Align Fructokinase (EC 2.7.1.4) (characterized)
to candidate AO353_25105 AO353_25105 sugar kinase
Query= reanno::pseudo6_N2E2:Pf6N2E2_1965 (306 letters) >FitnessBrowser__pseudo3_N2E3:AO353_25105 Length = 302 Score = 426 bits (1095), Expect = e-124 Identities = 206/296 (69%), Positives = 241/296 (81%) Query: 3 MQLPSVVVFGEALTDVVQHSPGRWQGYPGGAPWNVARAMSRLGVPTAFAGSISTDSLGDE 62 M LP VVFGEALTD+VQ +PG+W+GYPGGAPWNVAR++SRLGV +AFAG++S DSLGDE Sbjct: 1 MVLPRAVVFGEALTDLVQGTPGQWKGYPGGAPWNVARSLSRLGVSSAFAGAVSIDSLGDE 60 Query: 63 LAQQSKAAGLDMRFLQRVDADPLVAIVPSSHPPRYFFAGEADLLFDVDQLPAGWLDAARL 122 + QS+AA LDM F+QRVD DPLVAIVPSS PPRYFFAG+ADL FD D +P GW++ A L Sbjct: 61 IVAQSEAAALDMSFIQRVDRDPLVAIVPSSRPPRYFFAGDADLFFDPDLMPEGWINKAEL 120 Query: 123 CHFSCISLARQPLGDRLVEVARRVKEEDKLISYDPNWRNLMDTRYRELTFPAMVELADII 182 CHFSCISLARQPL DRLV++A++ KE K ISYDPNWRNLMD+ YRE TFP M LAD+I Sbjct: 121 CHFSCISLARQPLADRLVKIAQQAKEAGKRISYDPNWRNLMDSHYREQTFPTMTTLADMI 180 Query: 183 KLSDEDLRQIYPGLNEEQALHTLRTMNASAQILFTRGAKGMALYAADVKFEQPAIAVEVA 242 KLSDEDLR IYPGL E QA+ LR +N AQILFTRG GM L+ D + +QPAIAV+V Sbjct: 181 KLSDEDLRHIYPGLTEHQAMDELRALNPQAQILFTRGEHGMILHTPDSQLDQPAIAVKVE 240 Query: 243 DTVGAGDSSMAGWLASTLLGIQEPHARLEFSAACASVSCSHAGAYAPSREEVEDLL 298 DTVGAGD+ MAGWLA+ LLGI + RL FSAACAS+SC HAGA+AP+ +VE LL Sbjct: 241 DTVGAGDACMAGWLAAELLGIADLRERLRFSAACASISCRHAGAHAPALADVEGLL 296 Lambda K H 0.320 0.133 0.398 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: 323 Number of extensions: 7 Number of successful extensions: 1 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: 306 Length of database: 302 Length adjustment: 27 Effective length of query: 279 Effective length of database: 275 Effective search space: 76725 Effective search space used: 76725 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