Align Fructose import permease protein FruG (characterized)
to candidate RR42_RS03365 RR42_RS03365 ribose ABC transporter permease
Query= SwissProt::Q8G845 (340 letters) >FitnessBrowser__Cup4G11:RR42_RS03365 Length = 333 Score = 157 bits (397), Expect = 4e-43 Identities = 104/326 (31%), Positives = 170/326 (52%), Gaps = 11/326 (3%) Query: 4 ATANKVKAPKKGFKLDRQMIPTLAAVVIFILMIIMGQALFGTYIRLGFISSLFIDHAYLI 63 +T + A G ++ + L + + +L+ I L + +S + + + Sbjct: 7 STGAPLPAGTLGRLTTQERLRALGMLPVLVLLCIGFSVLTENFAGWQNLSIIAQQASINM 66 Query: 64 ILAVAMTLPILTGGIDLSVGAIVAITAVVGLKLANAGVPAFLVMIIMLLIGAVFGLLAGT 123 +LA MT ILTGGIDLSVG+I++I+AVV + ++ L + LL G +FG++ G Sbjct: 67 VLAAGMTFVILTGGIDLSVGSILSISAVVAMLVSLMPQLGMLSVPAALLCGLLFGIVNGA 126 Query: 124 LIEEFNMQPFIATLSTMFLARGLASIISTDSLTFPQGNDFSFISNVIKIIDNPKISNDLS 183 L+ + PFI TL T+ RGLA ++ DS + F+FI N +++ P + Sbjct: 127 LVAFMKLPPFIVTLGTLTAVRGLARLVGNDSTIYNPDIGFAFIGNG-EVLGVPWL----- 180 Query: 184 FNVGVIIALVVVVFGYVFLHHTRTGRTIYAIGGSRSSAELMGLPVKRTQYIIYLTSATLA 243 VIIA VV + L T G IYA+GG+ +A L G+ V +Y S LA Sbjct: 181 ----VIIAFAVVAVSWFVLRRTVLGLQIYAVGGNAEAARLSGIKVWVVLLFVYAVSGLLA 236 Query: 244 ALASIVYTANIGSAKN-TVGVGWELDAVASVVIGGTIITGGFGYVLGSVLGSLVRSILDP 302 L ++ +A + +A +G +ELDA+A+V++GGT GG G ++G+++G+L+ ++L Sbjct: 237 GLGGVMSSARLYAANGLQLGQSYELDAIAAVILGGTSFVGGTGSIVGTLVGALIIAVLSN 296 Query: 303 LTSDFGVPAEWTTIVIGLMILVFVVL 328 GV W I+ GL+I+ V L Sbjct: 297 GLVLLGVSDIWQYIIKGLVIIGAVAL 322 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: 271 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: 333 Length adjustment: 28 Effective length of query: 312 Effective length of database: 305 Effective search space: 95160 Effective search space used: 95160 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