Align Fructose import permease protein FruF (characterized)
to candidate 18255 b4230 predicted sugar transporter subunit: membrane component of ABC superfamily (RefSeq)
Query= SwissProt::Q8G846 (356 letters) >FitnessBrowser__Keio:18255 Length = 341 Score = 224 bits (571), Expect = 3e-63 Identities = 133/321 (41%), Positives = 196/321 (61%), Gaps = 8/321 (2%) Query: 25 IVAFILLVIICTIFQHDFLALSWNSNTGGLAGPLITMLQESARYLMIATGMTLVISTAGI 84 +VA +L++++ ++ F + G L G I +L +A ++A GMTLVI+T GI Sbjct: 25 LVALLLVLLVDSLVAPHFWQVVLQD--GRLFGSPIDILNRAAPVALLAIGMTLVIATGGI 82 Query: 85 DLSVGSVMAVAGAAAMQTLSNGMNVWLSILIALAVGLAIGCVNGALVSFLGLQPFITTLI 144 DLSVG+VMA+AGA G ++ + +L AL G+ G NG LV+ L +QPF+ TLI Sbjct: 83 DLSVGAVMAIAGATTAAMTVAGFSLPIVLLSALGTGILAGLWNGILVAILKIQPFVATLI 142 Query: 145 MMLAGRGMAKVITSGENTDASAVAGNEP-LKWFANGFILGIPANFVIAVIIVILVGLLCR 203 +M+AGRG+A++IT+G+ V N P L WF +G +L +P +IAV+ +IL LL R Sbjct: 143 LMVAGRGVAQLITAGQ-----IVTFNSPDLSWFGSGSLLFLPTPVIIAVLTLILFWLLTR 197 Query: 204 KTAMGMMIEAVGINQEASRMTGIKPKKILFLVYAISGFLAAIAGLFATASVMRVDVVKTG 263 KTA+GM IEAVGIN A++ G+ + I+ L Y +SG AAIAG+ A + D G Sbjct: 198 KTALGMFIEAVGINIRAAKNAGVNTRIIVMLTYVLSGLCAAIAGIIVAADIRGADANNAG 257 Query: 264 QDLEMYAILAVVIGGTSLLGGKFSLAGSAVGAVIIAMIRKTIITLGVNAEATPAFFAVVV 323 LE+ AILAVVIGG SL+GG+F+L S VGA+II + I+ G E AVVV Sbjct: 258 LWLELDAILAVVIGGGSLMGGRFNLLLSVVGALIIQGMNTGILLSGFPPEMNQVVKAVVV 317 Query: 324 IVICVMQAPKIHNLSANMKRK 344 + + ++Q+ + +L ++ + Sbjct: 318 LCVLIVQSQRFISLIKGVRSR 338 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: 326 Number of extensions: 29 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: 356 Length of database: 341 Length adjustment: 29 Effective length of query: 327 Effective length of database: 312 Effective search space: 102024 Effective search space used: 102024 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