Align Putative PTS IIA-like nitrogen-regulatory protein PtsN, component of Fructose Enzyme II complex (IIAFru - IIBFru - IICFru) (based on homology) (characterized)
to candidate PfGW456L13_5016 PTS IIA-like nitrogen-regulatory protein PtsN
Query= TCDB::D2RXA7 (156 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5016 Length = 138 Score = 84.7 bits (208), Expect = 5e-22 Identities = 47/132 (35%), Positives = 67/132 (50%) Query: 22 PPAEKAAAIEFLLDRAVDAGRVTDREAALEALLAREEETTTGVGMGIGIPHAKTDAVAEP 81 P K A+E + + + + EAL+ARE+ +TG G GI IPH + P Sbjct: 2 PGGSKKKALEQIANLIAREVPALEMQDVFEALIAREKLGSTGFGNGIAIPHCRLKGCVSP 61 Query: 82 TIVFARSSAGIDFDAMDDQPATLLFLLLVPAEGGEEHLELLSSLSRALMHDDVRERLHEA 141 A IDFDA+D P LLF+LLVP + HLELL ++ L +VRE+L A Sbjct: 62 ISALMHLDAPIDFDAIDGAPVDLLFVLLVPEAATDAHLELLRQIASMLDRKEVREKLRSA 121 Query: 142 DSKAAIEETITE 153 S A+ + + + Sbjct: 122 ASNEALYQVVLD 133 Lambda K H 0.313 0.130 0.347 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: 49 Number of extensions: 4 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: 156 Length of database: 138 Length adjustment: 16 Effective length of query: 140 Effective length of database: 122 Effective search space: 17080 Effective search space used: 17080 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 42 (20.8 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