Align Fructose import permease protein FruF (characterized)
to candidate Pf1N1B4_6033 Ribose ABC transport system, permease protein RbsC (TC 3.A.1.2.1)
Query= SwissProt::Q8G846 (356 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_6033 Length = 325 Score = 144 bits (363), Expect = 3e-39 Identities = 90/271 (33%), Positives = 147/271 (54%), Gaps = 8/271 (2%) Query: 60 TMLQESARYLMIATGMTLVISTAGIDLSVGSVMAVAGAA-AMQTLSNGMNVWLSILIALA 118 T+ + +++A GMT V+ GIDLSVGSV+A+A +A ++ L G +V + L+ +A Sbjct: 49 TLANQIPDLMVLAVGMTFVLIIGGIDLSVGSVLALAASAVSVAILGWGWSVLPAALLGMA 108 Query: 119 VGLAIGCVNGALVSFLGLQPFITTLIMMLAGRGMAKVITSGENTDASAVAGNEPLKWFAN 178 V G + G++ + FI +L ++ RG+A +T +A G + W +N Sbjct: 109 VAALAGTITGSITVAWRIPSFIVSLGVLEMARGLAYQMTGSR----TAYIG-DAFAWLSN 163 Query: 179 GFILGIPANFVIAVIIVILVGLLCRKTAMGMMIEAVGINQEASRMTGIKPKKILFLVYAI 238 GI +F+IA++I+ + + +T G + +G N+EA R+ GI PK LV+++ Sbjct: 164 PIAFGISPSFIIALLIIFIAQAVLTRTVFGRYLIGIGTNEEAVRLAGINPKPYKILVFSL 223 Query: 239 SGFLAAIAGLFATASVMRVDVVKTGQDLEMYAILAVVIGGTSLLGGKFSLAGSAVGAVII 298 G LA IA LF + + D G LE+ I AVVIGGTSL+GG+ S+ + G +II Sbjct: 224 MGLLAGIAALFQISRLEAAD-PNAGSGLELQVIAAVVIGGTSLMGGRGSVISTFFGVLII 282 Query: 299 AMIRKTIITLGVNAEATPAFFAVVVIVICVM 329 +++ + +G E T VIV+ V+ Sbjct: 283 SVLAAGLAQIGA-TEPTKRIITGAVIVVAVV 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: 319 Number of extensions: 22 Number of successful extensions: 4 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