Align Fructose import permease protein FruG (characterized)
to candidate H281DRAFT_00427 H281DRAFT_00427 monosaccharide ABC transporter membrane protein, CUT2 family
Query= SwissProt::Q8G845 (340 letters) >FitnessBrowser__Burk376:H281DRAFT_00427 Length = 341 Score = 159 bits (402), Expect = 1e-43 Identities = 98/306 (32%), Positives = 167/306 (54%), Gaps = 11/306 (3%) Query: 26 LAAVVIFILMIIMGQALFGTYIRLGFISSLFIDHAYLIILAVAMTLPILTGGIDLSVGAI 85 L A IL+++ ++++ I + A +LA+A T I+TGGIDLSVG + Sbjct: 32 LLAFASLILLLVFFSFASPAFMQMDNILGILQATAVNGVLAIASTFVIITGGIDLSVGTL 91 Query: 86 VAITAVV-GLKLANAGVPAFLVMIIMLLIGAVFGLLAGTLIEEFNMQPFIATLSTMFLAR 144 + TAV+ G+ L +P +L +I + GA+ G ++GTL + + PFIATL M L + Sbjct: 92 MTFTAVICGVFLTYWHLPMWLGVIAAIGTGAICGTISGTLTAKMKIPPFIATLGMMLLLK 151 Query: 145 GLASIISTDS-LTFPQGNDFSFISN---VIKIIDNPKISNDLSFNVGVIIALVVVVFGYV 200 GL+ ++S D + F +F IS + ++ + I N V+I + + V Sbjct: 152 GLSLVVSADKPIYFTDTENFYMISQDSLIGYLVPSLPIPN------AVLILFFLAIVSSV 205 Query: 201 FLHHTRTGRTIYAIGGSRSSAELMGLPVKRTQYIIYLTSATLAALASIVYTANIGSAKNT 260 L+ T GR +A+G + + L G+ V R + IY + +A ++ + + SA+ Sbjct: 206 TLNRTALGRYTFALGSNEEAVRLSGVNVDRWKIAIYGLGGAICGIAGLLIASRLNSAQPA 265 Query: 261 VGVGWELDAVASVVIGGTIITGGFGYVLGSVLGSLVRSILDPLTSDFGVPAEWTTIVIGL 320 +G G+EL+A+A+VVIGGT ++GG G +LG+++G+ + S+L V EW +V GL Sbjct: 266 LGQGYELEAIAAVVIGGTSLSGGSGTILGTIIGAFIMSVLTNGLRIMSVAQEWQIVVTGL 325 Query: 321 MILVFV 326 +I++ V Sbjct: 326 IIILAV 331 Lambda K H 0.327 0.142 0.400 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: 242 Number of extensions: 11 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: 340 Length of database: 341 Length adjustment: 28 Effective length of query: 312 Effective length of database: 313 Effective search space: 97656 Effective search space used: 97656 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 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