Align Fructose import permease protein FrcC (characterized)
to candidate 3609042 Dshi_2431 Monosaccharide-transporting ATPase (RefSeq)
Query= SwissProt::Q9F9B1 (360 letters) >FitnessBrowser__Dino:3609042 Length = 328 Score = 152 bits (383), Expect = 2e-41 Identities = 92/301 (30%), Positives = 161/301 (53%), Gaps = 13/301 (4%) Query: 56 VLSLIAFGVILGGKFFS-----AFTMTLILQQVAIVGIVGAAQTLVILTAGIDLSVGAIM 110 +L L+A G+ + F S A+ ++ ++ A L+I++ IDLSV +I+ Sbjct: 26 LLLLVAIGIFVANSFASPYFLNAWNLSDATFNFTEKAMIAFAMALLIISGEIDLSVASII 85 Query: 111 VLSSVIMGQFTFRYGFPPALSVICGLGVGALCGYINGTLVARMKLPPFIVTLGMWQIVLA 170 L+S MG P L V+ GLGVG LCG NG LV RM LP +VT+G + Sbjct: 86 ALASTAMGAAVQMGVGTPGL-VLIGLGVGLLCGAFNGVLVTRMGLPSIVVTIGTMSLFRG 144 Query: 171 SNFLYSANETIRAQDISANASILQFFGQNFRIGNAVFTYGVVVMVLLVCLLWYVLNRTAW 230 +++ ++ R S +FGQ + V ++ +V+ ++ + +L++T + Sbjct: 145 ISYIVLGDQAFRGYPES-----FSWFGQGYVWW--VISFELVLFAIIAVIYAMLLHKTNF 197 Query: 231 GRYVYAVGDDPEAAKLAGVNVTRMLISIYTLSGLICALAGWALIGRIGSVSPTAGQFANI 290 GR VYA+G++ A +G+ V R+ ++ L+GL+ +A L R+GS P+ + Sbjct: 198 GRAVYAIGNNATGAMFSGIRVQRVKFILFLLTGLMSGVAAICLTARLGSTRPSIAMGWEL 257 Query: 291 ESITAVVIGGISLFGGRGSIMGMLFGALIVGVFSLGLRLMGTDPQWTYLLIGLLIIIAVA 350 E +T VV+GG+S+ GG G+I+G++ A ++G+ + GL L+ ++IG L+I +A Sbjct: 258 EVVTMVVLGGVSILGGSGTILGVVIAAFVMGLVTFGLGLLNVPGIVMSIVIGALLIGVIA 317 Query: 351 I 351 + Sbjct: 318 L 318 Lambda K H 0.327 0.141 0.420 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: 356 Number of extensions: 28 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: 360 Length of database: 328 Length adjustment: 29 Effective length of query: 331 Effective length of database: 299 Effective search space: 98969 Effective search space used: 98969 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