Align Monosaccharide-transporting ATPase; EC 3.6.3.17; Flags: Precursor (characterized, see rationale)
to candidate RR42_RS03365 RR42_RS03365 ribose ABC transporter permease
Query= uniprot:B2T9V8 (351 letters) >FitnessBrowser__Cup4G11:RR42_RS03365 Length = 333 Score = 158 bits (400), Expect = 2e-43 Identities = 115/330 (34%), Positives = 177/330 (53%), Gaps = 16/330 (4%) Query: 12 AAQAGAQSQLALPASRGKRARSELARLRELALLPALALLIVIGAFISPSFLTKANLISVL 71 AA GA LPA R ++ RLR L +LP L LL + + ++ +F NL S++ Sbjct: 5 AASTGAP----LPAGTLGRLTTQ-ERLRALGMLPVLVLLCIGFSVLTENFAGWQNL-SII 58 Query: 72 GASAALALVVLAE-SLIVLTGKFDLSLESTVGIAPAVGAMLVMPAASAGFGMQWPAAAGL 130 A++ +V+ A + ++LTG DLS+ S + I+ AV AMLV G + PAA Sbjct: 59 AQQASINMVLAAGMTFVILTGGIDLSVGSILSIS-AVVAMLVSLMPQLGM-LSVPAA--- 113 Query: 131 LAIVVVGAVIGFINGFLVVRLRLNAFIVTLAMLIVLRGMLVGATKGGTLFDMPTSFFALA 190 ++ G + G +NG LV ++L FIVTL L +RG+ T+++ F + Sbjct: 114 ---LLCGLLFGIVNGALVAFMKLPPFIVTLGTLTAVRGLARLVGNDSTIYNPDIGFAFIG 170 Query: 191 TTIVLGLPLSVWLAAAAFAIAAFMLRYHRLGRALYAIGGNPEAARAAGIRVERITWGVFV 250 VLG+P V +A A A++ F+LR LG +YA+GGN EAAR +GI+V + V+ Sbjct: 171 NGEVLGVPWLVIIAFAVVAVSWFVLRRTVLGLQIYAVGGNAEAARLSGIKVWVVLLFVYA 230 Query: 251 LGSILASVGGLIVTGYVGAINANQ-GNGMIFTVFAAAVIGGISLDGGKGTMFGALTGVLL 309 + +LA +GG++ + + A N Q G AA ++GG S GG G++ G L G L+ Sbjct: 231 VSGLLAGLGGVMSSARLYAANGLQLGQSYELDAIAAVILGGTSFVGGTGSIVGTLVGALI 290 Query: 310 LGVVQNLLTLAQVPSFWIQAIYGAIILGSL 339 + V+ N L L V W I G +I+G++ Sbjct: 291 IAVLSNGLVLLGVSDIWQYIIKGLVIIGAV 320 Lambda K H 0.326 0.140 0.397 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: 312 Number of extensions: 18 Number of successful extensions: 2 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: 351 Length of database: 333 Length adjustment: 29 Effective length of query: 322 Effective length of database: 304 Effective search space: 97888 Effective search space used: 97888 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 (21.6 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