Align Fructose import permease protein FruF (characterized)
to candidate RR42_RS32895 RR42_RS32895 ABC transporter permease
Query= SwissProt::Q8G846 (356 letters) >FitnessBrowser__Cup4G11:RR42_RS32895 Length = 318 Score = 137 bits (344), Expect = 5e-37 Identities = 89/276 (32%), Positives = 145/276 (52%), Gaps = 5/276 (1%) Query: 58 LITMLQESARYLMIATGMTLVISTAGIDLSVGSVMAVAGAAAMQTLSNGMNVWLSILIAL 117 L+ + +S L+IA MTL+I T G+DLS+G+V+ + G + ++ L++ AL Sbjct: 45 LLNIGAQSTILLLIALPMTLIIMTEGLDLSMGAVLTLCGVVLAMVMVATESLPLALGAAL 104 Query: 118 AVGLAIGCVNGALVSFLGLQPFITTLIMMLAGRGMAKVITSGENTDASAVAGNEPLKWFA 177 GLA G +NGALVS+L + PF+ TL + +G+A V T G+ S E + Sbjct: 105 LTGLAFGLLNGALVSWLEIPPFVATLGTLGVAQGLALVATDGQ----SVTGIGEAIPLIY 160 Query: 178 NGFILGIPANFVIAVIIVILVGLLCRKTAMGMMIEAVGINQEASRMTGIKPKKILFLVYA 237 G +LG+P IA + L L T G + A+G N+EA + +G++ L VYA Sbjct: 161 AGQLLGVPLPIWIAAVFYGLFHWLLYHTRFGAYVFALGGNREALKFSGVRINVYLIAVYA 220 Query: 238 ISGFLAAIAGLFATASVMRVDVVKTGQDLEMYAILAVVIGGTSLLGGKFSLAGSAVGAVI 297 + G +A +A L TA M LE AI AV +GGT+ G L G+ +G + Sbjct: 221 LGGLMAGVAALLLTAR-MNAGHPTAAIGLEFDAIAAVAVGGTTFDRGNGWLPGTVLGVLA 279 Query: 298 IAMIRKTIITLGVNAEATPAFFAVVVIVICVMQAPK 333 + ++R + +GV + A ++V+V+ ++++ K Sbjct: 280 VGVLRNGLNLVGVPSSVQVAAIGLLVLVVLLIESFK 315 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: 286 Number of extensions: 16 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: 318 Length adjustment: 28 Effective length of query: 328 Effective length of database: 290 Effective search space: 95120 Effective search space used: 95120 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