Align Monosaccharide-transporting ATPase; EC 3.6.3.17; Flags: Precursor (characterized, see rationale)
to candidate 17810 b3750 ribose ABC transporter permease protein (NCBI)
Query= uniprot:B2T9V8 (351 letters) >FitnessBrowser__Keio:17810 Length = 321 Score = 173 bits (439), Expect = 5e-48 Identities = 110/310 (35%), Positives = 167/310 (53%), Gaps = 12/310 (3%) Query: 36 ARLRELALLPALALLIVIGAFISPSFLTKANLISVLGASAALALVVLAESLIVLTGKFDL 95 A L E L AL +LI I + +SP+F T NL ++L ++ A++ + +L++LT DL Sbjct: 15 AWLMEQKSLIALLVLIAIVSTLSPNFFTINNLFNILQQTSVNAIMAVGMTLVILTSGIDL 74 Query: 96 SLESTVGIAPAVGAMLVMPAASAGFGMQWPAAAGLLAIVVVGAVIGFINGFLVVRLRLNA 155 S+ S + + AV A +V G++ A + A + +GA IG + G +V + R+ A Sbjct: 75 SVGSLLALTGAVAASIV--------GIEVNALVAVAAALALGAAIGAVTGVIVAKGRVQA 126 Query: 156 FIVTLAMLIVLRGMLVGATKGG---TLFDMPTSFFA-LATTIVLGLPLSVWLAAAAFAIA 211 FI TL M+++LRG+ + T G T F F LG+P VW+ F A Sbjct: 127 FIATLVMMLLLRGVTMVYTNGSPVNTGFTENADLFGWFGIGRPLGVPTPVWIMGIVFLAA 186 Query: 212 AFMLRYHRLGRALYAIGGNPEAARAAGIRVERITWGVFVLGSILASVGGLIVTGYVGAIN 271 +ML + RLGR +YA+GGN A R +GI V +I V+ L +LAS+ G+I + + Sbjct: 187 WYMLHHTRLGRYIYALGGNEAATRLSGINVNKIKIIVYSLCGLLASLAGIIEVARLSSAQ 246 Query: 272 ANQGNGMIFTVFAAAVIGGISLDGGKGTMFGALTGVLLLGVVQNLLTLAQVPSFWIQAIY 331 G G AA V+GG SL GGKG + G L G L+LG + N L L V S++ + Sbjct: 247 PTAGTGYELDAIAAVVLGGTSLAGGKGRIVGTLIGALILGFLNNGLNLLGVSSYYQMIVK 306 Query: 332 GAIILGSLMV 341 +IL +++V Sbjct: 307 AVVILLAVLV 316 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: 244 Number of extensions: 12 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: 351 Length of database: 321 Length adjustment: 28 Effective length of query: 323 Effective length of database: 293 Effective search space: 94639 Effective search space used: 94639 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