Align protein-Npi-phosphohistidine-D-fructose phosphotransferase (subunit 1/2) (EC 2.7.1.202) (characterized)
to candidate H281DRAFT_01929 H281DRAFT_01929 PTS IIA-like nitrogen-regulatory protein PtsN
Query= BRENDA::Q8DWE6 (150 letters) >FitnessBrowser__Burk376:H281DRAFT_01929 Length = 171 Score = 74.7 bits (182), Expect = 7e-19 Identities = 48/141 (34%), Positives = 80/141 (56%), Gaps = 3/141 (2%) Query: 4 ENLIKINLICESQDEVFHYLATLVVDNGYANNTESVVQALKLRESEGTTGMMEGFAIPHA 63 EN++ + L S+ VF A L+ +N +V L RE G+TG+ EG AIPH Sbjct: 31 ENVV-VGLSVTSKKRVFEQ-AGLIFENQNGIARSTVTDNLFARERLGSTGLGEGVAIPHG 88 Query: 64 KDKSIVKPSIAILKLKTGVEWHSMDGQLINNVIALFIPEKEAGTTHLKVLSQIARLLVNK 123 + K + +P A ++L + + S DGQ ++ +I L +PE +A HL++LS+IA+LL ++ Sbjct: 89 RIKGLKQPLAAFVRLAEPIPFESPDGQPVSLLIFLLVPE-QATQQHLEILSEIAQLLSDR 147 Query: 124 TFKEKIKEADTILELKELLTE 144 +E++ + L LLT+ Sbjct: 148 EARERLHTEEDRESLHRLLTQ 168 Lambda K H 0.315 0.133 0.358 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: 46 Number of extensions: 3 Number of successful extensions: 2 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: 150 Length of database: 171 Length adjustment: 17 Effective length of query: 133 Effective length of database: 154 Effective search space: 20482 Effective search space used: 20482 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 (21.6 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