Align Putative PTS IIA-like nitrogen-regulatory protein PtsN, component of Fructose Enzyme II complex (IIAFru - IIBFru - IICFru) (based on homology) (characterized)
to candidate BPHYT_RS02895 BPHYT_RS02895 PTS sugar transporter subunit IIA
Query= TCDB::D2RXA7 (156 letters) >FitnessBrowser__BFirm:BPHYT_RS02895 Length = 151 Score = 83.6 bits (205), Expect = 1e-21 Identities = 38/108 (35%), Positives = 63/108 (58%) Query: 46 REAALEALLAREEETTTGVGMGIGIPHAKTDAVAEPTIVFARSSAGIDFDAMDDQPATLL 105 R + L ARE +TG+G G+ IPH + + +P F R + I F++ D QP +LL Sbjct: 41 RSTVTDNLFARERLGSTGLGEGVAIPHGRIKGLKQPLAAFVRLAEPIPFESPDGQPVSLL 100 Query: 106 FLLLVPAEGGEEHLELLSSLSRALMHDDVRERLHEADSKAAIEETITE 153 LLVP + ++HLE+LS +++ L + RERLH + + ++ +T+ Sbjct: 101 IFLLVPEQATQQHLEILSEIAQLLSDREARERLHTEEDRESLHRLLTQ 148 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: 43 Number of extensions: 1 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: 151 Length adjustment: 17 Effective length of query: 139 Effective length of database: 134 Effective search space: 18626 Effective search space used: 18626 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: 43 (21.2 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