Align Fructose import permease protein FruF (characterized)
to candidate BPHYT_RS23880 BPHYT_RS23880 sugar ABC transporter permease
Query= SwissProt::Q8G846 (356 letters) >FitnessBrowser__BFirm:BPHYT_RS23880 Length = 343 Score = 229 bits (585), Expect = 6e-65 Identities = 136/341 (39%), Positives = 205/341 (60%), Gaps = 11/341 (3%) Query: 10 NNFVKKLLSSNLTWSIVAFILLVIICTIFQHDFLALSWNSNTGGLAGPLITMLQESARYL 69 N FV+ L W V +LL + FL+L G L G I +L +A + Sbjct: 5 NWFVRDGAERPLIWPCVTLVLLCGLNLWVNPHFLSLRMLD--GHLFGAPIDVLNRAAPLV 62 Query: 70 MIATGMTLVISTAGIDLSVGSVMAVAGAAAMQTLS-----NGMNVWLSILIALAVGLAIG 124 ++ATGMTLVI+T GID+SVG+V+A+AGAAA L+ + + +++ AL VG+ G Sbjct: 63 LVATGMTLVIATRGIDISVGAVVAIAGAAAATILAAQPEPSSALIAQALIAALIVGVLSG 122 Query: 125 CVNGALVSFLGLQPFITTLIMMLAGRGMAKVITSGENTDASAVAGNEPLKWFANGFILGI 184 NG LVSF+G+QP I TLI+M+AGRG+A+++T+G+ A + G++LG+ Sbjct: 123 MWNGVLVSFVGMQPIIATLILMVAGRGIAQLLTAGQIIPIGAPG----YLFVGGGYLLGV 178 Query: 185 PANFVIAVIIVILVGLLCRKTAMGMMIEAVGINQEASRMTGIKPKKILFLVYAISGFLAA 244 P++ IA + V+ L TA+G+ I A+G+N A+R+ G++ K ++F VY SG AA Sbjct: 179 PSSVWIATVAVLATAALVEGTALGLFIRAIGVNPVATRLVGLRSKALVFAVYGFSGLTAA 238 Query: 245 IAGLFATASVMRVDVVKTGQDLEMYAILAVVIGGTSLLGGKFSLAGSAVGAVIIAMIRKT 304 +AG+ +++V D G LE+ AILAV +GGTSLLGG+FSLAG+ +GA+II + T Sbjct: 239 MAGILISSNVRSADGNNAGLLLELDAILAVTLGGTSLLGGRFSLAGTVLGALIIQTLTYT 298 Query: 305 IITLGVNAEATPAFFAVVVIVICVMQAPKIHNLSANMKRKR 345 ++GV EAT A VV+ + V+Q+P L ++ R Sbjct: 299 TYSIGVPPEATLVVKAAVVLAVSVIQSPSARALGMSLVTHR 339 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: 331 Number of extensions: 19 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: 343 Length adjustment: 29 Effective length of query: 327 Effective length of database: 314 Effective search space: 102678 Effective search space used: 102678 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