Align Fructose import permease protein FruF (characterized)
to candidate 16645 b2546 predicted sugar transporter subunit: membrane component of ABC superfamily (NCBI)
Query= SwissProt::Q8G846 (356 letters) >FitnessBrowser__Keio:16645 Length = 332 Score = 133 bits (334), Expect = 8e-36 Identities = 97/318 (30%), Positives = 162/318 (50%), Gaps = 18/318 (5%) Query: 30 LLVIICTIFQHDFLALSWNSNTGGLAGPLITMLQESARYLMIATGMTLVISTAGIDLSVG 89 LLV+I ++ L S N+ + +L+++A + A MTL+I + ID+SVG Sbjct: 29 LLVVIAILY----LVFSLNAPGFISLNNQMNVLRDAATIGIAAWAMTLIIISGEIDVSVG 84 Query: 90 SVMAVAGAAAMQTLSNGMNVWLSILIALAVGLAIGCVNGALVSFLGLQPFITTLIMMLAG 149 ++A L + + ++ L+ L +G +G + G L + F+ TL + A Sbjct: 85 PMVAFVSVCLAFLLQFEVPLAVACLLVLLLGALMGTLAGVLRGVFNVPSFVATLGLWSAL 144 Query: 150 RGMAKVITSGENTDASAVAGNEPLKWFANGFILGIPANFVIAVIIVILVGLLCRKTAMGM 209 RGM +T N + NE L W F LG+P + +I +++ L + RKTA G Sbjct: 145 RGMGLFMT---NALPVPIDENEVLDWLGGQF-LGVPVSALIMIVLFALFVFISRKTAFGR 200 Query: 210 MIEAVGINQEASRMTGIKPKKILFLVYAISGFLAAIAGLFATASVMRVDVVKTGQDLEMY 269 + AVG N A+++ GI +++ L++ +SG LAA+ G+ A + + LE Sbjct: 201 SVFAVGGNATAAQLCGINVRRVRILIFTLSGLLAAVTGILLAARLGSGN-AGAANGLEFD 259 Query: 270 AILAVVIGGTSLLGGKFSLAGSAVGAVIIAMIRKTIITLGVNAEATPAFFAVVV----IV 325 I AVV+GGT+L GG+ SL G+ +G ++I +I ++ LG+N +FF VV IV Sbjct: 260 VIAAVVVGGTALSGGRGSLFGTLLGVLVITLIGNGLVLLGIN-----SFFQQVVRGVIIV 314 Query: 326 ICVMQAPKIHNLSANMKR 343 + V+ + S+ KR Sbjct: 315 VAVLANILLTQRSSKAKR 332 Lambda K H 0.325 0.136 0.384 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: 295 Number of extensions: 19 Number of successful extensions: 3 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: 356 Length of database: 332 Length adjustment: 29 Effective length of query: 327 Effective length of database: 303 Effective search space: 99081 Effective search space used: 99081 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 49 (23.5 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