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 YP_004140887.1 Mesci_1682 inner-membrane translocator
Query= TCDB::Q7BSH3 (333 letters) >NCBI__GCF_000185905.1:YP_004140887.1 Length = 321 Score = 187 bits (475), Expect = 3e-52 Identities = 100/303 (33%), Positives = 173/303 (57%), Gaps = 4/303 (1%) Query: 12 LFLIIVVMIVVFSTRAADFATPGNLAGIFNDTSILIILALAQMTVILTKSIDLSVAANLA 71 L ++V++ ++ S FA+ N+A + S++ I+A+ Q VI+T IDLSV A + Sbjct: 23 LLALLVLLWILLSVTTTSFASANNIANLLRQGSMIAIMAVGQTFVIITGGIDLSVGAVVG 82 Query: 72 FTGMAIAMMNAAHPDLPLVVLILMAVVIGACLGAINGFLVWALEIPPIVVTLGTLTIYRG 131 F + +AMM A P+ + IL+ +++G +G +GF + + +PP ++TL TLT RG Sbjct: 83 FATVVVAMMINA--GFPIWLAILVTLLVGVAIGMFHGFGIVKMGLPPFIITLATLTSLRG 140 Query: 132 MAFVLSGGAWVNAHQMTPIFLSVPRTPVLGLPVLSWVGIIIVILMYVLLRYTQFGRSAYA 191 + +++ G +N + T F + R +G+P L W+ I++ I Y+ L ++++GR ++ Sbjct: 141 IGLLMTNGNSININSDT--FTAFSRNSFIGIPNLFWMVILVGIPAYIFLHHSRWGRYLFS 198 Query: 192 TGGNPTAAVYAGIDTGWTKFLAFVLSGALAGLASYLWVSRYAVAYVDIANGFELDSVAAC 251 G N A+ +G++ T ++A+ LSG A L +R + A G+EL ++A+ Sbjct: 199 VGSNAEASRLSGVNVQRTIYMAYTLSGLCAAFVGVLLAARIGIGNPTQAEGWELQAIASS 258 Query: 252 VIGGISIAGGVGSVAGTVLGALFLGVIKNALPVIGISPFTQMAISGTVIILAVAFNARRE 311 VIGG S+ G VGSV G +LGA L I N ++ ++ F Q I+G +II+ V F+ R Sbjct: 259 VIGGTSLFGAVGSVHGPLLGAFILATINNGANLLNVNSFWQRIITGALIIIIVYFDGLRR 318 Query: 312 RNR 314 R + Sbjct: 319 RGK 321 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: 249 Number of extensions: 15 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: 321 Length adjustment: 28 Effective length of query: 305 Effective length of database: 293 Effective search space: 89365 Effective search space used: 89365 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: 48 (23.1 bits)
This GapMind analysis is from Sep 24 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