Align Fructokinase (EC 2.7.1.4) (characterized)
to candidate Pf6N2E2_804 Fructokinase (EC 2.7.1.4)
Query= reanno::pseudo3_N2E3:AO353_25910 (314 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_804 Length = 312 Score = 524 bits (1350), Expect = e-153 Identities = 259/311 (83%), Positives = 281/311 (90%) Query: 1 MYLVCGEALFDFFSENAASSQASTVNYKAIAGGSPFNVAVGLRRLGVDSALFAGLSTDYL 60 MYLVCGEALFDFFSE A AS VNYKAIAGGSPFNVAVGLRRLGV+SALF GLSTDYL Sbjct: 1 MYLVCGEALFDFFSETEADGPASQVNYKAIAGGSPFNVAVGLRRLGVESALFTGLSTDYL 60 Query: 61 GRRLQQVLADEGVRADYLLDFDAPTTLAMVAVGANGSPHYSFRGEGCADRQLTLAHLPEL 120 GRRL QVL +EGV A YL+DFDAPTTLAMVAVGANGSPHYSFRGEGCADRQL+LAHLP+L Sbjct: 61 GRRLHQVLLNEGVSAQYLVDFDAPTTLAMVAVGANGSPHYSFRGEGCADRQLSLAHLPDL 120 Query: 121 SDEVRGLHIGSFSLVVQPIADTLLALVRRESGKRLISLDPNVRLNPEPDIELWRSRIAEL 180 EVRGLH GSFSLVVQPIADTLLAL++RESG+RLISLDPNVRLNP+PDIELWRSRIA L Sbjct: 121 GPEVRGLHFGSFSLVVQPIADTLLALMQRESGRRLISLDPNVRLNPQPDIELWRSRIATL 180 Query: 181 MKYADLIKVSDEDLSLLYPGREPQSVIDSWLEHRCQLVFLTRGGQGATVFSRRHGSWSAP 240 ++YADLIKVSDEDL LLYP +EP+++I+ WL +RCQLVFLTRGGQGATVFSR+HGSWS P Sbjct: 181 VQYADLIKVSDEDLDLLYPAKEPEAIIEGWLGNRCQLVFLTRGGQGATVFSRQHGSWSLP 240 Query: 241 ASKVVIADTVGAGDTFQAALITWLTEQQLDSVDGLQRLSREQIDAMLRFAISAAALTCSK 300 + V IADTVGAGDTFQAALI WLTEQQLDS++GL L+REQI AML FAI AAALTC K Sbjct: 241 SCPVKIADTVGAGDTFQAALIAWLTEQQLDSIEGLHTLTREQISAMLEFAIRAAALTCGK 300 Query: 301 TGPDLPYRHQL 311 TGPDLPYRHQL Sbjct: 301 TGPDLPYRHQL 311 Lambda K H 0.320 0.136 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: 398 Number of extensions: 10 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: 314 Length of database: 312 Length adjustment: 27 Effective length of query: 287 Effective length of database: 285 Effective search space: 81795 Effective search space used: 81795 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