Align Fructose import permease protein FruF (characterized)
to candidate Ac3H11_1841 Ribose ABC transport system, ATP-binding protein RbsA (TC 3.A.1.2.1)
Query= SwissProt::Q8G846 (356 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1841 Length = 892 Score = 160 bits (405), Expect = 1e-43 Identities = 98/276 (35%), Positives = 153/276 (55%), Gaps = 7/276 (2%) Query: 55 AGPLITMLQESARYLMIATGMTLVISTAGIDLSVGSVMAVAGA-AAMQTLSNGMNVWLSI 113 A IT+ E ++A GMT V+ AGIDLSVGSVMA+A A +A L G V + Sbjct: 613 AETFITIANEIPALAVMAVGMTFVLIIAGIDLSVGSVMALAAATSAAAILQWGWTVPAAA 672 Query: 114 LIALAVGLAIGCVNGALVSFLGLQPFITTLIMMLAGRGMAKVITSGENTDASAVAGNEPL 173 +ALA GL G + GA+ L FI +L M+ A RG A V+T D+ + + Sbjct: 673 ALALATGLVCGTITGAISVAWRLPSFIVSLGMLEAVRGSAYVVT-----DSRTQYVGDAI 727 Query: 174 KWFANGFILGIPANFVIAVIIVILVGLLCRKTAMGMMIEAVGINQEASRMTGIKPKKILF 233 W + F GI F++AV++V++ L+ +T G + +G N+EA R+ G+ P+ I Sbjct: 728 SWLSAPFFGGISFAFLLAVVLVVVAQLVLSRTVFGRCVVGIGTNEEAMRLAGVDPRPIRV 787 Query: 234 LVYAISGFLAAIAGLFATASVMRVDVVKTGQDLEMYAILAVVIGGTSLLGGKFSLAGSAV 293 +V+A++G LA +AGL +A + D G +E+ I AVVIGGTSL+GG+ S+ +A Sbjct: 788 IVFAMTGLLAGLAGLMQSARLEAAD-PNAGTGMELQVIAAVVIGGTSLMGGRGSVVNTAF 846 Query: 294 GAVIIAMIRKTIITLGVNAEATPAFFAVVVIVICVM 329 G +IIA++ + +G + + V++ ++ Sbjct: 847 GVLIIAVLEAGLAQVGASEPSKRIITGFVIVAAVIV 882 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: 612 Number of extensions: 30 Number of successful extensions: 4 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: 892 Length adjustment: 36 Effective length of query: 320 Effective length of database: 856 Effective search space: 273920 Effective search space used: 273920 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: 53 (25.0 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