Align Fructose import permease protein FruF (characterized)
to candidate WP_085121058.1 B9O00_RS01465 ABC transporter permease
Query= SwissProt::Q8G846 (356 letters) >NCBI__GCF_900177295.1:WP_085121058.1 Length = 335 Score = 140 bits (353), Expect = 5e-38 Identities = 101/313 (32%), Positives = 161/313 (51%), Gaps = 27/313 (8%) Query: 5 AKAEGNNFVKKLLSSNLTWSIVAFILLV-IICTIFQHDFLALSWNSNTGGLAGPLITMLQ 63 A A G + K L+++L ++ L++ + ++ FL S + +L Sbjct: 16 AAAAGEGRLLKQLATSLELRMLGLALVIGAVLSLLSPYFLTES----------NIFNILD 65 Query: 64 ESARYLMIATGMTLVISTAGIDLSVGSVMAVAGAAAMQTLSNGMNVWLSILIALAVGLAI 123 +S +++ GMT VI T GIDLSVGSV ++G L + + ++IL+ + G + Sbjct: 66 QSVVIGILSIGMTFVILTGGIDLSVGSVAGLSGIVLGLALKD-YPIPVAILLGVLTGAGV 124 Query: 124 GCVNGALVSFLGLQPFITTLIMMLAGRGMAKVIT-----SGENTDASAVAGNEPLKWFAN 178 G V+G L+ + L F+ TL MM GR +A + + SG +D S++ + Sbjct: 125 GLVSGILIGYFRLAAFVVTLGMMAIGRSLAYIFSGQTAISGFPSDLSSIVYTD------- 177 Query: 179 GFILGIPANFVIAVIIVILVGLLCRKTAMGMMIEAVGINQEASRMTGIKPKKILFLVYAI 238 + GIP N + +L T G I A+G N+EA+R G+ L Y + Sbjct: 178 --VFGIPTNVLFLGFAYLLAWGYLTYTKGGRTIYAIGSNKEAARAAGLGVLFYSILPYVV 235 Query: 239 SGFLAAIAGLFATASVMRVDVVKTGQDLEMYAILAVVIGGTSLLGGKFSLAGSAVGAVII 298 SG LAA+A F+ A ++ VD + TG +E+ AI AVVIGG SL GG+ S+ G+ +G +I+ Sbjct: 236 SGALAAVAITFSVAQILSVDPL-TGNGMELDAIAAVVIGGASLYGGRGSIVGTLIGVLIM 294 Query: 299 AMIRKTIITLGVN 311 MIR + LGV+ Sbjct: 295 VMIRNGLNLLGVS 307 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: 304 Number of extensions: 21 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 356 Length of database: 335 Length adjustment: 29 Effective length of query: 327 Effective length of database: 306 Effective search space: 100062 Effective search space used: 100062 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 Apr 09 2024. 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