Align Fructose import permease protein FruF (characterized)
to candidate PP_2456 PP_2456 D-ribose ABC transporter - permease subunit
Query= SwissProt::Q8G846 (356 letters) >FitnessBrowser__Putida:PP_2456 Length = 331 Score = 147 bits (371), Expect = 4e-40 Identities = 91/275 (33%), Positives = 147/275 (53%), Gaps = 8/275 (2%) Query: 56 GPLITMLQESARYLMIATGMTLVISTAGIDLSVGSVMAVAGAA-AMQTLSNGMNVWLSIL 114 G T+ + +++A GMT V+ GIDLSVGSV+A+A + ++ L G V S L Sbjct: 51 GTFSTLANQIPDLMVLAVGMTFVLIIGGIDLSVGSVLALAASTVSVAILGWGWGVLPSAL 110 Query: 115 IALAVGLAIGCVNGALVSFLGLQPFITTLIMMLAGRGMAKVITSGENTDASAVAGNEPLK 174 + +AV G + G + + FI +L ++ RG+A + TD+ + Sbjct: 111 LGMAVAALAGSITGGVTVAWRIPSFIVSLGVLEMARGLAY-----QFTDSRTAYIGDAYA 165 Query: 175 WFANGFILGIPANFVIAVIIVILVGLLCRKTAMGMMIEAVGINQEASRMTGIKPKKILFL 234 WF+N G+ F+IA+++++L L+ +T G + +G N+EA R+ GI P+ L Sbjct: 166 WFSNPVAFGVSPAFIIALLVIVLAQLVLTRTVFGRYLIGIGTNEEAVRLAGIDPRPYKVL 225 Query: 235 VYAISGFLAAIAGLFATASVMRVDVVKTGQDLEMYAILAVVIGGTSLLGGKFSLAGSAVG 294 V+A+ G LA +A LF + + D G LE+ I AVVIGGTSL+GG+ S+ + G Sbjct: 226 VFALMGLLAGLAALFQISRLEAAD-PNAGSGLELQVIAAVVIGGTSLMGGRGSVISTFFG 284 Query: 295 AVIIAMIRKTIITLGVNAEATPAFFAVVVIVICVM 329 +II+++ + +G +E T VIVI V+ Sbjct: 285 VLIISVLAAGLAQIGA-SEPTKRIITGAVIVIAVV 318 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: 307 Number of extensions: 21 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: 331 Length adjustment: 29 Effective length of query: 327 Effective length of database: 302 Effective search space: 98754 Effective search space used: 98754 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