Align 1-phosphofructokinase; EC 2.7.1.56; Fructose 1-phosphate kinase (uncharacterized)
to candidate RR42_RS01370 RR42_RS01370 phosphomethylpyrimidine kinase
Query= curated2:P23386 (316 letters) >FitnessBrowser__Cup4G11:RR42_RS01370 Length = 276 Score = 46.2 bits (108), Expect = 9e-10 Identities = 41/131 (31%), Positives = 61/131 (46%), Gaps = 10/131 (7%) Query: 107 LNFPGIAAGPADL-----DAVAATLTELLAQG--LDWVALCGSLPAGIGAEAYAELAA-- 157 L G+ A PAD+ DAVA+ + A+ L A+ ++ A + +L Sbjct: 52 LGVTGVHAIPADMVAAQIDAVASDIGVDAAKTGMLGTAAIVEAVAAAVDRHGIRQLVVDP 111 Query: 158 -LARKGGARVALDTSGPALGLALAARPDIVKPNVAELGAHLGRTLTGLESVREAARDLAA 216 + GA +A D + A+ L R +V PN+ E LGR +T E + +AARDLAA Sbjct: 112 VMISTSGATLADDATTQAMVRLLFPRAVLVTPNLPEASYLLGREITRREEMEQAARDLAA 171 Query: 217 SGVGLVAVSMG 227 G V + G Sbjct: 172 LGCPAVLLKGG 182 Lambda K H 0.318 0.133 0.377 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: 220 Number of extensions: 6 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: 316 Length of database: 276 Length adjustment: 26 Effective length of query: 290 Effective length of database: 250 Effective search space: 72500 Effective search space used: 72500 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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