Align Fructose import permease protein FruF (characterized)
to candidate 7024901 Shewana3_2075 inner-membrane translocator (RefSeq)
Query= SwissProt::Q8G846 (356 letters) >FitnessBrowser__ANA3:7024901 Length = 405 Score = 218 bits (556), Expect = 2e-61 Identities = 140/344 (40%), Positives = 198/344 (57%), Gaps = 17/344 (4%) Query: 23 WSIVAFILLVIICTIFQHDFLALSWNSNTGGLAGPLITMLQESARYLMIATGMTLVISTA 82 W ++A +L++ F +S+ + L G LI +L SA +++ GM+LVI+T Sbjct: 64 WPLLALSILLLANLFIDSSFFNISYQDDR--LYGSLIDILNRSAPVALLSIGMSLVIATG 121 Query: 83 GIDLSVGSVMAVAGAA-AMQTLSNGMNVWLSILIALAVGLAIGCVNGALVSFLGLQPFIT 141 GIDLSVG+VMA+AGA A L +++ I L VGL GC+NG LVSFLG+QP + Sbjct: 122 GIDLSVGAVMAIAGAVCANLLLVPDISLVTVIAAGLIVGLLAGCINGGLVSFLGIQPIVA 181 Query: 142 TLIMMLAGRGMAKVITSGENTDASAVAGNEP-LKWFANGFILGIPANFVIAVIIVILVGL 200 TL++M+AGRG+A++I G+ + P G LG+P I + ++ L Sbjct: 182 TLLLMVAGRGVAQLINQGQ-----IITFQHPGFAAIGVGQFLGLPMPVWIVIGMLTFSQL 236 Query: 201 LCRKTAMGMMIEAVGINQEASRMTGIKPKKILFLVYAISGFLAAIAGLFATASVMRVDVV 260 L RKTA+G+ IEAVG N +ASR GI K I Y I+G AA+AG+ +TA + D Sbjct: 237 LLRKTALGLFIEAVGCNAKASRYLGINDKSIKLFAYGIAGLCAALAGMISTADIQGSDAN 296 Query: 261 KTGQDLEMYAILAVVIGGTSLLGGKFSLAGSAVGAVIIAMIRKTIITLGVNAEATPAFFA 320 G LE+ A+LAVVIGG +L GG+FSL S VGA+II + TII G+ A+ A Sbjct: 297 NAGLWLELDAVLAVVIGGAALTGGRFSLILSVVGALIIQTLATTIIVSGLPAKFNLLIKA 356 Query: 321 VVVIVICVMQAPKI-HNLSANMKRKRALKAQ-------AKAVAA 356 +V++ + ++Q+ K LSA K KR A+ AKA AA Sbjct: 357 IVILTVLLLQSAKFRRQLSALFKSKRHADAKPAEKATSAKASAA 400 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: 347 Number of extensions: 17 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: 405 Length adjustment: 30 Effective length of query: 326 Effective length of database: 375 Effective search space: 122250 Effective search space used: 122250 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: 50 (23.9 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