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 WP_007730024.1 C1M55_RS26585 ABC transporter permease
Query= TCDB::Q7BSH3 (333 letters) >NCBI__GCF_002893965.1:WP_007730024.1 Length = 347 Score = 169 bits (427), Expect = 1e-46 Identities = 101/305 (33%), Positives = 160/305 (52%), Gaps = 3/305 (0%) Query: 5 IRKRETLLFLIIVVMIVVFSTRAADFATPGNLAGIFNDTSILIILALAQMTVILTKSIDL 64 + K + + V + VFS + F T NL+ + + ++I+A+A VI IDL Sbjct: 25 VNKPTLAMLAVTVAVAAVFSATTSSFLTFTNLSNLATQIAPVLIIAVAMTFVITAGQIDL 84 Query: 65 SVAANLAFTGMAIAMMNAAHPDLPLVVLILMAVVIGACLGAINGFLVWALEIPPIVVTLG 124 SV A +AF A + A D LV + A V+GA G +NG+L IPP +VTL Sbjct: 85 SVGAIVAFVAAMSAELIQAGVDSSLV--FVAAPVMGAAWGLVNGWLAAYQGIPPFIVTLA 142 Query: 125 TLTIYRGMAFVLSGGAWVNAHQMTPIFLSVPRTPVLGLPVLSWVGIIIVILMYVLLRYTQ 184 T+++ RG+A + G V T F + + LG +W+ +++V++ + L + Sbjct: 143 TMSVIRGIALYRTEGFSVPVPADT-YFAKLGTSEFLGFSASAWIALVVVVIGAIALNRMR 201 Query: 185 FGRSAYATGGNPTAAVYAGIDTGWTKFLAFVLSGALAGLASYLWVSRYAVAYVDIANGFE 244 FGR G N + +G++T + V +G AG+A L +R + A GFE Sbjct: 202 FGRYVTGIGSNVESVRRSGVNTRRVLMMTLVFTGLAAGIAGLLIAARLGSGSANSATGFE 261 Query: 245 LDSVAACVIGGISIAGGVGSVAGTVLGALFLGVIKNALPVIGISPFTQMAISGTVIILAV 304 L + A V+GG ++ GG G+V GTV+GA+ G+I N L ++G+SPF I+G V++LA+ Sbjct: 262 LTVITAVVLGGTNLFGGRGTVIGTVIGAVLTGIIANGLTLLGVSPFLTPIITGVVLLLAI 321 Query: 305 AFNAR 309 N R Sbjct: 322 WINMR 326 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: 294 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: 347 Length adjustment: 28 Effective length of query: 305 Effective length of database: 319 Effective search space: 97295 Effective search space used: 97295 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 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