Align PTS system fructose-specific EIIA component; EIIA-Fru; Fructose-specific phosphotransferase enzyme IIA component (characterized)
to candidate WP_011386292.1 AMB_RS19930 PTS IIA-like nitrogen-regulatory protein PtsN
Query= SwissProt::D4GYE4 (154 letters) >NCBI__GCF_000009985.1:WP_011386292.1 Length = 154 Score = 90.9 bits (224), Expect = 8e-24 Identities = 57/151 (37%), Positives = 88/151 (58%), Gaps = 4/151 (2%) Query: 1 MDVTDISTITPLELISLEEPPATKEGAIEFLLDLAVDAGRVDDRDAALDALLEREGEATT 60 M++TD+ I+P +I A+K+ A++ L A + + +R A D LLERE TT Sbjct: 1 MEITDL--ISPAAVIP-NLRAASKKQALQDLAKKAAEITGLHER-AIFDVLLERERLGTT 56 Query: 61 GVGFGIGIPHAKTDAVSKPTVAFARSAEGIDFDAMDDKPAKLLFMILVPAAGGEDHLQIL 120 GVG GI IPH K A+ K FAR + I F+++D++P L+F++L P + G DHL+ L Sbjct: 57 GVGNGIAIPHGKLPAMEKLYGVFARLEKPIAFESIDEQPVDLIFLLLAPESAGADHLKAL 116 Query: 121 SALSRSLMHEDVREKLLEAESKQTVQDVLAE 151 + +SR L + V EKL ++ + +L E Sbjct: 117 ARVSRLLRDKSVCEKLRGTDNADALYALLTE 147 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: 64 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: 154 Length adjustment: 17 Effective length of query: 137 Effective length of database: 137 Effective search space: 18769 Effective search space used: 18769 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: 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