Align Fructose import permease protein FruF (characterized)
to candidate H281DRAFT_05271 H281DRAFT_05271 monosaccharide ABC transporter membrane protein, CUT2 family
Query= SwissProt::Q8G846 (356 letters) >FitnessBrowser__Burk376:H281DRAFT_05271 Length = 347 Score = 225 bits (574), Expect = 1e-63 Identities = 134/326 (41%), Positives = 197/326 (60%), Gaps = 11/326 (3%) Query: 21 LTWSIVAFILLVIICTIFQHDFLALSWNSNTGGLAGPLITMLQESARYLMIATGMTLVIS 80 L W V LL + FL+L G L G I +L +A +++ATGMTLVI+ Sbjct: 16 LIWPCVTLALLCALNLWVNPHFLSLRMLD--GHLFGAPIDVLNRAAPLVLVATGMTLVIA 73 Query: 81 TAGIDLSVGSVMAVAGAAAM-----QTLSNGMNVWLSILIALAVGLAIGCVNGALVSFLG 135 T GID+SVG+V+A+AGAAA Q + G + ++L AL VG+ G NG LVSF+G Sbjct: 74 TRGIDISVGAVVAIAGAAAATILATQPVPTGNLIAQALLAALIVGVLSGMWNGLLVSFVG 133 Query: 136 LQPFITTLIMMLAGRGMAKVITSGENTDASAVAGNEPLKWFANGFILGIPANFVIAVIIV 195 +QP I TLI+M+AGRG+A+++T+G+ A + G+ LG+P + IA I V Sbjct: 134 MQPIIATLILMVAGRGIAQLLTAGQIIPIGAPG----YLFVGGGYWLGVPCSVWIATIAV 189 Query: 196 ILVGLLCRKTAMGMMIEAVGINQEASRMTGIKPKKILFLVYAISGFLAAIAGLFATASVM 255 + L TA+G+ I A+G+N A+R+ G++ K ++F VY SG AA+AG+ +++V Sbjct: 190 LATAALVEGTALGLFIRAIGVNPVATRLVGLRSKALVFAVYGFSGLTAAMAGILISSNVR 249 Query: 256 RVDVVKTGQDLEMYAILAVVIGGTSLLGGKFSLAGSAVGAVIIAMIRKTIITLGVNAEAT 315 D G LE+ AILAV +GGTSLLGG+FS AG+ +GA+II + T ++GV EAT Sbjct: 250 SADGNNAGLLLELDAILAVTLGGTSLLGGRFSFAGTVLGALIIQTLTYTTYSIGVPPEAT 309 Query: 316 PAFFAVVVIVICVMQAPKIHNLSANM 341 A VV+ + V+Q+P L+ ++ Sbjct: 310 LVVKAAVVLTVSVIQSPAARALAMSV 335 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: 324 Number of extensions: 21 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: 347 Length adjustment: 29 Effective length of query: 327 Effective length of database: 318 Effective search space: 103986 Effective search space used: 103986 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