Align RhaP, component of Rhamnose porter (Richardson et al., 2004) (Transport activity is dependent on rhamnokinase (RhaK; AAQ92412) activity (Richardson and Oresnik, 2007) This could be an example of group translocation!) (characterized)
to candidate HSERO_RS03645 HSERO_RS03645 ribose ABC transporter permease
Query= TCDB::Q7BSH3 (333 letters) >FitnessBrowser__HerbieS:HSERO_RS03645 Length = 339 Score = 181 bits (460), Expect = 2e-50 Identities = 111/289 (38%), Positives = 164/289 (56%), Gaps = 10/289 (3%) Query: 28 ADFATPGNLAGIFNDTSILIILALAQMTVILTKSIDLSVAANLAFT---GMAIAMMNAAH 84 ++FA+ N I +I ++LA VILT IDLSV + LA + GM +++ A Sbjct: 53 SNFASAENTMNILRQVAINLVLAAGMTFVILTAGIDLSVGSVLAVSAVLGMQVSLGAAPG 112 Query: 85 PDLPLVVLILMAVVIGACLGAINGFLVWALEIPPIVVTLGTLTIYRGMAFVLSGGAWVNA 144 +P M + G +G +NG +V L I VVTLGT+T +RG A++L+ G V Sbjct: 113 WAIP------MFIFSGLVMGMVNGAMVALLNINAFVVTLGTMTAFRGAAYLLADGTTVLN 166 Query: 145 HQMTPIFLSVPRTPVLGLPVLSWVGIIIVILMYVLLRYTQFGRSAYATGGNPTAAVYAGI 204 + + P F + L +P L WV + +V+L +V+LR T G YA GGN AA GI Sbjct: 167 NDI-PSFEWIGNGDFLHVPWLIWVAVAVVLLSWVILRKTVLGMHIYAIGGNLQAARLTGI 225 Query: 205 DTGWTKFLAFVLSGALAGLASYLWVSRYAVAYVDIANGFELDSVAACVIGGISIAGGVGS 264 G + +SG +GLA + SR A + +G+ELD++AA V+GG S+ GGVGS Sbjct: 226 RVGLVLLFVYSISGLFSGLAGAMSASRLYGANGNWGSGYELDAIAAVVLGGTSLMGGVGS 285 Query: 265 VAGTVLGALFLGVIKNALPVIGISPFTQMAISGTVIILAVAFNARRERN 313 + GTV+GAL +GV+ N L ++G+S F Q G VI+LAV + R+++ Sbjct: 286 IWGTVVGALIIGVMNNGLTILGLSSFWQYVAKGAVIVLAVILDKWRQKD 334 Lambda K H 0.328 0.141 0.413 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: 301 Number of extensions: 19 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: 333 Length of database: 339 Length adjustment: 28 Effective length of query: 305 Effective length of database: 311 Effective search space: 94855 Effective search space used: 94855 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 (21.8 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