Align Fructokinase (EC 2.7.1.4) (characterized)
to candidate HSERO_RS02180 HSERO_RS02180 fructokinase
Query= reanno::pseudo6_N2E2:Pf6N2E2_1965 (306 letters) >FitnessBrowser__HerbieS:HSERO_RS02180 Length = 301 Score = 285 bits (728), Expect = 1e-81 Identities = 148/300 (49%), Positives = 204/300 (68%), Gaps = 5/300 (1%) Query: 4 QLPSVVVFGEALTDVVQHSPGRWQGYPGGAPWNVARAMSRLGVPTAFAGSISTDSLGDEL 63 Q + VVFGEALTD ++ +W+ PGGA WNVARA +RLGVPT +AGS+STD G EL Sbjct: 3 QSAAFVVFGEALTDFIRQPDEQWRAIPGGACWNVARAAARLGVPTGYAGSVSTDVFGAEL 62 Query: 64 AQQSKAAGLDMRFLQRVDADPLVAIVPSSHPPRYFFAGE--ADLLFDVDQLPAGWLDAAR 121 ++AAGLDMRF Q+ PL+A+V S+ PP YFF G+ ADL FD +LPAGWLD A+ Sbjct: 63 YALTQAAGLDMRFTQQYAKAPLLAMVTSTTPPDYFFIGDDSADLHFDPQRLPAGWLDDAQ 122 Query: 122 LCHFSCISLARQPLGDRLVEVARRVKEEDKLISYDPNWRNLMDTRYRELTFPAMVELADI 181 + HF CISL R+PL RL+++A+ +K I++DPNWR LMD+ L F ++ L+ Sbjct: 123 VLHFGCISLTREPLASRLLQIAQEAARRNKKIAFDPNWRKLMDSPSYRLLFQQLLSLSHY 182 Query: 182 IKLSDEDLRQIYPGLNEEQALHTLRTMNASAQILFTRGAKGMALYAADVKFEQPAIAVEV 241 +K+SDEDL +++PG + AL TL+++ A+IL+T GAKGM + +QPA VEV Sbjct: 183 VKVSDEDLERLFPG--DTNALATLQSLAPQAEILYTLGAKGMQWIKGEQVIDQPAYRVEV 240 Query: 242 ADTVGAGDSSMAGWLASTLLGIQEP-HARLEFSAACASVSCSHAGAYAPSREEVEDLLSN 300 DTVG GD+SM GW+AS L P L+ +AA A+++ S AGAYA + +EV+ L+++ Sbjct: 241 IDTVGCGDASMGGWIASQLRQPDAPAQVHLQCAAAGAAIAASKAGAYAATWDEVQALIAH 300 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: 270 Number of extensions: 5 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: 306 Length of database: 301 Length adjustment: 27 Effective length of query: 279 Effective length of database: 274 Effective search space: 76446 Effective search space used: 76446 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