Align Fructose import binding protein FruE (characterized)
to candidate 18252 b4227 predicted sugar transporter subunit: periplasmic-binding component of ABC superfamily (NCBI)
Query= SwissProt::Q8G848 (327 letters) >FitnessBrowser__Keio:18252 Length = 318 Score = 140 bits (353), Expect = 4e-38 Identities = 104/325 (32%), Positives = 162/325 (49%), Gaps = 22/325 (6%) Query: 4 WKKAIALVASAAALVSVAACGSSNAGGSSDSGKKTVGFVAVGPEGGFRTANEKDIQKAFE 63 WK+ + + A +AA+ S+A + TVGF VG E G+R A + E Sbjct: 2 WKRLLIVSAVSAAMSSMAL-----------AAPLTVGFSQVGSESGWRAAETNVAKSEAE 50 Query: 64 DAGFDLTYSPTQNNDQQKQIQAFNKFVNDEVDAIILSSTEDSGWDDSLKKAAEAEIPVFT 123 G L + Q Q+ QI+A FV VDAI ++ +GW+ LK+A +AEIPVF Sbjct: 51 KRGITLKIADGQQK-QENQIKAVRSFVAQGVDAIFIAPVVATGWEPVLKEAKDAEIPVFL 109 Query: 124 VDRNVDVKDAEAKKAIVAHIGPSNVWCGEQAAEFVNKNF-PDGANGFILEGPAGLSVVKD 182 +DR++DVKD K + + N+ G+ +++ K N L+G G SV D Sbjct: 110 LDRSIDVKD---KSLYMTTVTADNILEGKLIGDWLVKEVNGKPCNVVELQGTVGASVAID 166 Query: 183 RGTGWGN--KVASNVKVLESQSANWSTDEAKTVTAGLLD-KYKSDNPQFIFAQNDEMGLG 239 R G+ K A N+K++ SQS +++ + K V + + N ++A ND+M +G Sbjct: 167 RKKGFAEAIKNAPNIKIIRSQSGDFTRSKGKEVMESFIKAENNGKNICMVYAHNDDMVIG 226 Query: 240 AAQAVDAAGLKGKVKIIT--IDGTKNALQALVDGDLSYVIEYNPIFGKETAQAVKDY-LD 296 A QA+ AGLK I+T IDG + +A++DG+ + +E P A++ Y D Sbjct: 227 AIQAIKEAGLKPGKDILTGSIDGVPDIYKAMMDGEANASVELTPNMAGPAFDALEKYKKD 286 Query: 297 GKTVEKDIEIESKTFDAASAKEALD 321 G EK +S + +AKE L+ Sbjct: 287 GTMPEKLTLTKSTLYLPDTAKEELE 311 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: 272 Number of extensions: 19 Number of successful extensions: 5 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: 318 Length adjustment: 28 Effective length of query: 299 Effective length of database: 290 Effective search space: 86710 Effective search space used: 86710 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