Align Fructose import binding protein FruE (characterized)
to candidate 7024899 Shewana3_2073 periplasmic binding protein/LacI transcriptional regulator (RefSeq)
Query= SwissProt::Q8G848 (327 letters) >FitnessBrowser__ANA3:7024899 Length = 313 Score = 137 bits (346), Expect = 3e-37 Identities = 85/264 (32%), Positives = 136/264 (51%), Gaps = 8/264 (3%) Query: 38 TVGFVAVGPEGGFRTANEKDIQKAFEDAGFDLTYSPTQNNDQQKQIQAFNKFVNDEVDAI 97 TVGF VG E G+RT+ + ++ + G DL ++ Q Q+ QI+A F+ VDAI Sbjct: 24 TVGFSQVGSESGWRTSFSEAVKAEAKQRGIDLKFADAQQK-QENQIKAVRSFIAQGVDAI 82 Query: 98 ILSSTEDSGWDDSLKKAAEAEIPVFTVDRNVDVKDAEAKKAIVAHIGPSNVWCGEQAAEF 157 I++ ++GW LK+A A+IPV VDRN+ V D + I G + ++ Sbjct: 83 IIAPVVETGWKPVLKEAKRAKIPVVIVDRNIKVDD---DSLFLTRIASDFSEEGRKIGQW 139 Query: 158 VNKNFPDGANGFILEGPAGLSVVKDRGTGWGNKVAS--NVKVLESQSANWSTDEAKTVTA 215 + + L+G G + DR G+ +A+ N K++ SQ+ ++ + K V Sbjct: 140 LMDKTQGNCDIAELQGTVGATAAIDRAAGFNQVIANYPNAKIVRSQTGEFTRAKGKEVME 199 Query: 216 GLLDKYKSDNPQFIFAQNDEMGLGAAQAVDAAGLK-GK-VKIITIDGTKNALQALVDGDL 273 G L +++ NDEM LGA QA+ AGLK GK + I+++DG + +A+ DGD+ Sbjct: 200 GFLKAQNGQPLCAVWSHNDEMALGAVQAIKEAGLKPGKDILIVSVDGVPDYFKAMADGDV 259 Query: 274 SYVIEYNPIFGKETAQAVKDYLDG 297 + +E +P G A+ YL G Sbjct: 260 NATVELSPYLGGPAFDAIDAYLKG 283 Lambda K H 0.310 0.128 0.360 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: 250 Number of extensions: 12 Number of successful extensions: 4 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: 327 Length of database: 313 Length adjustment: 28 Effective length of query: 299 Effective length of database: 285 Effective search space: 85215 Effective search space used: 85215 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 (21.8 bits) S2: 48 (23.1 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