Align Fructose import permease protein FruF (characterized)
to candidate PfGW456L13_3910 Ribose ABC transport system, permease protein RbsC (TC 3.A.1.2.1)
Query= SwissProt::Q8G846 (356 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3910 Length = 325 Score = 142 bits (357), Expect = 2e-38 Identities = 92/304 (30%), Positives = 157/304 (51%), Gaps = 18/304 (5%) Query: 27 AFILLVIICTIFQHDFLALSWNSNTGGLAGPLITMLQESARYLMIATGMTLVISTAGIDL 86 A + ++++ ++ FL+ S T+ + +++A GMT V+ GIDL Sbjct: 26 ALLAMIVLFSVLSSHFLSYDTFS----------TLANQIPDLMVLAVGMTFVLIIGGIDL 75 Query: 87 SVGSVMAVAGAA-AMQTLSNGMNVWLSILIALAVGLAIGCVNGALVSFLGLQPFITTLIM 145 SVGSV+A+A + ++ L G V + L+ +AV G + G++ + FI +L + Sbjct: 76 SVGSVLALAASTVSVAILGWGWGVLPAALLGMAVAALAGTITGSITVAWRIPSFIVSLGV 135 Query: 146 MLAGRGMAKVITSGENTDASAVAGNEPLKWFANGFILGIPANFVIAVIIVILVGLLCRKT 205 + RG+A +T +A G + W +N GI +F+IA++I+ + + +T Sbjct: 136 LEMARGVAYQMTGSR----TAYIG-DAFAWLSNPIAFGISPSFIIALLIIFVAQAVLTRT 190 Query: 206 AMGMMIEAVGINQEASRMTGIKPKKILFLVYAISGFLAAIAGLFATASVMRVDVVKTGQD 265 G + +G N+EA R+ GI PK LV+++ G LA +A LF + + D G Sbjct: 191 VFGRYLIGIGTNEEAVRLAGINPKPYKVLVFSLMGLLAGVAALFQISRLEAAD-PNAGSG 249 Query: 266 LEMYAILAVVIGGTSLLGGKFSLAGSAVGAVIIAMIRKTIITLGVNAEATPAFFAVVVIV 325 LE+ I AVVIGGTSL+GG+ S+ + G +II+++ + +G E T VIV Sbjct: 250 LELQVIAAVVIGGTSLMGGRGSVISTFFGVLIISVLAAGLAQIGA-TEPTKRIITGAVIV 308 Query: 326 ICVM 329 + V+ Sbjct: 309 VAVV 312 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: 305 Number of extensions: 19 Number of successful extensions: 3 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: 325 Length adjustment: 28 Effective length of query: 328 Effective length of database: 297 Effective search space: 97416 Effective search space used: 97416 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