQPEPVQQVTSLAVVNLDAHGHPDYAFYREGVADRAVSAAGLGDSCTALP 132 Query: 138 ELQVVATGCLALVAQDAALYLPWLAAQRAAGRMVVVDANLRLSAVDDADAYRANVMAALQ 197 LQ+V TG LAL A+D A+YLPWLAAQRAAG VVVDANLR S + D AYR V AAL Sbjct: 133 ALQLVCTGALALDARDTAIYLPWLAAQRAAGCCVVVDANLRPSVMPDLAAYRTAVHAALA 192 Query: 198 HAHLIKVSDDDLEALAIPGANALERA-HFLQQQTQAQWLALTLGPNGAWLLQRDGLAVHA 256 HAH+IK SD+DLE LA+PG +AL RA H L QA LALTLG GAWLL R+G A Sbjct: 193 HAHIIKASDEDLEHLAVPGGDALARAQHLLAAHPQAHLLALTLGAAGAWLLHRNGAQCFA 252 Query: 257 REEAPITVVDTVGAGDCFLAGLITAWLAGPERGEDA-LALRAGGLTAPVTEARLRAVLHH 315 +E P+ VVDTVGAGD FLAGL+ L + E A A GLTA + LR H Sbjct: 253 KEAQPLPVVDTVGAGDSFLAGLLAHLLRQSQAAELASFAQFVDGLTADACQQALR----H 308 Query: 316 ALASASHCVERAGCTPPRYEEVRERLSLR 344 ALASAS CV GC PP +E + R R Sbjct: 309 ALASASLCVMEQGCVPPAWEAAQARALAR 337 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: 355 Number of extensions: 12 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: 350 Length of database: 337 Length adjustment: 29 Effective length of query: 321 Effective length of database: 308 Effective search space: 98868 Effective search space used: 98868 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: 49 (23.5 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