Align PTS system fructose-specific EIIA component; EIIA-Fru; Fructose-specific phosphotransferase enzyme IIA component (characterized)
to candidate WP_106711955.1 CU102_RS15020 PTS sugar transporter subunit IIA
Query= SwissProt::D4GYE4 (154 letters) >NCBI__GCF_003010955.1:WP_106711955.1 Length = 149 Score = 79.0 bits (193), Expect = 3e-20 Identities = 39/101 (38%), Positives = 59/101 (58%) Query: 45 DAALDALLEREGEATTGVGFGIGIPHAKTDAVSKPTVAFARSAEGIDFDAMDDKPAKLLF 104 DA L AL +RE +TGVG GI IPH + D + KP AR + IDF+++DD P ++F Sbjct: 41 DAILTALQKRENLGSTGVGQGIAIPHTRIDGIEKPIGLLARMRKPIDFESIDDLPVDIIF 100 Query: 105 MILVPAAGGEDHLQILSALSRSLMHEDVREKLLEAESKQTV 145 ++L P HL +L+A SR L +++ A+ Q++ Sbjct: 101 VLLTPNRDTNKHLNVLAAFSRKLRSPGALKQMRTAKDAQSL 141 Lambda K H 0.315 0.134 0.359 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: 57 Number of extensions: 2 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: 154 Length of database: 149 Length adjustment: 17 Effective length of query: 137 Effective length of database: 132 Effective search space: 18084 Effective search space used: 18084 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: 42 (22.0 bits) S2: 42 (20.8 bits)
This GapMind analysis is from Sep 24 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